def create_summary(first,amosbnk,prefix,ref_asm,utils,img,rund,nLibs,taxa_level,dbdir):
#if __name__ == "__main__":
# if len(sys.argv) < 5:
# print "usage: create_report.py <metaphyler tab file> <AMOS bnk> <output prefix> <ref_asm> <Utils dir> <run dir> <# of libs> <taxa level of classifications>"
# sys.exit(0)
html_prefix = prefix
prefix = prefix.replace("/html/", "")
MA_dir = prefix
MA_dir = MA_dir.replace("/Postprocess/out","")
mp = open(first,'r')
#mp2 = open(sys.argv[1].replace("s12","s3"),'r')
# set working dir
os.chdir(html_prefix)
if not os.path.exists(html_prefix+"asmstats.out"):
libPath = rund.replace("bin", "lib")
#print "perl -I %s %s/perl/statistics.pl %s > %sasmstats.out"%(libPath,utils,ref_asm,html_prefix)
run_process(_settings,"perl -I %s %s/perl/statistics.pl %s > %sasmstats.out"%(libPath,utils,ref_asm,html_prefix),"Classify")
report = open(html_prefix+"asmstats.out",'r')
initialStep = "Browse Results"
steps = []
steps.append("Preprocess")
steps.append("Assemble")
steps.append("MapReads")
steps.append("FindORFS")
steps.append("FindRepeats")
steps.append("Scaffold")
steps.append("FindScaffoldORFS")
steps.append("Abundance")
steps.append("Annotate")
steps.append("FunctionalAnnotation")
steps.append("Propagate")
steps.append("Classify")
steps.append("Browse Results")
step_status = {}
step_status["Preprocess"] = "OK"
step_status["Assemble"] = "OK"
step_status["MapReads"] = "OK"
step_status["FindORFS"] = "OK"
step_status["FindRepeats"] = "OK"
step_status["Scaffold"] = "OK"
step_status["FindScaffoldORFS"] = "OK"
step_status["Abundance"] = "FAIL"
step_status["Annotate"] = "FAIL"
step_status["FunctionalAnnotation"] = "FAIL"
step_status["Propagate"] = "NONE"
step_status["Classify"] = "NONE"
step_status["Browse Results"] = "OK"
##get status of each step from Log dir
for step in steps:
if step == "Browse Results":
continue
stepn = step.lower()
started = False
completed = False
skipped = False
if os.path.exists("%s/Logs/%s.started"%(MA_dir,stepn)):
started = True
if os.path.exists("%s/Logs/%s.ok"%(MA_dir,stepn)):
completed = True
if os.path.exists("%s/Logs/%s.skip"%(MA_dir,stepn)):
skipped = True
if completed and not skipped:
step_status[step] = "OK"
elif skipped:
step_status[step] = "SKIP"
elif started and not completed:
step_status[step] = "FAIL"
elif not started:
step_status[step] = "NONE"
else:
step_status[step] = "NONE"
#+male1 /cbcb/project-scratch/sergek/metAMOS/individualAsms/m1_asm proba b- metaphyler=1
## call Dan's script, for now on a single sample/run
cpfile = open("%s/plot.tab"%(html_prefix),'w')
cpfile.write("+sample1\t%s\tproba\tb-\tmetaphyler=1\n"%(MA_dir))
cpfile.close()
#os.system("python %s/python/create_plots.py %s/plot.tab proba1"%(utils,html_prefix))
create_plots("%s/plot.tab"%(html_prefix),"%s"%("proba1"))
##update counts
#count reads
os.system("cat %s/Preprocess/out/*.*.fasta | grep -c \">\" > readcount.txt"%(MA_dir))
readcount = open("readcount.txt",'r').read().replace("\n","")
#print readcount
os.system("rm readcount.txt")
#count contigs
os.system("grep -c \">\" %s/Assemble/out/proba.asm.contig > contigcount.txt"%(MA_dir))
contigcount = open("contigcount.txt",'r').read().replace("\n","")
#print contigcount
os.system("rm contigcount.txt")
#count scaffolds
os.system("grep -c \">\" %s/Scaffold/out/proba.scaffolds.final > scafcount.txt"%(MA_dir))
scaffoldcount = open("scafcount.txt",'r').read().replace("\n","")
#print scaffoldcount
os.system("rm scafcount.txt")
#count scaffolds
os.system("grep -c \">\" %s/Scaffold/out/proba.motifs > motifcount.txt"%(MA_dir))
motifcount = open("motifcount.txt",'r').read().replace("\n","")
#print motifcount
os.system("rm motifcount.txt")
#count ORFs
os.system("grep -c \">\" %s/FindORFS/out/proba.fna > orfcount.txt"%(MA_dir))
orfcount = open("orfcount.txt",'r').read().replace("\n","")
#print orfcount
os.system("rm orfcount.txt")
##copy stuff
for step in steps:
# step = step.lower()
if os.path.exists("%s/javascript/%s.html"%(utils,step)):
os.system("cp %s/javascript/%s.html %s/"%(utils,step,html_prefix))
os.system("cp %s/Logs/COMMANDS.log %s/pipeline.commands"%(MA_dir,html_prefix))
os.system("cp %s/pipeline.run %s/pipeline.summary"%(MA_dir,html_prefix))
os.system("cp %s/javascript/style.css %s/"%(utils,html_prefix)) # TEMP: change back to cp
os.system("cp -r %s/../KronaTools/src %s/../KronaTools/img %s/"%(utils, utils, html_prefix)) # TODO: unhack KronaTools path
# os.system("cp %s/blocks.jpg %s/"%(img,html_prefix))
# os.system("cp %s/blocks_small.jpg %s/"%(img,html_prefix))
os.system("cp %s/blocks_dark_tiny.png %s/"%(img,html_prefix))
os.system("cp %s/name.png %s/"%(img,html_prefix))
# generate dynamic java scripts
# first classify and propagate
#os.system("python %s/python/get_classify_stats.py %s/propagate.in.clusters %s/propagate.out.clusters %s/DB/tax_key.tab %s Classify.html Propagate.html %s"%(utils, html_prefix, html_prefix, utils, html_prefix, taxa_level))
get_classify_stats("%s/propagate.in.clusters"%(html_prefix),"%s/propagate.out.clusters"%(html_prefix),"%s/tax_key.tab"%(dbdir),"%s"%(html_prefix),"Classify.html","Propagate.html","%s"%(taxa_level))
# generate preprocess
preprocess = markup.page()
preprocess.init()#bodyattrs={'style':"margin:0px"})
preprocess.p()
nQC = 0
for i in range(1, nLibs + 1):
if os.path.exists("%s/lib%d.1.fastqc/fastqc_report.html"%(html_prefix, i)):
nQC = nQC + 1
summary = open("%s/pipeline.ini"%(MA_dir), 'r')
libcnt = 1
format = None
mmin = 0
mmax = 0
mated = False
interleaved = False
innie = False
linkerType = ""
libadded = False
firstLib = True
for line in summary:
line = line.replace("\n","")
if "#" in line:
continue
elif "asmcontigs:" in line:
asmc = line.replace("\n","").split("\t")[-1]
if len(asmc) <= 2:
continue
preprocess.add("Supplied assembly: %s"%(asmc))
preprocess.br()
elif "format:" in line:
if format and not libadded:
outputLibraryInfo(html_prefix, preprocess, firstLib, libcnt, format, mated, interleaved, mmin, mmax, nQC > 0)
libcnt += 1
libadded = False
format = line.replace("\n","").split("\t")[-1]
elif "mated:" in line:
mated = line.replace("\n","").split("\t")[-1]
elif "innie:" in line:
innie = line.replace("\n","").split("\t")[-1]
elif "linker:" in line:
linkerType = line.replace("\n","").split("\t")[-1]
elif "interleaved:" in line:
interleaved = line.replace("\n","").split("\t")[-1]
elif "f1:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "f2:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
libadded = True
elif "frg" in line:
data = line.split("\t")
mated = False
libadded = True
if format and not libadded:
outputLibraryInfo(html_prefix, preprocess, firstLib, libcnt, format, mated, interleaved, mmin, mmax, nQC > 0)
preprocess.table.close()
summary.close()
preprocess_out = open("%s/Preprocess.html"%(html_prefix), 'w')
preprocess_out.write(preprocess.__str__())
preprocess_out.close()
# todo, need to add report for MapReads including # reads mapped (%), contig coverage histogram, and % reads between contigs and number of links histogram. Also re-estimated insert sizes for each lib
#mapreads = markup.page()
#mapreads.init(bodyattrs={'style':"margin:0px"})
#mapreads.img(src_="hist_ctgcvg.png",height_="100%",width_="100%")
#mapreads_out = open("%s/MapReads.html"%(html_prefix), 'w')
#mapreads_out.write(mapreads.__str__())
##This will create ScaffoldSizes.png,ContigSizes.png
##create code to automatically generate .js files for HTML report
## let's start with Abundance
#abundance_js = open(html_prefix+"abundance.js",'w')
rdata = []
for line in report:
rdata.append(line)
if not os.path.exists(html_prefix+"covstats.out"):
run_process(_settings,"%s/analyze-read-depth -x 2 %s > %scovstats.out"%(rund,amosbnk,html_prefix),"Classify")
ff = open(html_prefix+"covstats.out",'r')
covdata = []
#covdata = ff.readlines()
#zflag = 0
for line in ff:
covdata.append(line)
if not os.path.exists(html_prefix+"stats.out"):
#os.system("%s/astats %s > %sstats.out"%(rund,amosbnk,html_prefix))
run_process(_settings,"%s/astats %s > %sstats.out"%(rund,amosbnk,html_prefix),"Classify")
dd = open(html_prefix+"stats.out",'r')
ddata = dd.readlines()
ddf = ""
bflag = 0
cflag = 0
rflag = 0
for line in ddata:
if "<body>" in line:
bflag = 1
ddf += "<table border=\"1\">"
elif "[Contigs]" in line:
cflag = 1
ddf += line
elif "[Small" in line:
cflag = 0
elif "[Big" in line:
cflag = 0
elif "[Reads]" in line:
rflag = 1
ddf += line
elif cflag != 0 or rflag != 0:
if "N50" not in line:
ddf += line
else:
continue
mp.readline()
cov = []
abund = []
ids = []
mpd = mp.readlines()
phylum = False
for line in mpd:
if ">phylum" in line:
phylum = True
if len(line) < 3:
continue
data = line.split("\t")
if len(data) < 2:
continue
if not phylum:
continue
ids.append(data[0])
#cov.append(int(float(data[2])))
abund.append(100*float(data[1]))
# Create a chart object of 200x100 pixels
# chart2 = StackedVerticalBarChart(600, 300)
chart2 = PieChart3D(550, 300)
chart2.set_colours(["0A8C8A","EBB671","DE091A"])
# Add some data
chart2.add_data(abund)
# chart2.add_data(abund2)
# Assign the labels to the pie data
chart2.set_pie_labels(ids)
# chart2.set_axis_labels(Axis.BOTTOM, ids)
# Download the chart
try:
chart2.download(html_prefix+'abund.png')
except:
print "Warning: could not download abund.png"
chart = GroupedHorizontalBarChart(600, 500, x_range=(0,100))
chart.set_bar_width(30)
chart.set_colours(("FF0000","0000FF"))
#chart.set_colours_within_series(("FF0000","FF7F00","FFFF00","00FF00","0000FF","8B00FF","FFFFFF"))
# chart.set_colours(['00ff00', 'ff0000'])
chart.add_data(abund)
#chart.add_data(abund2)
#chart.add_data([1,4,9,16,25])
#category = ["even","staggered"]
#chart.set_legend(category)
ids = ids[::-1]
chart.set_axis_labels(Axis.LEFT, ids)
chart.set_axis_labels(Axis.BOTTOM, [0,10,20,30,40,50,60,70,80,90,100])
#chart.set_axis_labels(Axis.LEFT, ["0)
index = chart.set_axis_labels(Axis.BOTTOM, ['Abundance (%)'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
index = chart.set_axis_labels(Axis.LEFT, ['Phylum'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
try:
chart.download(html_prefix+'bar-phylum.png')
except:
print "Warning: could not download bar-phylum.png"
dt = datetime.now()
ds = dt.strftime("%d %b %Y,<br/>%l:%M%p")
title = "metAMOS report"
# header is blank for now
header = []
# write the javascript we need on the page
script = []
script.append("<script type=\"text/javascript\">")
script.append("var steps = ['%s'];"%("','".join(steps)))
script.append("function load(step) {")
script.append(" for (var i = 0; i < steps.length; i++) {")
script.append(" var current = steps[i].toLowerCase();")
script.append(" if (current == step) {")
script.append(" document.getElementById(step + 'Button').className = 'menuItemSelected';")
script.append(" document.getElementById(step).style.display = 'block';")
script.append(" document.getElementById(step + 'Marker').className = 'markerSelected';")
script.append(" } else {")
script.append(" document.getElementById(current + 'Button').className = 'menuItemUnselected';")
script.append(" document.getElementById(current).style.display = 'none';")
script.append(" document.getElementById(current + 'Marker').className = 'markerUnselected';")
script.append(" }")
script.append(" }")
script.append("}")
script.append("")
script.append("</script>")
#<link rel="shortcut icon" href="../assets/ico/favicon.ico">
#<link rel="apple-touch-icon-precomposed" sizes="144x144" href="../assets/ico/apple-touch-icon-144-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="114x114" href="../assets/ico/apple-touch-icon-114-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="72x72" href="../assets/ico/apple-touch-icon-72-precomposed.png">
#<link rel="apple-touch-icon-precomposed" href="../assets/ico/apple-touch-icon-57-precomposed.png">
# generate the dictionary of javascript pages we need
scripts = {}
# scripts["file://%s/javascript/jquery-latest.js"%(utils)] = "javascript"
# scripts["http://code.jquery.com/jquery-latest.js"] = "javascript"
# now a javascript for each page
for step in steps:
scripts["%s.js"%(step.lower())] = "javascript"
# attributes for the body tax
body = {}
body["onload"] = "load('%s')"%(initialStep.lower())
# the footer for the page
footer = ""#"Generated %s"%(ds)
#styles = ( 'style2.css')#'./html/bootstrap.css', './html/boostrap-responsive.css')#'style2.css')#'layout.css', 'alt.css', 'images.css' )
#styles = ( 'layout.css', 'alt.css', 'images.css' )
#meta = ('viewport':"width=device-width, initial-scale=1.0",'description':'','author':'')
# create HTML page
page = markup.page( )
# add the javascript free form
page.add("\n".join(script))
# initialize the rest of the body/html headers
page.init( title=title, \
css='style.css', \
script=scripts,\
header='\n'.join(header), \
bodyattrs=body, \
footer=footer )
# page.br()
#page.div( class_ = 'navbar navbar-fixed-top')
#page.div( class_ = 'navbar-inner')
#page.div( class_ = 'container', style_='width:100%;height=100%')
#page.div.close()
#page.div.close()
#page.div.close()
#page.div( id_='page' )
# header
# page.add('<table style="width:100%;"><tr><td><img src="blocks_small.jpg"/></td><td><a target="_blank" href="https://github.com/treangen/metAMOS/wiki"><div><img src="name.jpg"/><br/>Under peer review</a></div></td><td class="title" style="width:100%"></td></tr></table>')
'''
page.div( id_='header', style="background-color:#B8B8B8;clear:both;text-align:center;width:100%;height:7%;border:1px solid black")
page.h1("<u>MetAMOS <font color=\"blue\">v1.0</font> metagenomic assembly & analysis report</u>" , style_="text-align:center;vertical-align:top")
page.h1.close()
#page.div( id_='title')# style="vertical-align:bottom;")
#page.font( size=14)
#page.br( )
page.div.close()
'''
#<frameset rows="40%,60%"cols="80%,20%">
#<frame src="report.krona.html">
#<frameset rows="20%,20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#<frameset rows="60%" cols="40%,40%">
#<frame src="report.krona.html">
#<frame src="report.krona2.html">
#</frameset>f
#<frameset rows="20%,20%,20%" cols="20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#</frameset>
#</html>
#font, estimate
#page.div.close()
#page.frameset( rows_="40%,60%", cols_ = "80%,20%")
#page.div()
page.table(style_="width:100%;height:100%;")
page.tr()
page.td( id_="menu", style_="padding:0px;")
page.div(style_="height:100%;")
# page.table(style_="height:100%")
# page.tr()
# page.td()#style_="border-right:1px solid black")
# page.div(style_="box-shadow:inset -1px -1px 5px #555555;")
page.add("<a target=\"_blank\" href=\"https://github.com/treangen/metAMOS/wiki\"><img style=\"padding-top:5px;\" src=\"name.png\"/>")
page.add("<img src=\"blocks_dark_tiny.png\"/></a>")
# page.add("<img src=\"blocks_tiny2.jpg\"/>")
page.add("<div style=\"padding:2px;font-size:12px;\"><a target=\"_blank\" href=\"https://github.com/treangen/metAMOS/wiki\">Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 2013 Jan 15;14(1):R2. PMID: 23320958.</a></div>")
page.add("<br/>")
# page.div.close()
# page.td.close()
# page.tr.close()
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
# page.tr()
# page.td(style_="padding:0px;")
page.table( id_="links", class_="menu" )
for step in steps:
page.tr()
status = "NA"
try:
if step_status[step] == "OK":
status = "OK"
elif step_status[step] == "FAIL":
status = "FAIL"
elif step_status[step] == "SKIP":
status = "SKIPPED"
except KeyError:
continue
tableHTML = []
tableHTML.append("<td class=\"menuItemTd\"><a class=\"menuLink\" href=\"javascript:void(0)\"><div class=\"menuItem %s\"><div id=\"%sButton\" class=\"menuItemUnselected\" onclick=\"load('%s');\">"%(status.lower(), step.lower(), step.lower()))
tableHTML.append("<table style='width:100%%;'><tr><td style='width:100%%;'><span class='step %sText'>%s</span>"%(status.lower(), step))
tableHTML.append("<br>")
tableHTML.append("<span class='status %sText'>%s</span></td></tr></table>"%(status.lower(), status))
tableHTML.append("</div></div></a></td><td><div id='%sMarker' class='markerUnselected'>●</div></td>"%(step.lower()))
page.add("\n".join(tableHTML))
page.tr.close()
page.table.close()
# page.td.close()
# page.tr.close()
#page.ul.close()
# page.tr()
# page.td(style_="height:100%;")#border-right:1px solid black")
page.div(class_="notes")
page.add("<div style=\"font-size:14px;\"><br/><a target=\"_blank\" href=\"pipeline.summary\">Pipeline summary</a><br/>")
page.add("<a target=\"_blank\" href=\"pipeline.commands\">Run commands</a><br/><br/></div>")
tableHTML = []
tableHTML.append("<table style=\"font-size:12px\"><tr>")
tableHTML.append("<tr><td>Version:</td><td>1.0</td></tr>")
tableHTML.append("<tr><td>Created:<br/> </td><td>%s</td></tr>"%(ds))
tableHTML.append("</table>")
page.add("\n".join(tableHTML))
page.div.close()
# page.td.close()
# page.tr.close()
# page.table.close()
page.div.close()
page.td.close()
page.td( id_="krona", style_="width:100%;height:100%padding:0px;")
page.table(class_="charts",style_="width:100%;height:100%")
page.tr()
page.td(class_="main", style_="height:100%", colspan_="4")
page.div(class_="shadow")
page.table(style_="width:100%;height:100%")
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.tr()
page.td()
page.td.close()
page.td(class_="inset")
for step in steps:
if step == "Browse Results":
page.iframe( id_=step.lower(), src_="../.", style_="display:none;" )
else:
page.iframe( id_=step.lower(), src_="%s.html"%(step), style_="display:none;" )
page.iframe.close()
page.td.close()
page.td()
page.td.close()
page.tr.close()
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.table.close()
page.div.close()
page.td.close()
page.tr.close()
#page.tr()
#page.div(id_="sideplots")#, style_="background-color:#FFFFFF;width:20.5%%;height:88%%;float:right;border:1px")
#page.div(id_="sideplot1", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.td(style_="width:25%")
#page.img(class_="chart", src_="ContigSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot2", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_contigs.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot3", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="ScaffoldSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot4", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_scaffold.png")
#page.td.close()
#page.div.close()
#page.div.close()
#page.td.close()
#page.tr.close()
page.table.close()
#page.iframe(src_="bar-phylum.png",style_="width:100%;height:100%;hspace=10")
#page.frameset(rows_="100%" ,cols_="100%")
page.td.close()
#page.li("<a target=\"_blank\" href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>")
#page.li("<a href=\"http://cbcb.umd.edu/~mpop/Software.shtml\">Related software</a>")
#page.li("<a href=\"http://cbcb.umd.edu\">CBCB</a>")
# page.li( items[1] )
#page.ul.close( )
#page.div.close()
page.div( id_="content")
#page.div( id_='wrapper')
#page.div( id_="content")
#page.a( "Reference assembly:", class_='internal', href='%s'%(ref_asm) )
#paragraphs = ( ddf )
cnt = 0
#table_html = ""
if 0:
page.table(border="1",style_="width=80%")
for contig in covdata:
if cnt == 0:
#table_html += "<table border=\"1\">\n"
page.tr()
page.td("High Coverage Contig ID")
page.td("Coverage")
page.tr.close()
#table_html += "<tr><td> High Coverage Contig ID </td> <td> Coverage </td></tr>\n"
page.tr()
page.td(contig.split("\t")[0])
page.td(contig.split(" ")[-1])
cnt +=1
'''
#page.table.close()
#page.p( paragraphs )
#page.p(style_="font-size:6px")
page.table(border="0")
#page.tr()
#page.(
if 1:
#table_html = ""
#table_html += "<table border=\"1\">\n"
for contig in rdata:
page.tr()
#table_html += "<tr>\n"
index = 0
for item in contig.split("\t"):
index +=1
if index == 8 or index == 7:
continue
elif index == 1 and "File" not in item:
page.td("<a target=\"_blank\" href=\""+ref_asm+"\">%s</a>"%(ref_asm.split("/")[-1]))
continue
page.td("<p style=\"font-size:15px\">"+item+"</p>")
#table_html += "<td> %s </td> \n"%(item)
page.tr.close()
#table_html += "</tr>\n"
page.table.close()
#table_html += "</table>\n"
#page.p( table_html )
#page.p.close()
page.div.close()
'''
page.td( id_="quick" )
page.div(style_="height:100%")
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
page.br()
page.div(class_="stats")
page.table(class_="stats")
page.add("<tr><td class=\"number\">%s</td><td>Reads</td></tr>"%intOrZero(readcount))
page.add("<tr><td class=\"number\">%s</td><td>Contigs</td></tr>"%intOrZero(contigcount))
page.add("<tr><td class=\"number\">%s</td><td>Scaffolds</td></tr>"%intOrZero(scaffoldcount))
page.add("<tr><td class=\"number\">%s</td><td>ORFs</td></tr>"%intOrZero(orfcount))
page.add("<tr><td class=\"number\">%s</td><td>Motifs</td></tr>"%intOrZero(motifcount))
page.table.close()
page.div.close()
page.div.close()
page.td.close()
page.tr.close()
page.table.close()
#page.div( id_="metaphyler", style="float:left;width:28%;height:70%")
#page.img( hspace=10, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
#page.img( hspace=10, width=600, height=500, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
fout = open(html_prefix+"summary.html",'w')
fout.write(page.__str__())
fout.close()
def create_summary(first,amosbnk,prefix,ref_asm,utils,img,rund,nLibs,taxa_level,dbdir):
#if __name__ == "__main__":
# if len(sys.argv) < 5:
# print "usage: create_report.py <metaphyler tab file> <AMOS bnk> <output prefix> <ref_asm> <Utils dir> <run dir> <# of libs> <taxa level of classifications>"
# sys.exit(0)
html_prefix = prefix
prefix = prefix.replace("/html/", "")
MA_dir = prefix
MA_dir = MA_dir.replace("/Postprocess/out","")
mp = open(first,'r')
#mp2 = open(sys.argv[1].replace("s12","s3"),'r')
# set working dir
os.chdir(html_prefix)
if not os.path.exists(html_prefix+"asmstats.out"):
libPath = rund.rsplit(os.sep,1)[0] + os.sep + rund.rsplit(os.sep,1)[-1].replace("bin", "lib")
#print "perl -I %s %s/perl/statistics.pl %s > %sasmstats.out"%(libPath,utils,ref_asm,html_prefix)
run_process(_settings,"perl -I %s %s/perl/statistics.pl %s > %sasmstats.out"%(libPath,utils,ref_asm,html_prefix),"Postprocess")
report = open(html_prefix+"asmstats.out",'r')
initialStep = "Classify"
# get metamos version
version = "1.0"
summary = open("%s/pipeline.run"%(MA_dir), 'r')
for line in summary:
line = line.replace("\n","")
if "#" in line:
continue
elif "metAMOS Version:" in line:
version = line.replace("\n","").split("\t")[-1]
summary.close()
steps = []
steps.append("Preprocess")
steps.append("Assemble")
steps.append("MapReads")
steps.append("Validate")
#steps.append("MultiAlign")
steps.append("FindORFS")
steps.append("FindRepeats")
steps.append("Scaffold")
steps.append("FindScaffoldORFS")
steps.append("Abundance")
steps.append("Classify")
steps.append("FunctionalAnnotation")
steps.append("Propagate")
steps.append("Bin")
steps.append("Browse Results")
step_status = {}
step_status["Preprocess"] = "OK"
step_status["Assemble"] = "OK"
step_status["MapReads"] = "OK"
step_status["Validate"] = "OK"
#step_status["MultiAlign"] = "OK"
step_status["FindORFS"] = "OK"
step_status["FindRepeats"] = "OK"
step_status["Scaffold"] = "OK"
step_status["FindScaffoldORFS"] = "OK"
step_status["Abundance"] = "FAIL"
step_status["Classify"] = "FAIL"
step_status["FunctionalAnnotation"] = "FAIL"
step_status["Propagate"] = "NONE"
step_status["Bin"] = "NONE"
step_status["Browse Results"] = "OK"
##get status of each step from Log dir
for step in steps:
if step == "Browse Results":
continue
stepn = step.lower()
started = False
completed = False
skipped = False
if os.path.exists("%s/Logs/%s.started"%(MA_dir,stepn)):
started = True
if os.path.exists("%s/Logs/%s.ok"%(MA_dir,stepn)):
completed = True
if os.path.exists("%s/Logs/%s.skip"%(MA_dir,stepn)):
skipped = True
if completed and not skipped:
step_status[step] = "OK"
elif skipped:
step_status[step] = "SKIP"
elif started and not completed:
step_status[step] = "FAIL"
elif not started:
step_status[step] = "NONE"
else:
step_status[step] = "NONE"
#+male1 /cbcb/project-scratch/sergek/metAMOS/individualAsms/m1_asm proba b- metaphyler=1
## call Dan's script, for now on a single sample/run
cpfile = open("%s/plot.tab"%(html_prefix),'w')
cpfile.write("+sample1\t%s\tproba\tb-\tmetaphyler=1\n"%(MA_dir))
cpfile.close()
#os.system("python %s/python/create_plots.py %s/plot.tab proba1"%(utils,html_prefix))
if _havePlots:
create_plots("%s/plot.tab"%(html_prefix),"%s"%("proba1"))
##update counts
#count reads
os.system("cat `ls %s/Preprocess/out/* |egrep 'lib[0-9]*\.fasta$'` | grep -c \">\" > readcount.txt"%(MA_dir))
readcount = open("readcount.txt",'r').read().replace("\n","")
#print readcount
os.system("rm readcount.txt")
#count contigs
os.system("grep -c \">\" %s/Assemble/out/proba.asm.contig > contigcount.txt"%(MA_dir))
contigcount = open("contigcount.txt",'r').read().replace("\n","")
#print contigcount
os.system("rm contigcount.txt")
#count scaffolds
os.system("grep -c \">\" %s/Scaffold/out/proba.scaffolds.final > scafcount.txt"%(MA_dir))
scaffoldcount = open("scafcount.txt",'r').read().replace("\n","")
#print scaffoldcount
os.system("rm scafcount.txt")
#count scaffolds
os.system("grep -c \">\" %s/Scaffold/out/proba.motifs > motifcount.txt"%(MA_dir))
motifcount = open("motifcount.txt",'r').read().replace("\n","")
#print motifcount
os.system("rm motifcount.txt")
#count ORFs
os.system("grep -c \">\" %s/FindORFS/out/proba.fna > orfcount.txt"%(MA_dir))
orfcount = open("orfcount.txt",'r').read().replace("\n","")
#print orfcount
os.system("rm orfcount.txt")
##copy stuff
for step in steps:
# step = step.lower()
if os.path.exists("%s/javascript/%s.html"%(utils,step)):
os.system("cp %s/javascript/%s.html %s/"%(utils,step,html_prefix))
os.system("cp %s/Logs/COMMANDS.log %s/pipeline.commands"%(MA_dir,html_prefix))
os.system("cp %s/pipeline.run %s/pipeline.summary"%(MA_dir,html_prefix))
os.system("cp %s/javascript/style.css %s/"%(utils,html_prefix)) # TEMP: change back to cp
os.system("cp -r %s/../KronaTools/src %s/../KronaTools/img %s/"%(utils, utils, html_prefix)) # TODO: unhack KronaTools path
# os.system("cp %s/blocks.jpg %s/"%(img,html_prefix))
# os.system("cp %s/blocks_small.jpg %s/"%(img,html_prefix))
os.system("cp %s/blocks_dark_tiny.png %s/"%(img,html_prefix))
os.system("cp %s/name.png %s/"%(img,html_prefix))
# generate dynamic java scripts
# first classify and propagate
#os.system("python %s/python/get_classify_stats.py %s/propagate.in.clusters %s/propagate.out.clusters %s/DB/tax_key.tab %s Classify.html Propagate.html %s"%(utils, html_prefix, html_prefix, utils, html_prefix, taxa_level))
get_classify_stats("%s/propagate.in.clusters"%(html_prefix),"%s/propagate.out.clusters"%(html_prefix),"%s/tax_key.tab"%(dbdir),"%s"%(html_prefix),"Bin.html","Propagate.html","%s"%(taxa_level))
# generate preprocess
preprocess = markup.page()
preprocess.init(css="style.css")#bodyattrs={'style':"margin:0px"})
preprocess.p()
nQC = 0
for i in range(1, nLibs + 1):
if os.path.exists("%s/lib%d.1.fastqc/fastqc_report.html"%(html_prefix, i)):
nQC = nQC + 1
summary = open("%s/pipeline.ini"%(MA_dir), 'r')
libcnt = 1
format = None
mmin = 0
mmax = 0
mated = False
interleaved = False
innie = False
linkerType = ""
libadded = False
firstLib = True
headerArray = []
dataArray = []
for line in summary:
line = line.replace("\n","")
if "#" in line:
continue
elif "asmcontigs:" in line:
asmc = line.replace("\n","").split("\t")[-1]
if len(asmc) <= 2:
continue
preprocess.add("<div class=\"datagrid\">Pre-assembled contigs input: %s</div>"%(asmc))
preprocess.br()
elif "format:" in line:
if format and not libadded:
outputLibraryInfo(headerArray, dataArray, firstLib, libcnt, format, mated, interleaved, mmin, mmax, nQC > 0)
libcnt += 1
libadded = False
format = line.replace("\n","").split("\t")[-1]
elif "mated:" in line:
mated = str2bool(line.replace("\n","").split("\t")[-1])
elif "innie:" in line:
innie = str2bool(line.replace("\n","").split("\t")[-1])
elif "linker:" in line:
linkerType = line.replace("\n","").split("\t")[-1]
elif "interleaved:" in line:
interleaved = str2bool(line.replace("\n","").split("\t")[-1])
elif "f1:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "f2:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "frg" in line:
data = line.split("\t")
if format and not libadded:
outputLibraryInfo(headerArray, dataArray, firstLib, libcnt, format, mated, interleaved, mmin, mmax, nQC > 0)
preprocess.add(getTable(headerArray, dataArray))
summary.close()
if os.path.exists("%s/Postprocess/out/html/kmergenie_report.html"%(MA_dir)):
preprocess.iframe(id_="KmerGenie", src_="kmergenie_report.html", width="800", height="5000")
preprocess_out = open("%s/Preprocess.html"%(html_prefix), 'w')
preprocess_out.write(preprocess.__str__())
preprocess_out.close()
validate_out = open("%s/Validate.html"%(html_prefix), 'w')
validate = markup.page()
validate.init(css="style.css", bodyattrs={'style':"background-color:#FFFFFF;"})
headerArray = []
dataArray = []
firstScore = True
bestAsm = ""
refs = []
if os.path.exists("%s/Postprocess/out/asm.scores"%(MA_dir)):
best = open("%s/Postprocess/out/best.asm"%(MA_dir), 'r')
bestAsm = best.read()
best.close()
laps = open("%s/Postprocess/out/asm.scores"%(MA_dir), 'r')
validate.p()
validate.add("<div class=\"datagrid\">")
validate.add("Selected assembler: %s"%(bestAsm))
ref = open("%s/Postprocess/out/ref.name"%(MA_dir), 'r')
first = True
for r in ref.xreadlines():
refs.append(r)
if first:
validate.br()
first = False
validate.add("Selected reference: %s"%(r))
ref.close()
if os.path.exists("%s/Bin/out/contaminant.true"%(MA_dir)):
cont = open("%s/Bin/out/contaminant.true"%(MA_dir), 'r')
contPercent = cont.read().split()
cont.close()
validate.br()
validate.add("<b>Sample may have contaminants, only %s%% contigs/reads >%sbp assigned to %s. Check Classify output</b>"%(contPercent[0], contPercent[2], contPercent[1]))
validate.br()
for line in laps:
line = line.replace("\n","")
if "#" in line:
continue
else:
res = line.split("\t")
outputValidate(headerArray, dataArray, firstScore, bestAsm, res)
firstScore = False
validate.add(getTable(headerArray, dataArray))
validate.add("</div>")
laps.close()
# when we have quast, we will add our table to their report, otherwise write standalone report
if os.path.exists("%s/Postprocess/out/html/quast/combined_quast_output/report.html"%(MA_dir)):
os.system("cp %s/Postprocess/out/html/quast/combined_quast_output/report.html %s/Postprocess/out/html/quast/combined_quast_output/~report.html"%(MA_dir, MA_dir))
quastIn = open("%s/Postprocess/out/html/quast/combined_quast_output/~report.html"%(MA_dir), 'r')
quastOut = open("%s/Postprocess/out/html/quast/combined_quast_output/report.html"%(MA_dir), 'w')
skip = False
output = False
for line in quastIn.xreadlines():
if not skip:
quastOut.write(line.strip().replace("<br>", "") + "\n")
elif output:
quastOut.write("margin-left: 50px;\n")
quastOut.write("padding-top: 10px;\n")
quastOut.write("background: #ffffff;\n")
output = False
if ".content" in line:
skip = True
output = True
elif "clear:" in line:
quastOut.write(line.strip() + "\n")
skip = False
output = False
quastIn.close()
quastOut.close()
validate.iframe(id_="quast", src_="quast/combined_quast_output/report.html", width="800", height="1000")
validate_out.write(validate.__str__())
validate_out.close()
# multialign step
treeScripts= {}
treeScripts["http://www.jsphylosvg.com/js/jquery/jquery-1.4.2.min.js"] = "javascript"
treeScripts["http://www.jsphylosvg.com/js/jquery/jquery.simplemodal.1.4.1.min.js"] = "javascript"
treeScripts["http://www.jsphylosvg.com/js/raphael/raphael-min.js"] = "javascript"
treeScripts["http://www.jsphylosvg.com/js/jsphylosvg-min.js?1.29"] = "javascript"
treeScripts["http://www.jsphylosvg.com/js/unitip/js/unitip.js"] = "javascript"
treeScript = []
treeScript.append("<script type=\"text/javascript\">")
treeScript.append(" var dataObject = { newick: '(M_canettii_CIPT_d:0.059437,(M_canettii_CIPT_e:0.07845,((((M_africanum_GM04118:0.00646,(M_bovis_AF2122_97:0.00269,(M_bovis_BCG_Tokyo_1:0.00013,((M_bovis_BCG_Korea_1:0.0,M_bovis_BCG_Pasteur:0.0):0.00014,M_bovis_BCG_Mexico:0.00013):0.00014):0.00294):0.00514):0.00207,(((MTBC_Beijing_NITR20:0.00914,(MTBC_CCDC5180:0.00102,(MTBC_CCDC5079:0.00423,MTBC_CCDC5079:0.00014):0.00078):0.00016):0.00368,((((MTBC_Erdman_ATCC_35:0.00075,MTBC:0.00123):0.00129,(MTBC_CDC1551:0.00245,MTBC_Haarlem3_NITR2:0.01398):0.00093):0.00065,((((MTBC_CTRI_2:0.001,(MTBC_KZN_4207:0.00014,(MTBC_KZN_605:0.00012,MTBC_KZN_1435:0.00014):0.00012):0.00071):0.00061,(MTBC_RGTB327:0.00462,MTBC_UT205:0.0012):0.00037):0.00014,MTBC_F11:0.00158):0.00109,(MTBC_H37Ra:0.00016,(MTBC_H37Rv:0.00028,MTBC_H37Rv:0.00014):0.00014):0.00281):0.00047):0.00112,MTBC_CAS_NITR204:0.009827):0.00022):0.00247,((MTBC_EAI5:0.0023,MTBC_EAI5_NITR206:0.00933):0.0035,(MTBC_RGTB423:0.00868,spades.45.asm.contig:0.0035):0.00066):0.00289):0.00015):0.07224,(M_canettii_CIPT_a:0.01891,M_canettii_CIPT_b:0.05096):0.03720):0.03909,M_canettii_CIPT_c:0.056869):0.00469):0.02099);' };")
treeScript.append(" function load() {")
treeScript.append(" var divVal = $('#svgCanvas').empty();")
treeScript.append(" var isCircular = $('#circularize-value')[0].value;")
treeScript.append(" Smits.PhyloCanvas.Render.Parameters.Rectangular.bufferX = 150;")
treeScript.append(" Smits.PhyloCanvas.Render.Parameters.Circular.bufferRadius = 0.35;")
treeScript.append(" Smits.PhyloCanvas.Render.Style.line.stroke = 'rgb(0,0,255)';")
treeScript.append(" Smits.PhyloCanvas.Render.Style.text[\"font-size\"] = 10;")
treeScript.append(" if (isCircular.toLowerCase() == 'true') {")
treeScript.append(" phylocanvas = new Smits.PhyloCanvas(")
treeScript.append(" dataObject,")
treeScript.append(" 'svgCanvas',")
treeScript.append(" 1000, 1000, 'circular'")
treeScript.append(" );")
treeScript.append(" $('#circularize-value')[0].value = 'false';")
treeScript.append(" } else {")
treeScript.append(" phylocanvas = new Smits.PhyloCanvas(")
treeScript.append(" dataObject,")
treeScript.append(" 'svgCanvas',")
treeScript.append(" 500, 500")
treeScript.append(" );")
treeScript.append(" $('#circularize-value')[0].value = 'true';")
treeScript.append(" }")
treeScript.append(" init();")
treeScript.append(" }")
treeScript.append("function snapshot() {")
treeScript.append(" var svgSource = phylocanvas.getSvgSource();")
treeScript.append(" if(svgSource) {")
treeScript.append(" var url = 'data:image/svg+xml,' + svgSource")
treeScript.append(" window.open(url);")
treeScript.append(" }")
treeScript.append(" }")
treeScript.append("</script>")
treeBody = {}
treeBody["onload"] = "load()"
maStep = markup.page()
maStep.add("\n".join(treeScript))
maStep.init(
css=("http://www.jsphylosvg.com//js/yui/build/cssfonts/fonts-min.css", "http://www.jsphylosvg.com/js/unitip/css/unitip.css"),
script=treeScripts,
bodyattrs=treeBody)
maStep.div()
maStep.add("<input type=\"button\" id=\"download-link\" onclick=\"snapshot()\" value=\"Snapshot\" />")
maStep.div.close()
maStep.div()
maStep.add("<input type=\"button\" id=\"circularize-link\" onclick=\"load()\" value=\"Toggle Circular\" />")
maStep.add("<input type=\"hidden\" id=\"circularize-value\" value=\"false\">")
maStep.div.close()
maStep.div(id_="svgCanvas")
maStep.div.close()
maStep_out = open("%s/MultiAlign.html"%(html_prefix), 'w')
maStep_out.write(maStep.__str__())
maStep_out.close()
# todo, need to add report for MapReads including # reads mapped (%), contig coverage histogram, and % reads between contigs and number of links histogram. Also re-estimated insert sizes for each lib
#mapreads = markup.page()
#mapreads.init(bodyattrs={'style':"margin:0px"})
#mapreads.img(src_="hist_ctgcvg.png",height_="100%",width_="100%")
#mapreads_out = open("%s/MapReads.html"%(html_prefix), 'w')
#mapreads_out.write(mapreads.__str__())
##This will create ScaffoldSizes.png,ContigSizes.png
##create code to automatically generate .js files for HTML report
## let's start with Abundance
#abundance_js = open(html_prefix+"abundance.js",'w')
rdata = []
for line in report:
rdata.append(line)
if not os.path.exists(html_prefix+"covstats.out"):
run_process(_settings,"%s/analyze-read-depth -x 2 %s > %scovstats.out"%(rund,amosbnk,html_prefix),"Postprocess")
ff = open(html_prefix+"covstats.out",'r')
covdata = []
#covdata = ff.readlines()
#zflag = 0
for line in ff:
covdata.append(line)
if not os.path.exists(html_prefix+"stats.out"):
if os.path.getsize("%s/Assemble/out/proba.asm.contig"%(MA_dir)) == 0:
run_process(_settings, "touch %sstats.out"%(html_prefix), "Postprocess")
else:
#os.system("%s/astats %s > %sstats.out"%(rund,amosbnk,html_prefix))
run_process(_settings,"%s/astats %s > %sstats.out"%(rund,amosbnk,html_prefix),"Postprocess")
dd = open(html_prefix+"stats.out",'r')
ddata = dd.readlines()
ddf = ""
bflag = 0
cflag = 0
rflag = 0
for line in ddata:
if "<body>" in line:
bflag = 1
ddf += "<table border=\"1\">"
elif "[Contigs]" in line:
cflag = 1
ddf += line
elif "[Small" in line:
cflag = 0
elif "[Big" in line:
cflag = 0
elif "[Reads]" in line:
rflag = 1
ddf += line
elif cflag != 0 or rflag != 0:
if "N50" not in line:
ddf += line
else:
continue
mp.readline()
cov = []
abund = []
ids = []
mpd = mp.readlines()
phylum = False
for line in mpd:
if ">phylum" in line:
phylum = True
if len(line) < 3:
continue
data = line.split("\t")
if len(data) < 2:
continue
if not phylum:
continue
ids.append(data[0])
#cov.append(int(float(data[2])))
abund.append(100*float(data[1]))
# Create a chart object of 200x100 pixels
# chart2 = StackedVerticalBarChart(600, 300)
chart2 = PieChart3D(550, 300)
chart2.set_colours(["0A8C8A","EBB671","DE091A"])
# Add some data
chart2.add_data(abund)
# chart2.add_data(abund2)
# Assign the labels to the pie data
chart2.set_pie_labels(ids)
# chart2.set_axis_labels(Axis.BOTTOM, ids)
# Download the chart
try:
chart2.download(html_prefix+'abund.png')
except:
print "Warning: could not download abund.png"
chart = GroupedHorizontalBarChart(600, 500, x_range=(0,100))
chart.set_bar_width(30)
chart.set_colours(("FF0000","0000FF"))
#chart.set_colours_within_series(("FF0000","FF7F00","FFFF00","00FF00","0000FF","8B00FF","FFFFFF"))
# chart.set_colours(['00ff00', 'ff0000'])
chart.add_data(abund)
#chart.add_data(abund2)
#chart.add_data([1,4,9,16,25])
#category = ["even","staggered"]
#chart.set_legend(category)
ids = ids[::-1]
chart.set_axis_labels(Axis.LEFT, ids)
chart.set_axis_labels(Axis.BOTTOM, [0,10,20,30,40,50,60,70,80,90,100])
#chart.set_axis_labels(Axis.LEFT, ["0)
index = chart.set_axis_labels(Axis.BOTTOM, ['Abundance (%)'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
index = chart.set_axis_labels(Axis.LEFT, ['Phylum'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
try:
chart.download(html_prefix+'bar-phylum.png')
except:
print "Warning: could not download bar-phylum.png"
dt = datetime.now()
ds = dt.strftime("%d %b %Y,<br/>%l:%M%p")
title = "metAMOS report"
# header is blank for now
header = []
# write the javascript we need on the page
script = []
script.append("<script type=\"text/javascript\">")
script.append("var steps = ['%s'];"%("','".join(steps)))
script.append("function load(step) {")
for step in steps:
if step_status[step] != "OK":
script.append(" if (step.toLowerCase() == \"%s\".toLowerCase()) {"%(step))
script.append(" return;")
script.append(" }")
script.append(" for (var i = 0; i < steps.length; i++) {")
script.append(" var current = steps[i].toLowerCase();")
script.append(" if (current == step) {")
script.append(" document.getElementById(step + 'Button').className = 'menuItemSelected';")
script.append(" document.getElementById(step).style.display = 'block';")
script.append(" document.getElementById(step + 'Marker').className = 'markerSelected';")
script.append(" } else {")
script.append(" document.getElementById(current + 'Button').className = 'menuItemUnselected';")
script.append(" document.getElementById(current).style.display = 'none';")
script.append(" document.getElementById(current + 'Marker').className = 'markerUnselected';")
script.append(" }")
script.append(" }")
script.append("}")
script.append("")
script.append("</script>")
#<link rel="shortcut icon" href="../assets/ico/favicon.ico">
#<link rel="apple-touch-icon-precomposed" sizes="144x144" href="../assets/ico/apple-touch-icon-144-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="114x114" href="../assets/ico/apple-touch-icon-114-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="72x72" href="../assets/ico/apple-touch-icon-72-precomposed.png">
#<link rel="apple-touch-icon-precomposed" href="../assets/ico/apple-touch-icon-57-precomposed.png">
# generate the dictionary of javascript pages we need
scripts = {}
# scripts["file://%s/javascript/jquery-latest.js"%(utils)] = "javascript"
# scripts["http://code.jquery.com/jquery-latest.js"] = "javascript"
# now a javascript for each page
for step in steps:
scripts["%s.js"%(step.lower())] = "javascript"
# attributes for the body tax
body = {}
body["onload"] = "load('%s')"%(initialStep.lower())
# the footer for the page
footer = ""#"Generated %s"%(ds)
#styles = ( 'style2.css')#'./html/bootstrap.css', './html/boostrap-responsive.css')#'style2.css')#'layout.css', 'alt.css', 'images.css' )
#styles = ( 'layout.css', 'alt.css', 'images.css' )
#meta = ('viewport':"width=device-width, initial-scale=1.0",'description':'','author':'')
# create HTML page
page = markup.page( )
# add the javascript free form
page.add("\n".join(script))
# initialize the rest of the body/html headers
page.init( title=title, \
css='style.css', \
script=scripts,\
header='\n'.join(header), \
bodyattrs=body, \
footer=footer )
# page.br()
#page.div( class_ = 'navbar navbar-fixed-top')
#page.div( class_ = 'navbar-inner')
#page.div( class_ = 'container', style_='width:100%;height=100%')
#page.div.close()
#page.div.close()
#page.div.close()
#page.div( id_='page' )
# header
# page.add('<table style="width:100%;"><tr><td><img src="blocks_small.jpg"/></td><td><a target="_blank" href="https://github.com/treangen/metAMOS/wiki"><div><img src="name.jpg"/><br/>Under peer review</a></div></td><td class="title" style="width:100%"></td></tr></table>')
'''
page.div( id_='header', style="background-color:#B8B8B8;clear:both;text-align:center;width:100%;height:7%;border:1px solid black")
page.h1("<u>MetAMOS <font color=\"blue\">v1.0</font> metagenomic assembly & analysis report</u>" , style_="text-align:center;vertical-align:top")
page.h1.close()
#page.div( id_='title')# style="vertical-align:bottom;")
#page.font( size=14)
#page.br( )
page.div.close()
'''
#<frameset rows="40%,60%"cols="80%,20%">
#<frame src="report.krona.html">
#<frameset rows="20%,20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#<frameset rows="60%" cols="40%,40%">
#<frame src="report.krona.html">
#<frame src="report.krona2.html">
#</frameset>f
#<frameset rows="20%,20%,20%" cols="20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#</frameset>
#</html>
#font, estimate
#page.div.close()
#page.frameset( rows_="40%,60%", cols_ = "80%,20%")
#page.div()
page.table(style_="width:100%;height:100%;")
page.tr()
page.td( id_="menu", style_="padding:0px;")
page.div(style_="height:100%;")
# page.table(style_="height:100%")
# page.tr()
# page.td()#style_="border-right:1px solid black")
# page.div(style_="box-shadow:inset -1px -1px 5px #555555;")
page.add("<a target=\"_blank\" href=\"https://github.com/treangen/metAMOS/wiki\"><img style=\"padding-top:5px;\" src=\"name.png\"/>")
page.add("<img src=\"blocks_dark_tiny.png\"/></a>")
# page.add("<img src=\"blocks_tiny2.jpg\"/>")
page.add("<div style=\"padding:2px;font-size:12px;\"><a target=\"_blank\" href=\"http://genomebiology.com/2013/14/1/R2\">Treangen TJ, Koren S, et. al. Genome Biol. 2013 Jan 15;14(1):R2. PMID: 23320958.</a></div>")
page.add("<br/>")
# page.div.close()
# page.td.close()
# page.tr.close()
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
# page.tr()
# page.td(style_="padding:0px;")
page.table( id_="links", class_="menu" )
for step in steps:
page.tr()
status = "NA"
try:
if step_status[step] == "OK":
status = "OK"
elif step_status[step] == "FAIL":
status = "FAIL"
elif step_status[step] == "SKIP":
status = "SKIPPED"
except KeyError:
continue
tableHTML = []
tableHTML.append("<td class=\"menuItemTd\"><a class=\"menuLink\" href=\"javascript:void(0)\"><div class=\"menuItem %s\"><div id=\"%sButton\" class=\"menuItemUnselected\" onclick=\"load('%s');\">"%(status.lower(), step.lower(), step.lower()))
tableHTML.append("<table style='width:100%%;'><tr><td style='width:100%%;'><span class='step %sText'>%s</span>"%(status.lower(), step))
tableHTML.append("<br>")
tableHTML.append("<span class='status %sText'>%s</span></td></tr></table>"%(status.lower(), status))
tableHTML.append("</div></div></a></td><td><div id='%sMarker' class='markerUnselected'>●</div></td>"%(step.lower()))
page.add("\n".join(tableHTML))
page.tr.close()
page.table.close()
# page.td.close()
# page.tr.close()
#page.ul.close()
# page.tr()
# page.td(style_="height:100%;")#border-right:1px solid black")
page.div(class_="notes")
page.add("<div style=\"font-size:14px;\"><br/><a target=\"_blank\" href=\"pipeline.summary\">Pipeline summary</a><br/>")
page.add("<a target=\"_blank\" href=\"pipeline.commands\">Run commands</a><br/><br/></div>")
tableHTML = []
tableHTML.append("<table style=\"font-size:12px\"><tr>")
tableHTML.append("<tr><td>Version:</td><td>%s</td></tr>"%(version))
tableHTML.append("<tr><td>Created:<br/> </td><td>%s</td></tr>"%(ds))
tableHTML.append("</table>")
page.add("\n".join(tableHTML))
page.div.close()
# page.td.close()
# page.tr.close()
# page.table.close()
page.div.close()
page.td.close()
page.td( id_="krona", style_="width:100%;height:100%padding:0px;")
page.table(class_="charts",style_="width:100%;height:100%")
page.tr()
page.td(class_="main", style_="height:100%", colspan_="4")
page.div(class_="shadow")
page.table(style_="width:100%;height:100%")
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.tr()
page.td()
page.td.close()
page.td(class_="inset")
for step in steps:
if step == "Browse Results":
page.iframe( id_=step.lower(), src_="../.", style_="display:none;" )
else:
page.iframe( id_=step.lower(), src_="%s.html"%(step), style_="display:none;" )
page.iframe.close()
page.td.close()
page.td()
page.td.close()
page.tr.close()
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.table.close()
page.div.close()
page.td.close()
page.tr.close()
#page.tr()
#page.div(id_="sideplots")#, style_="background-color:#FFFFFF;width:20.5%%;height:88%%;float:right;border:1px")
#page.div(id_="sideplot1", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.td(style_="width:25%")
#page.img(class_="chart", src_="ContigSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot2", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_contigs.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot3", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="ScaffoldSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot4", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_scaffold.png")
#page.td.close()
#page.div.close()
#page.div.close()
#page.td.close()
#page.tr.close()
page.table.close()
#page.iframe(src_="bar-phylum.png",style_="width:100%;height:100%;hspace=10")
#page.frameset(rows_="100%" ,cols_="100%")
page.td.close()
#page.li("<a target=\"_blank\" href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>")
#page.li("<a href=\"http://cbcb.umd.edu/~mpop/Software.shtml\">Related software</a>")
#page.li("<a href=\"http://cbcb.umd.edu\">CBCB</a>")
# page.li( items[1] )
#page.ul.close( )
#page.div.close()
page.div( id_="content")
#page.div( id_='wrapper')
#page.div( id_="content")
#page.a( "Reference assembly:", class_='internal', href='%s'%(ref_asm) )
#paragraphs = ( ddf )
cnt = 0
#table_html = ""
if 0:
page.table(border="1",style_="width=80%")
for contig in covdata:
if cnt == 0:
#table_html += "<table border=\"1\">\n"
page.tr()
page.td("High Coverage Contig ID")
page.td("Coverage")
page.tr.close()
#table_html += "<tr><td> High Coverage Contig ID </td> <td> Coverage </td></tr>\n"
page.tr()
page.td(contig.split("\t")[0])
page.td(contig.split(" ")[-1])
cnt +=1
'''
#page.table.close()
#page.p( paragraphs )
#page.p(style_="font-size:6px")
page.table(border="0")
#page.tr()
#page.(
if 1:
#table_html = ""
#table_html += "<table border=\"1\">\n"
for contig in rdata:
page.tr()
#table_html += "<tr>\n"
index = 0
for item in contig.split("\t"):
index +=1
if index == 8 or index == 7:
continue
elif index == 1 and "File" not in item:
page.td("<a target=\"_blank\" href=\""+ref_asm+"\">%s</a>"%(ref_asm.split("/")[-1]))
continue
page.td("<p style=\"font-size:15px\">"+item+"</p>")
#table_html += "<td> %s </td> \n"%(item)
page.tr.close()
#table_html += "</tr>\n"
page.table.close()
#table_html += "</table>\n"
#page.p( table_html )
#page.p.close()
page.div.close()
'''
page.td( id_="quick" )
page.div(style_="height:100%")
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
page.br()
page.div(class_="stats")
page.table(class_="stats")
page.add("<tr><td class=\"number\">%s</td><td>Reads</td></tr>"%intOrZero(readcount))
page.add("<tr><td class=\"number\">%s</td><td>Contigs</td></tr>"%intOrZero(contigcount))
page.add("<tr><td class=\"number\">%s</td><td>Scaffolds</td></tr>"%intOrZero(scaffoldcount))
page.add("<tr><td class=\"number\">%s</td><td>ORFs</td></tr>"%intOrZero(orfcount))
page.add("<tr><td class=\"number\">%s</td><td>Motifs</td></tr>"%intOrZero(motifcount))
page.table.close()
page.div.close()
page.div.close()
page.td.close()
page.tr.close()
page.table.close()
#page.div( id_="metaphyler", style="float:left;width:28%;height:70%")
#page.img( hspace=10, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
#page.img( hspace=10, width=600, height=500, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
fout = open(html_prefix+"summary.html",'w')
fout.write(page.__str__())
fout.close()
def create_summary(first, amosbnk, prefix, ref_asm, utils, img, rund, nLibs,
taxa_level, dbdir):
#if __name__ == "__main__":
# if len(sys.argv) < 5:
# print "usage: create_report.py <metaphyler tab file> <AMOS bnk> <output prefix> <ref_asm> <Utils dir> <run dir> <# of libs> <taxa level of classifications>"
# sys.exit(0)
html_prefix = prefix
prefix = prefix.replace("/html/", "")
MA_dir = prefix
MA_dir = MA_dir.replace("/Postprocess/out", "")
mp = open(first, 'r')
#mp2 = open(sys.argv[1].replace("s12","s3"),'r')
# set working dir
os.chdir(html_prefix)
if not os.path.exists(html_prefix + "asmstats.out"):
libPath = rund.rsplit(os.sep, 1)[0] + os.sep + rund.rsplit(
os.sep, 1)[-1].replace("bin", "lib")
#print "perl -I %s %s/perl/statistics.pl %s > %sasmstats.out"%(libPath,utils,ref_asm,html_prefix)
run_process(
_settings, "perl -I %s %s/perl/statistics.pl %s > %sasmstats.out" %
(libPath, utils, ref_asm, html_prefix), "Postprocess")
report = open(html_prefix + "asmstats.out", 'r')
initialStep = "Classify"
# get metamos version
version = "1.0"
summary = open("%s/pipeline.run" % (MA_dir), 'r')
for line in summary:
line = line.replace("\n", "")
if "#" in line:
continue
elif "metAMOS Version:" in line:
version = line.replace("\n", "").split("\t")[-1]
summary.close()
steps = []
steps.append("Preprocess")
steps.append("Assemble")
steps.append("MapReads")
steps.append("Validate")
#steps.append("MultiAlign")
steps.append("FindORFS")
steps.append("FindRepeats")
steps.append("Scaffold")
steps.append("FindScaffoldORFS")
steps.append("Abundance")
steps.append("Classify")
steps.append("FunctionalAnnotation")
steps.append("Propagate")
steps.append("Bin")
steps.append("Browse Results")
step_status = {}
step_status["Preprocess"] = "OK"
step_status["Assemble"] = "OK"
step_status["MapReads"] = "OK"
step_status["Validate"] = "OK"
#step_status["MultiAlign"] = "OK"
step_status["FindORFS"] = "OK"
step_status["FindRepeats"] = "OK"
step_status["Scaffold"] = "OK"
step_status["FindScaffoldORFS"] = "OK"
step_status["Abundance"] = "FAIL"
step_status["Classify"] = "FAIL"
step_status["FunctionalAnnotation"] = "FAIL"
step_status["Propagate"] = "NONE"
step_status["Bin"] = "NONE"
step_status["Browse Results"] = "OK"
##get status of each step from Log dir
for step in steps:
if step == "Browse Results":
continue
stepn = step.lower()
started = False
completed = False
skipped = False
if os.path.exists("%s/Logs/%s.started" % (MA_dir, stepn)):
started = True
if os.path.exists("%s/Logs/%s.ok" % (MA_dir, stepn)):
completed = True
if os.path.exists("%s/Logs/%s.skip" % (MA_dir, stepn)):
skipped = True
if completed and not skipped:
step_status[step] = "OK"
elif skipped:
step_status[step] = "SKIP"
elif started and not completed:
step_status[step] = "FAIL"
elif not started:
step_status[step] = "NONE"
else:
step_status[step] = "NONE"
#+male1 /cbcb/project-scratch/sergek/metAMOS/individualAsms/m1_asm proba b- metaphyler=1
## call Dan's script, for now on a single sample/run
cpfile = open("%s/plot.tab" % (html_prefix), 'w')
cpfile.write("+sample1\t%s\tproba\tb-\tmetaphyler=1\n" % (MA_dir))
cpfile.close()
#os.system("python %s/python/create_plots.py %s/plot.tab proba1"%(utils,html_prefix))
if _havePlots:
create_plots("%s/plot.tab" % (html_prefix), "%s" % ("proba1"))
##update counts
#count reads
os.system(
"cat `ls %s/Preprocess/out/* |egrep 'lib[0-9]*\.fasta$'` | grep -c \">\" > readcount.txt"
% (MA_dir))
readcount = open("readcount.txt", 'r').read().replace("\n", "")
#print readcount
os.system("rm readcount.txt")
#count contigs
os.system(
"grep -c \">\" %s/Assemble/out/proba.asm.contig > contigcount.txt" %
(MA_dir))
contigcount = open("contigcount.txt", 'r').read().replace("\n", "")
#print contigcount
os.system("rm contigcount.txt")
#count scaffolds
os.system(
"grep -c \">\" %s/Scaffold/out/proba.scaffolds.final > scafcount.txt" %
(MA_dir))
scaffoldcount = open("scafcount.txt", 'r').read().replace("\n", "")
#print scaffoldcount
os.system("rm scafcount.txt")
#count scaffolds
os.system("grep -c \">\" %s/Scaffold/out/proba.motifs > motifcount.txt" %
(MA_dir))
motifcount = open("motifcount.txt", 'r').read().replace("\n", "")
#print motifcount
os.system("rm motifcount.txt")
#count ORFs
os.system("grep -c \">\" %s/FindORFS/out/proba.fna > orfcount.txt" %
(MA_dir))
orfcount = open("orfcount.txt", 'r').read().replace("\n", "")
#print orfcount
os.system("rm orfcount.txt")
##copy stuff
for step in steps:
# step = step.lower()
if os.path.exists("%s/javascript/%s.html" % (utils, step)):
os.system("cp %s/javascript/%s.html %s/" %
(utils, step, html_prefix))
os.system("cp %s/Logs/COMMANDS.log %s/pipeline.commands" %
(MA_dir, html_prefix))
os.system("cp %s/pipeline.run %s/pipeline.summary" % (MA_dir, html_prefix))
os.system("cp %s/javascript/style.css %s/" %
(utils, html_prefix)) # TEMP: change back to cp
os.system("cp -r %s/../KronaTools/src %s/../KronaTools/img %s/" %
(utils, utils, html_prefix)) # TODO: unhack KronaTools path
# os.system("cp %s/blocks.jpg %s/"%(img,html_prefix))
# os.system("cp %s/blocks_small.jpg %s/"%(img,html_prefix))
os.system("cp %s/blocks_dark_tiny.png %s/" % (img, html_prefix))
os.system("cp %s/name.png %s/" % (img, html_prefix))
# generate dynamic java scripts
# first classify and propagate
#os.system("python %s/python/get_classify_stats.py %s/propagate.in.clusters %s/propagate.out.clusters %s/DB/tax_key.tab %s Classify.html Propagate.html %s"%(utils, html_prefix, html_prefix, utils, html_prefix, taxa_level))
get_classify_stats("%s/propagate.in.clusters" % (html_prefix),
"%s/propagate.out.clusters" % (html_prefix),
"%s/tax_key.tab" % (dbdir), "%s" % (html_prefix),
"Bin.html", "Propagate.html", "%s" % (taxa_level))
# generate preprocess
preprocess = markup.page()
preprocess.init(css="style.css") #bodyattrs={'style':"margin:0px"})
preprocess.p()
nQC = 0
for i in range(1, nLibs + 1):
if os.path.exists("%s/lib%d.1.fastqc/fastqc_report.html" %
(html_prefix, i)):
nQC = nQC + 1
summary = open("%s/pipeline.ini" % (MA_dir), 'r')
libcnt = 1
format = None
mmin = 0
mmax = 0
mated = False
interleaved = False
innie = False
linkerType = ""
libadded = False
firstLib = True
headerArray = []
dataArray = []
for line in summary:
line = line.replace("\n", "")
if "#" in line:
continue
elif "asmcontigs:" in line:
asmc = line.replace("\n", "").split("\t")[-1]
if len(asmc) <= 2:
continue
preprocess.add(
"<div class=\"datagrid\">Pre-assembled contigs input: %s</div>"
% (asmc))
preprocess.br()
elif "format:" in line:
if format and not libadded:
outputLibraryInfo(headerArray, dataArray, firstLib, libcnt,
format, mated, interleaved, mmin, mmax,
nQC > 0)
libcnt += 1
libadded = False
format = line.replace("\n", "").split("\t")[-1]
elif "mated:" in line:
mated = str2bool(line.replace("\n", "").split("\t")[-1])
elif "innie:" in line:
innie = str2bool(line.replace("\n", "").split("\t")[-1])
elif "linker:" in line:
linkerType = line.replace("\n", "").split("\t")[-1]
elif "interleaved:" in line:
interleaved = str2bool(line.replace("\n", "").split("\t")[-1])
elif "f1:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "f2:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "frg" in line:
data = line.split("\t")
if format and not libadded:
outputLibraryInfo(headerArray, dataArray, firstLib, libcnt, format,
mated, interleaved, mmin, mmax, nQC > 0)
preprocess.add(getTable(headerArray, dataArray))
summary.close()
if os.path.exists("%s/Postprocess/out/html/kmergenie_report.html" %
(MA_dir)):
preprocess.iframe(id_="KmerGenie",
src_="kmergenie_report.html",
width="800",
height="5000")
preprocess_out = open("%s/Preprocess.html" % (html_prefix), 'w')
preprocess_out.write(preprocess.__str__())
preprocess_out.close()
validate_out = open("%s/Validate.html" % (html_prefix), 'w')
validate = markup.page()
validate.init(css="style.css",
bodyattrs={'style': "background-color:#FFFFFF;"})
headerArray = []
dataArray = []
firstScore = True
bestAsm = ""
refs = []
if os.path.exists("%s/Postprocess/out/asm.scores" % (MA_dir)):
best = open("%s/Postprocess/out/best.asm" % (MA_dir), 'r')
bestAsm = best.read()
best.close()
laps = open("%s/Postprocess/out/asm.scores" % (MA_dir), 'r')
validate.p()
validate.add("<div class=\"datagrid\">")
validate.add("Selected assembler: %s" % (bestAsm))
ref = open("%s/Postprocess/out/ref.name" % (MA_dir), 'r')
first = True
for r in ref.xreadlines():
refs.append(r)
if first:
validate.br()
first = False
validate.add("Selected reference: %s" % (r))
ref.close()
if os.path.exists("%s/Bin/out/contaminant.true" % (MA_dir)):
cont = open("%s/Bin/out/contaminant.true" % (MA_dir), 'r')
contPercent = cont.read().split()
cont.close()
validate.br()
validate.add(
"<b>Sample may have contaminants, only %s%% contigs/reads >%sbp assigned to %s. Check Classify output</b>"
% (contPercent[0], contPercent[2], contPercent[1]))
validate.br()
for line in laps:
line = line.replace("\n", "")
if "#" in line:
continue
else:
res = line.split("\t")
outputValidate(headerArray, dataArray, firstScore, bestAsm,
res)
firstScore = False
validate.add(getTable(headerArray, dataArray))
validate.add("</div>")
laps.close()
# when we have quast, we will add our table to their report, otherwise write standalone report
if os.path.exists(
"%s/Postprocess/out/html/quast/combined_quast_output/report.html" %
(MA_dir)):
os.system(
"cp %s/Postprocess/out/html/quast/combined_quast_output/report.html %s/Postprocess/out/html/quast/combined_quast_output/~report.html"
% (MA_dir, MA_dir))
quastIn = open(
"%s/Postprocess/out/html/quast/combined_quast_output/~report.html"
% (MA_dir), 'r')
quastOut = open(
"%s/Postprocess/out/html/quast/combined_quast_output/report.html" %
(MA_dir), 'w')
skip = False
output = False
for line in quastIn.xreadlines():
if not skip:
quastOut.write(line.strip().replace("<br>", "") + "\n")
elif output:
quastOut.write("margin-left: 50px;\n")
quastOut.write("padding-top: 10px;\n")
quastOut.write("background: #ffffff;\n")
output = False
if ".content" in line:
skip = True
output = True
elif "clear:" in line:
quastOut.write(line.strip() + "\n")
skip = False
output = False
quastIn.close()
quastOut.close()
validate.iframe(id_="quast",
src_="quast/combined_quast_output/report.html",
width="800",
height="1000")
validate_out.write(validate.__str__())
validate_out.close()
# multialign step
treeScripts = {}
treeScripts[
"http://www.jsphylosvg.com/js/jquery/jquery-1.4.2.min.js"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/jquery/jquery.simplemodal.1.4.1.min.js"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/raphael/raphael-min.js"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/jsphylosvg-min.js?1.29"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/unitip/js/unitip.js"] = "javascript"
treeScript = []
treeScript.append("<script type=\"text/javascript\">")
treeScript.append(
" var dataObject = { newick: '(M_canettii_CIPT_d:0.059437,(M_canettii_CIPT_e:0.07845,((((M_africanum_GM04118:0.00646,(M_bovis_AF2122_97:0.00269,(M_bovis_BCG_Tokyo_1:0.00013,((M_bovis_BCG_Korea_1:0.0,M_bovis_BCG_Pasteur:0.0):0.00014,M_bovis_BCG_Mexico:0.00013):0.00014):0.00294):0.00514):0.00207,(((MTBC_Beijing_NITR20:0.00914,(MTBC_CCDC5180:0.00102,(MTBC_CCDC5079:0.00423,MTBC_CCDC5079:0.00014):0.00078):0.00016):0.00368,((((MTBC_Erdman_ATCC_35:0.00075,MTBC:0.00123):0.00129,(MTBC_CDC1551:0.00245,MTBC_Haarlem3_NITR2:0.01398):0.00093):0.00065,((((MTBC_CTRI_2:0.001,(MTBC_KZN_4207:0.00014,(MTBC_KZN_605:0.00012,MTBC_KZN_1435:0.00014):0.00012):0.00071):0.00061,(MTBC_RGTB327:0.00462,MTBC_UT205:0.0012):0.00037):0.00014,MTBC_F11:0.00158):0.00109,(MTBC_H37Ra:0.00016,(MTBC_H37Rv:0.00028,MTBC_H37Rv:0.00014):0.00014):0.00281):0.00047):0.00112,MTBC_CAS_NITR204:0.009827):0.00022):0.00247,((MTBC_EAI5:0.0023,MTBC_EAI5_NITR206:0.00933):0.0035,(MTBC_RGTB423:0.00868,spades.45.asm.contig:0.0035):0.00066):0.00289):0.00015):0.07224,(M_canettii_CIPT_a:0.01891,M_canettii_CIPT_b:0.05096):0.03720):0.03909,M_canettii_CIPT_c:0.056869):0.00469):0.02099);' };"
)
treeScript.append(" function load() {")
treeScript.append(" var divVal = $('#svgCanvas').empty();")
treeScript.append(
" var isCircular = $('#circularize-value')[0].value;")
treeScript.append(
" Smits.PhyloCanvas.Render.Parameters.Rectangular.bufferX = 150;")
treeScript.append(
" Smits.PhyloCanvas.Render.Parameters.Circular.bufferRadius = 0.35;"
)
treeScript.append(
" Smits.PhyloCanvas.Render.Style.line.stroke = 'rgb(0,0,255)';")
treeScript.append(
" Smits.PhyloCanvas.Render.Style.text[\"font-size\"] = 10;")
treeScript.append(" if (isCircular.toLowerCase() == 'true') {")
treeScript.append(" phylocanvas = new Smits.PhyloCanvas(")
treeScript.append(" dataObject,")
treeScript.append(" 'svgCanvas',")
treeScript.append(
" 1000, 1000, 'circular'")
treeScript.append(" );")
treeScript.append(" $('#circularize-value')[0].value = 'false';")
treeScript.append(" } else {")
treeScript.append(" phylocanvas = new Smits.PhyloCanvas(")
treeScript.append(" dataObject,")
treeScript.append(" 'svgCanvas',")
treeScript.append(" 500, 500")
treeScript.append(" );")
treeScript.append(" $('#circularize-value')[0].value = 'true';")
treeScript.append(" }")
treeScript.append(" init();")
treeScript.append(" }")
treeScript.append("function snapshot() {")
treeScript.append(" var svgSource = phylocanvas.getSvgSource();")
treeScript.append(" if(svgSource) {")
treeScript.append(" var url = 'data:image/svg+xml,' + svgSource")
treeScript.append(" window.open(url);")
treeScript.append(" }")
treeScript.append(" }")
treeScript.append("</script>")
treeBody = {}
treeBody["onload"] = "load()"
maStep = markup.page()
maStep.add("\n".join(treeScript))
maStep.init(
css=("http://www.jsphylosvg.com//js/yui/build/cssfonts/fonts-min.css",
"http://www.jsphylosvg.com/js/unitip/css/unitip.css"),
script=treeScripts,
bodyattrs=treeBody)
maStep.div()
maStep.add(
"<input type=\"button\" id=\"download-link\" onclick=\"snapshot()\" value=\"Snapshot\" />"
)
maStep.div.close()
maStep.div()
maStep.add(
"<input type=\"button\" id=\"circularize-link\" onclick=\"load()\" value=\"Toggle Circular\" />"
)
maStep.add(
"<input type=\"hidden\" id=\"circularize-value\" value=\"false\">")
maStep.div.close()
maStep.div(id_="svgCanvas")
maStep.div.close()
maStep_out = open("%s/MultiAlign.html" % (html_prefix), 'w')
maStep_out.write(maStep.__str__())
maStep_out.close()
# todo, need to add report for MapReads including # reads mapped (%), contig coverage histogram, and % reads between contigs and number of links histogram. Also re-estimated insert sizes for each lib
#mapreads = markup.page()
#mapreads.init(bodyattrs={'style':"margin:0px"})
#mapreads.img(src_="hist_ctgcvg.png",height_="100%",width_="100%")
#mapreads_out = open("%s/MapReads.html"%(html_prefix), 'w')
#mapreads_out.write(mapreads.__str__())
##This will create ScaffoldSizes.png,ContigSizes.png
##create code to automatically generate .js files for HTML report
## let's start with Abundance
#abundance_js = open(html_prefix+"abundance.js",'w')
rdata = []
for line in report:
rdata.append(line)
if not os.path.exists(html_prefix + "covstats.out"):
run_process(
_settings, "%s/analyze-read-depth -x 2 %s > %scovstats.out" %
(rund, amosbnk, html_prefix), "Postprocess")
ff = open(html_prefix + "covstats.out", 'r')
covdata = []
#covdata = ff.readlines()
#zflag = 0
for line in ff:
covdata.append(line)
if not os.path.exists(html_prefix + "stats.out"):
if os.path.getsize("%s/Assemble/out/proba.asm.contig" % (MA_dir)) == 0:
run_process(_settings, "touch %sstats.out" % (html_prefix),
"Postprocess")
else:
#os.system("%s/astats %s > %sstats.out"%(rund,amosbnk,html_prefix))
run_process(
_settings,
"%s/astats %s > %sstats.out" % (rund, amosbnk, html_prefix),
"Postprocess")
dd = open(html_prefix + "stats.out", 'r')
ddata = dd.readlines()
ddf = ""
bflag = 0
cflag = 0
rflag = 0
for line in ddata:
if "<body>" in line:
bflag = 1
ddf += "<table border=\"1\">"
elif "[Contigs]" in line:
cflag = 1
ddf += line
elif "[Small" in line:
cflag = 0
elif "[Big" in line:
cflag = 0
elif "[Reads]" in line:
rflag = 1
ddf += line
elif cflag != 0 or rflag != 0:
if "N50" not in line:
ddf += line
else:
continue
mp.readline()
cov = []
abund = []
ids = []
mpd = mp.readlines()
phylum = False
for line in mpd:
if ">phylum" in line:
phylum = True
if len(line) < 3:
continue
data = line.split("\t")
if len(data) < 2:
continue
if not phylum:
continue
ids.append(data[0])
#cov.append(int(float(data[2])))
abund.append(100 * float(data[1]))
# Create a chart object of 200x100 pixels
# chart2 = StackedVerticalBarChart(600, 300)
chart2 = PieChart3D(550, 300)
chart2.set_colours(["0A8C8A", "EBB671", "DE091A"])
# Add some data
chart2.add_data(abund)
# chart2.add_data(abund2)
# Assign the labels to the pie data
chart2.set_pie_labels(ids)
# chart2.set_axis_labels(Axis.BOTTOM, ids)
# Download the chart
try:
chart2.download(html_prefix + 'abund.png')
except:
print "Warning: could not download abund.png"
chart = GroupedHorizontalBarChart(600, 500, x_range=(0, 100))
chart.set_bar_width(30)
chart.set_colours(("FF0000", "0000FF"))
#chart.set_colours_within_series(("FF0000","FF7F00","FFFF00","00FF00","0000FF","8B00FF","FFFFFF"))
# chart.set_colours(['00ff00', 'ff0000'])
chart.add_data(abund)
#chart.add_data(abund2)
#chart.add_data([1,4,9,16,25])
#category = ["even","staggered"]
#chart.set_legend(category)
ids = ids[::-1]
chart.set_axis_labels(Axis.LEFT, ids)
chart.set_axis_labels(Axis.BOTTOM,
[0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
#chart.set_axis_labels(Axis.LEFT, ["0)
index = chart.set_axis_labels(Axis.BOTTOM, ['Abundance (%)'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
index = chart.set_axis_labels(Axis.LEFT, ['Phylum'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
try:
chart.download(html_prefix + 'bar-phylum.png')
except:
print "Warning: could not download bar-phylum.png"
dt = datetime.now()
ds = dt.strftime("%d %b %Y,<br/>%l:%M%p")
title = "metAMOS report"
# header is blank for now
header = []
# write the javascript we need on the page
script = []
script.append("<script type=\"text/javascript\">")
script.append("var steps = ['%s'];" % ("','".join(steps)))
script.append("function load(step) {")
for step in steps:
if step_status[step] != "OK":
script.append(
" if (step.toLowerCase() == \"%s\".toLowerCase()) {" %
(step))
script.append(" return;")
script.append(" }")
script.append(" for (var i = 0; i < steps.length; i++) {")
script.append(" var current = steps[i].toLowerCase();")
script.append(" if (current == step) {")
script.append(
" document.getElementById(step + 'Button').className = 'menuItemSelected';"
)
script.append(
" document.getElementById(step).style.display = 'block';")
script.append(
" document.getElementById(step + 'Marker').className = 'markerSelected';"
)
script.append(" } else {")
script.append(
" document.getElementById(current + 'Button').className = 'menuItemUnselected';"
)
script.append(
" document.getElementById(current).style.display = 'none';")
script.append(
" document.getElementById(current + 'Marker').className = 'markerUnselected';"
)
script.append(" }")
script.append(" }")
script.append("}")
script.append("")
script.append("</script>")
#<link rel="shortcut icon" href="../assets/ico/favicon.ico">
#<link rel="apple-touch-icon-precomposed" sizes="144x144" href="../assets/ico/apple-touch-icon-144-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="114x114" href="../assets/ico/apple-touch-icon-114-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="72x72" href="../assets/ico/apple-touch-icon-72-precomposed.png">
#<link rel="apple-touch-icon-precomposed" href="../assets/ico/apple-touch-icon-57-precomposed.png">
# generate the dictionary of javascript pages we need
scripts = {}
# scripts["file://%s/javascript/jquery-latest.js"%(utils)] = "javascript"
# scripts["http://code.jquery.com/jquery-latest.js"] = "javascript"
# now a javascript for each page
for step in steps:
scripts["%s.js" % (step.lower())] = "javascript"
# attributes for the body tax
body = {}
body["onload"] = "load('%s')" % (initialStep.lower())
# the footer for the page
footer = "" #"Generated %s"%(ds)
#styles = ( 'style2.css')#'./html/bootstrap.css', './html/boostrap-responsive.css')#'style2.css')#'layout.css', 'alt.css', 'images.css' )
#styles = ( 'layout.css', 'alt.css', 'images.css' )
#meta = ('viewport':"width=device-width, initial-scale=1.0",'description':'','author':'')
# create HTML page
page = markup.page()
# add the javascript free form
page.add("\n".join(script))
# initialize the rest of the body/html headers
page.init( title=title, \
css='style.css', \
script=scripts,\
header='\n'.join(header), \
bodyattrs=body, \
footer=footer )
# page.br()
#page.div( class_ = 'navbar navbar-fixed-top')
#page.div( class_ = 'navbar-inner')
#page.div( class_ = 'container', style_='width:100%;height=100%')
#page.div.close()
#page.div.close()
#page.div.close()
#page.div( id_='page' )
# header
# page.add('<table style="width:100%;"><tr><td><img src="blocks_small.jpg"/></td><td><a target="_blank" href="https://github.com/treangen/metAMOS/wiki"><div><img src="name.jpg"/><br/>Under peer review</a></div></td><td class="title" style="width:100%"></td></tr></table>')
'''
page.div( id_='header', style="background-color:#B8B8B8;clear:both;text-align:center;width:100%;height:7%;border:1px solid black")
page.h1("<u>MetAMOS <font color=\"blue\">v1.0</font> metagenomic assembly & analysis report</u>" , style_="text-align:center;vertical-align:top")
page.h1.close()
#page.div( id_='title')# style="vertical-align:bottom;")
#page.font( size=14)
#page.br( )
page.div.close()
'''
#<frameset rows="40%,60%"cols="80%,20%">
#<frame src="report.krona.html">
#<frameset rows="20%,20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#<frameset rows="60%" cols="40%,40%">
#<frame src="report.krona.html">
#<frame src="report.krona2.html">
#</frameset>f
#<frameset rows="20%,20%,20%" cols="20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#</frameset>
#</html>
#font, estimate
#page.div.close()
#page.frameset( rows_="40%,60%", cols_ = "80%,20%")
#page.div()
page.table(style_="width:100%;height:100%;")
page.tr()
page.td(id_="menu", style_="padding:0px;")
page.div(style_="height:100%;")
# page.table(style_="height:100%")
# page.tr()
# page.td()#style_="border-right:1px solid black")
# page.div(style_="box-shadow:inset -1px -1px 5px #555555;")
page.add(
"<a target=\"_blank\" href=\"https://github.com/treangen/metAMOS/wiki\"><img style=\"padding-top:5px;\" src=\"name.png\"/>"
)
page.add("<img src=\"blocks_dark_tiny.png\"/></a>")
# page.add("<img src=\"blocks_tiny2.jpg\"/>")
page.add(
"<div style=\"padding:2px;font-size:12px;\"><a target=\"_blank\" href=\"http://genomebiology.com/2013/14/1/R2\">Treangen TJ, Koren S, et. al. Genome Biol. 2013 Jan 15;14(1):R2. PMID: 23320958.</a></div>"
)
page.add("<br/>")
# page.div.close()
# page.td.close()
# page.tr.close()
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
# page.tr()
# page.td(style_="padding:0px;")
page.table(id_="links", class_="menu")
for step in steps:
page.tr()
status = "NA"
try:
if step_status[step] == "OK":
status = "OK"
elif step_status[step] == "FAIL":
status = "FAIL"
elif step_status[step] == "SKIP":
status = "SKIPPED"
except KeyError:
continue
tableHTML = []
tableHTML.append(
"<td class=\"menuItemTd\"><a class=\"menuLink\" href=\"javascript:void(0)\"><div class=\"menuItem %s\"><div id=\"%sButton\" class=\"menuItemUnselected\" onclick=\"load('%s');\">"
% (status.lower(), step.lower(), step.lower()))
tableHTML.append(
"<table style='width:100%%;'><tr><td style='width:100%%;'><span class='step %sText'>%s</span>"
% (status.lower(), step))
tableHTML.append("<br>")
tableHTML.append(
"<span class='status %sText'>%s</span></td></tr></table>" %
(status.lower(), status))
tableHTML.append(
"</div></div></a></td><td><div id='%sMarker' class='markerUnselected'>●</div></td>"
% (step.lower()))
page.add("\n".join(tableHTML))
page.tr.close()
page.table.close()
# page.td.close()
# page.tr.close()
#page.ul.close()
# page.tr()
# page.td(style_="height:100%;")#border-right:1px solid black")
page.div(class_="notes")
page.add(
"<div style=\"font-size:14px;\"><br/><a target=\"_blank\" href=\"pipeline.summary\">Pipeline summary</a><br/>"
)
page.add(
"<a target=\"_blank\" href=\"pipeline.commands\">Run commands</a><br/><br/></div>"
)
tableHTML = []
tableHTML.append("<table style=\"font-size:12px\"><tr>")
tableHTML.append("<tr><td>Version:</td><td>%s</td></tr>" % (version))
tableHTML.append("<tr><td>Created:<br/> </td><td>%s</td></tr>" % (ds))
tableHTML.append("</table>")
page.add("\n".join(tableHTML))
page.div.close()
# page.td.close()
# page.tr.close()
# page.table.close()
page.div.close()
page.td.close()
page.td(id_="krona", style_="width:100%;height:100%padding:0px;")
page.table(class_="charts", style_="width:100%;height:100%")
page.tr()
page.td(class_="main", style_="height:100%", colspan_="4")
page.div(class_="shadow")
page.table(style_="width:100%;height:100%")
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.tr()
page.td()
page.td.close()
page.td(class_="inset")
for step in steps:
if step == "Browse Results":
page.iframe(id_=step.lower(), src_="../.", style_="display:none;")
else:
page.iframe(id_=step.lower(),
src_="%s.html" % (step),
style_="display:none;")
page.iframe.close()
page.td.close()
page.td()
page.td.close()
page.tr.close()
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.table.close()
page.div.close()
page.td.close()
page.tr.close()
#page.tr()
#page.div(id_="sideplots")#, style_="background-color:#FFFFFF;width:20.5%%;height:88%%;float:right;border:1px")
#page.div(id_="sideplot1", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.td(style_="width:25%")
#page.img(class_="chart", src_="ContigSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot2", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_contigs.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot3", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="ScaffoldSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot4", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_scaffold.png")
#page.td.close()
#page.div.close()
#page.div.close()
#page.td.close()
#page.tr.close()
page.table.close()
#page.iframe(src_="bar-phylum.png",style_="width:100%;height:100%;hspace=10")
#page.frameset(rows_="100%" ,cols_="100%")
page.td.close()
#page.li("<a target=\"_blank\" href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>")
#page.li("<a href=\"http://cbcb.umd.edu/~mpop/Software.shtml\">Related software</a>")
#page.li("<a href=\"http://cbcb.umd.edu\">CBCB</a>")
# page.li( items[1] )
#page.ul.close( )
#page.div.close()
page.div(id_="content")
#page.div( id_='wrapper')
#page.div( id_="content")
#page.a( "Reference assembly:", class_='internal', href='%s'%(ref_asm) )
#paragraphs = ( ddf )
cnt = 0
#table_html = ""
if 0:
page.table(border="1", style_="width=80%")
for contig in covdata:
if cnt == 0:
#table_html += "<table border=\"1\">\n"
page.tr()
page.td("High Coverage Contig ID")
page.td("Coverage")
page.tr.close()
#table_html += "<tr><td> High Coverage Contig ID </td> <td> Coverage </td></tr>\n"
page.tr()
page.td(contig.split("\t")[0])
page.td(contig.split(" ")[-1])
cnt += 1
'''
#page.table.close()
#page.p( paragraphs )
#page.p(style_="font-size:6px")
page.table(border="0")
#page.tr()
#page.(
if 1:
#table_html = ""
#table_html += "<table border=\"1\">\n"
for contig in rdata:
page.tr()
#table_html += "<tr>\n"
index = 0
for item in contig.split("\t"):
index +=1
if index == 8 or index == 7:
continue
elif index == 1 and "File" not in item:
page.td("<a target=\"_blank\" href=\""+ref_asm+"\">%s</a>"%(ref_asm.split("/")[-1]))
continue
page.td("<p style=\"font-size:15px\">"+item+"</p>")
#table_html += "<td> %s </td> \n"%(item)
page.tr.close()
#table_html += "</tr>\n"
page.table.close()
#table_html += "</table>\n"
#page.p( table_html )
#page.p.close()
page.div.close()
'''
page.td(id_="quick")
page.div(style_="height:100%")
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
page.br()
page.div(class_="stats")
page.table(class_="stats")
page.add("<tr><td class=\"number\">%s</td><td>Reads</td></tr>" %
intOrZero(readcount))
page.add("<tr><td class=\"number\">%s</td><td>Contigs</td></tr>" %
intOrZero(contigcount))
page.add("<tr><td class=\"number\">%s</td><td>Scaffolds</td></tr>" %
intOrZero(scaffoldcount))
page.add("<tr><td class=\"number\">%s</td><td>ORFs</td></tr>" %
intOrZero(orfcount))
page.add("<tr><td class=\"number\">%s</td><td>Motifs</td></tr>" %
intOrZero(motifcount))
page.table.close()
page.div.close()
page.div.close()
page.td.close()
page.tr.close()
page.table.close()
#page.div( id_="metaphyler", style="float:left;width:28%;height:70%")
#page.img( hspace=10, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
#page.img( hspace=10, width=600, height=500, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
fout = open(html_prefix + "summary.html", 'w')
fout.write(page.__str__())
fout.close()
#chart.set_colours_within_series(("FF0000","FF7F00","FFFF00","00FF00","0000FF","8B00FF","FFFFFF"))
# chart.set_colours(['00ff00', 'ff0000'])
chart.add_data(abund)
#chart.add_data(abund2)
#chart.add_data([1,4,9,16,25])
#category = ["even","staggered"]
#chart.set_legend(category)
ids = ids[::-1]
chart.set_axis_labels(Axis.LEFT, ids)
chart.set_axis_labels(Axis.BOTTOM, [0,10,20,30,40,50,60,70,80,90,100])
#chart.set_axis_labels(Axis.LEFT, ["0)
index = chart.set_axis_labels(Axis.BOTTOM, ['Abundance (%)'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
index = chart.set_axis_labels(Axis.LEFT, ['Phylum'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
try:
chart.download(prefix+'bar-phylum.png')
except:
print "Warning: could not download bar-phylum.png"
dt = datetime.now()
ds = dt.strftime("%A, %d. %B %Y %I:%M%p")
title = "metAMOS: a metagenomic assembly pipeline for AMOS"
header = ""#metAMOS Metagenomic assembly report"
#<link rel="shortcut icon" href="../assets/ico/favicon.ico">
# chart.set_colours(['00ff00', 'ff0000'])
chart.add_data(abund)
#chart.add_data(abund2)
#chart.add_data([1,4,9,16,25])
#category = ["even","staggered"]
#chart.set_legend(category)
ids = ids[::-1]
chart.set_axis_labels(Axis.LEFT, ids)
chart.set_axis_labels(Axis.BOTTOM,
[0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
#chart.set_axis_labels(Axis.LEFT, ["0)
index = chart.set_axis_labels(Axis.BOTTOM, ['Abundance (%)'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
index = chart.set_axis_labels(Axis.LEFT, ['Phylum'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
try:
chart.download(prefix + 'bar-phylum.png')
except:
print "Warning: could not download bar-phylum.png"
dt = datetime.now()
ds = dt.strftime("%A, %d. %B %Y %I:%M%p")
title = "metAMOS: a metagenomic assembly pipeline for AMOS"
header = "" #metAMOS Metagenomic assembly report"
#<link rel="shortcut icon" href="../assets/ico/favicon.ico">