def GetTreeListOrder(treefile, outpath):
#Create the Itol class
itl = Itol.Itol()
#Set the tree file
tree = treefile
dirname = os.path.dirname(treefile)
if dirname == "":
dirname = "."
if outpath == "":
outpath = dirname
elif not os.path.exists(outpath):
os.system("mkdir -p %s" % (outpath))
rootname = os.path.basename(os.path.splitext(treefile)[0])
#===================================
itl.add_variable('treeFile', tree)
itl.add_variable('treeName', rootname)
itl.add_variable('treeFormat', 'newick')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print ''
good_upload = itl.upload()
if good_upload == False:
print 'There was an error:' + itl.comm.upload_output
return 1
#Export to pdf
print 'Exporting to pdf'
tree_id = itl.comm.tree_id
itol_exporter = itl.get_itol_export()
itol_exporter.set_export_param_value('format', "eps")
itol_exporter.set_export_param_value('displayMode', "normal")
itol_exporter.set_export_param_value('lineWidth', "1")
epsfile = outpath + os.sep + rootname + '.itolnormal.eps'
pdffile = outpath + os.sep + rootname + '.itolnormal.pdf'
itol_exporter.export(epsfile)
orderfile = outpath + os.sep + rootname + '.listorder.txt'
os.system("epstopdf %s" % epsfile)
os.system("pdftotext -nopgbrk %s %s" % (pdffile, orderfile))
os.system("rm -f %s" % pdffile)
os.system("rm -f %s" % epsfile)
print 'list order output to ', orderfile
def Itol_Tree_m0(pfamid, datapath, outpath): #{{{
#Create the Itol class
itl = Itol.Itol()
#Set the tree file
tree = datapath + os.sep + pfamid + '.kalignp.fasttree'
(dataset1, dataset2, dataset3, dataset4) = ("", "", "", "")
if not os.path.exists(tree):
print >> sys.stderr, "tree file %s does not exist. Ignore" % (tree)
return 1
t = Tree(tree)
leaves = t.get_leaves()
numLeave = len(leaves)
fontsize = GetFontSize(numLeave)
dataset1 = datapath + os.sep + pfamid + '.numTM_and_io.txt'
dataset2 = datapath + os.sep + pfamid + '.cmpclass.colordef.txt'
# dataset3 = datapath + os.sep + pfamid + '.ntermstate.colordef.txt'
dataset4 = datapath + os.sep + pfamid + '.cluster.colordef.txt'
colordeffile = datapath + os.sep + pfamid + '.pfam.colordef.txt'
branchlabelfile = datapath + os.sep + pfamid + '.branchlabel.txt'
#===================================
itl.add_variable('treeFile', tree)
itl.add_variable('treeName', 'PF00854')
itl.add_variable('treeFormat', 'newick')
if os.path.exists(colordeffile):
itl.add_variable('colorDefinitionFile', colordeffile)
if os.path.exists(branchlabelfile):
itl.add_variable('branchLabelsFile', branchlabelfile)
#===================================
if os.path.exists(dataset1):
itl.add_variable('dataset1File', dataset1)
itl.add_variable('dataset1Label', 'numTM_and_io')
itl.add_variable('dataset1Separator', 'comma')
itl.add_variable('dataset1Type', 'multibar')
itl.add_variable('dataset1PreventOverlap', '1')
itl.add_variable('dataset1Color', '#FF0000')
#===================================
if os.path.exists(dataset2):
itl.add_variable('dataset2File', dataset2)
itl.add_variable('dataset2Label', 'cmpclass')
itl.add_variable('dataset2Separator', 'comma')
itl.add_variable('dataset2Type', 'colorstrip')
itl.add_variable('dataset2StripWidth', '200')
itl.add_variable('dataset2PreventOverlap', '1')
itl.add_variable('dataset2ColoringType', 'both')
#===================================
if os.path.exists(dataset3):
itl.add_variable('dataset3File', dataset3)
itl.add_variable('dataset3Label', 'NtermState')
itl.add_variable('dataset3Separator', 'comma')
itl.add_variable('dataset3Type', 'colorstrip')
itl.add_variable('dataset3StripWidth', '200')
itl.add_variable('dataset3PreventOverlap', '1')
itl.add_variable('dataset3ColoringType', 'both')
#===================================
if os.path.exists(dataset4):
itl.add_variable('dataset4File', dataset4)
itl.add_variable('dataset4Label', 'cluster')
itl.add_variable('dataset4Separator', 'comma')
itl.add_variable('dataset4Type', 'colorstrip')
itl.add_variable('dataset4StripWidth', '200')
itl.add_variable('dataset4PreventOverlap', '1')
itl.add_variable('dataset4ColoringType', 'both')
itl.add_variable('dataset4BranchColoringType', 'both')
#itl.add_variable('dataset1BarSizeMax','1')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print ''
print 'Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server'
good_upload = itl.upload()
if good_upload == False:
print 'There was an error:' + itl.comm.upload_output
sys.exit(1)
#Read the tree ID
print 'Tree ID: ' + str(itl.comm.tree_id)
#Read the iTOL API return statement
print 'iTOL output: ' + str(itl.comm.upload_output)
#Website to be redirected to iTOL tree
print 'Tree Web Page URL: ' + itl.get_webpage()
# Warnings associated with the upload
print 'Warnings: ' + str(itl.comm.warnings)
#Export to pdf
print 'Exporting to pdf'
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('displayMode', "circular")
itol_exporter.set_export_param_value('showBS', "0")
itol_exporter.set_export_param_value('fontSize', fontsize)
itol_exporter.set_export_param_value('alignLabels', "1")
itol_exporter.set_export_param_value(
'datasetList', 'dataset1,dataset2,dataset3,dataset4')
epsfile = outpath + os.sep + pfamid + '-itol.eps'
pdffile = outpath + os.sep + pfamid + '-itol.pdf'
jpgfile = outpath + os.sep + pfamid + '-itol.jpg'
thumbfile = outpath + os.sep + "thumb." + pfamid + '-itol.jpg'
itol_exporter.export(epsfile)
os.system("epstopdf %s" % epsfile)
os.system("convert %s %s" % (epsfile, jpgfile))
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print 'exported tree to ', pdffile
def Itol_Tree_m0(treefile, outpath, method): #{{{
#Create the Itol class
itl = Itol.Itol()
#Set the tree file
tree = treefile
dirname = os.path.dirname(treefile)
if dirname == "":
dirname = "."
if outpath == "":
outpath = dirname
elif not os.path.exists(outpath):
os.system("mkdir -p %s" % (outpath))
treefile_without_ext = os.path.splitext(treefile)[0]
rootname = os.path.basename(os.path.splitext(treefile)[0])
if not os.path.exists(tree):
print >> sys.stderr, "tree file %s does not exist. Ignore" % (tree)
return 1
#t = Tree(tree)
#leaves = t.get_leaves()
#numLeave = len(leaves)
colordeffile = treefile_without_ext + '.pfam.colordef.txt'
branchlabelfile = treefile_without_ext + '.branchlabel.txt'
dataset1 = ""
dataset2 = ""
dataset3 = ""
dataset4 = ""
dataset1 = treefile_without_ext + '.numTM_and_io.txt'
dataset2 = treefile_without_ext + '.domain.txt'
dataset3 = treefile_without_ext + '.taxo.colordef.txt'
dataset4 = treefile_without_ext + '.cluster.colordef.txt'
numLeave = len(open(dataset1, "r").readlines()) - 2
fontsize = GetFontSize(numLeave)
#===================================
itl.add_variable('treeFile', tree)
itl.add_variable('treeName', rootname)
itl.add_variable('treeFormat', 'newick')
if os.path.exists(colordeffile):
itl.add_variable('colorDefinitionFile', colordeffile)
if os.path.exists(branchlabelfile):
itl.add_variable('branchLabelsFile', branchlabelfile)
#===================================
if os.path.exists(dataset1):
itl.add_variable('dataset1File', dataset1)
itl.add_variable('dataset1Label', 'numTM_and_io')
itl.add_variable('dataset1Separator', 'comma')
itl.add_variable('dataset1Type', 'multibar')
itl.add_variable('dataset1PreventOverlap', '1')
itl.add_variable('dataset1MultiBarAlign', '0')
itl.add_variable('dataset1Color', '#FF0000')
itl.add_variable('dataset1BarSizeMax', '1000')
#===================================
if os.path.exists(dataset2):
itl.add_variable('dataset2File', dataset2)
itl.add_variable('dataset2Label', 'Domain')
itl.add_variable('dataset2Separator', 'comma')
itl.add_variable('dataset2Type', 'domains')
itl.add_variable('dataset2ProtSizeMax', '1000')
itl.add_variable('dataset2PreventOverlap', '1')
itl.add_variable('dataset2CirclesSpacing', '100')
#===================================
if os.path.exists(dataset3):
itl.add_variable('dataset3File', dataset3)
itl.add_variable('dataset3Label', 'taxonomy')
itl.add_variable('dataset3Separator', 'comma')
itl.add_variable('dataset3Type', 'colorstrip')
itl.add_variable('dataset3StripWidth', '300')
itl.add_variable('dataset3PreventOverlap', '1')
itl.add_variable('dataset3ColoringType', 'both')
itl.add_variable('dataset3CirclesSpacing', '100')
#===================================
if os.path.exists(dataset4):
itl.add_variable('dataset4File', dataset4)
itl.add_variable('dataset4Label', 'cluster')
itl.add_variable('dataset4Separator', 'comma')
itl.add_variable('dataset4Type', 'colorstrip')
itl.add_variable('dataset4StripWidth', '200')
itl.add_variable('dataset4PreventOverlap', '1')
itl.add_variable('dataset4ColoringType', 'both')
#itl.add_variable('dataset1BarSizeMax','1')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print ''
print 'Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server'
good_upload = itl.upload()
if good_upload == False:
print 'There was an error:' + itl.comm.upload_output
return 1
#Read the tree ID
print 'Tree ID: ' + str(itl.comm.tree_id)
#Read the iTOL API return statement
print 'iTOL output: ' + str(itl.comm.upload_output)
#Website to be redirected to iTOL tree
print 'Tree Web Page URL: ' + itl.get_webpage()
# Warnings associated with the upload
print 'Warnings: ' + str(itl.comm.warnings)
#Export to pdf
print 'Exporting to pdf'
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('displayMode', "circular")
itol_exporter.set_export_param_value('showBS', "0")
itol_exporter.set_export_param_value('fontSize', fontsize)
itol_exporter.set_export_param_value('alignLabels', "1")
itol_exporter.set_export_param_value(
'datasetList', 'dataset1,dataset2,dataset3,dataset4')
epsfile = treefile_without_ext + '.m%d.itol.eps' % (method)
pdffile = treefile_without_ext + '.m%d.itol.pdf' % (method)
jpgfile = treefile_without_ext + '.m%d.itol.jpg' % (method)
svgfile = treefile_without_ext + '.m%d.itol.svg' % (method)
thumbfile = treefile_without_ext + '.m%d.itol.thumb.jpg' % (method)
itol_exporter.export(epsfile)
os.system("epstopdf %s" % epsfile)
os.system("convert %s %s" % (epsfile, jpgfile))
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print 'exported tree to ', pdffile
itol_exporter.set_export_param_value('format', 'svg')
itol_exporter.export(svgfile)
def Itol_Tree(pfamid, datapath, outpath):
#Create the Itol class
itl = Itol.Itol()
#Set the tree file
treefile = "%s%s%s%s"%(datapath , os.sep , pfamid ,
".TMpro.clustalo10.fasttree")
taxofile = "%s%s%s%s"%(datapath , os.sep , pfamid ,
"-taxonomy-file.txt")
TMdeffile = "%s%s%s%s"%(datapath , os.sep , pfamid ,
"tms.txt")
if not os.path.exists(treefile):
print >> sys.stderr, "tree file %s does not exist. Ignore" %(treefile)
return 1
if myfunc.checkfile(taxofile, "taxofile") != 0:
return 1
numLeave = len(open(taxofile, "r").readlines())
# t = Tree(treefile)
# leaves = t.get_leaves()
fontsize = GetFontSize(numLeave)
colordeffile = taxofile
branchlabelfile = ""
dataset1 = ""
dataset2 = ""
dataset3 = ""
dataset4 = ""
dataset1 = TMdeffile
#===================================
itl.add_variable('treeFile',treefile)
itl.add_variable('treeName', pfamid)
itl.add_variable('treeFormat','newick')
if os.path.exists(colordeffile):
itl.add_variable('colorDefinitionFile', colordeffile)
if os.path.exists(branchlabelfile):
itl.add_variable('branchLabelsFile', branchlabelfile)
if os.path.exists(dataset1):
itl.add_variable('dataset1File',dataset1)
itl.add_variable('dataset1Label','numTM_and_repeat')
itl.add_variable('dataset1Separator','comma')
itl.add_variable('dataset1Type','domains')
itl.add_variable('dataset1PreventOverlap','1')
itl.add_variable('dataset1Color','#FF0000')
# itl.add_variable('dataset1BarSizeMax','300')
#===================================
# itl.add_variable('dataset1File',dataset1)
# itl.add_variable('dataset1Label','numTM')
# itl.add_variable('dataset1Separator','comma')
# itl.add_variable('dataset1Type','simplebar')
# itl.add_variable('dataset1Color','#FF0000')
#===================================
if os.path.exists(dataset2):
itl.add_variable('dataset2File', dataset2)
itl.add_variable('dataset2Label', 'taxonomy')
itl.add_variable('dataset2Separator','comma')
itl.add_variable('dataset2Type','colorstrip')
itl.add_variable('dataset2StripWidth','300')
itl.add_variable('dataset2PreventOverlap','1')
itl.add_variable('dataset2ColoringType','both')
itl.add_variable('dataset2CirclesSpacing','100')
#===================================
if os.path.exists(dataset3):
itl.add_variable('dataset3File', dataset3)
itl.add_variable('dataset3Label', 'pfam')
itl.add_variable('dataset3Separator','tab')
itl.add_variable('dataset3Type','colorstrip')
# itl.add_variable('dataset3Type','ColorDefinitionFile')
# itl.add_variable('dataset3StripWidth','300')
# itl.add_variable('dataset3PreventOverlap','1')
# itl.add_variable('dataset3ColoringType','both')
# itl.add_variable('dataset3CirclesSpacing','100')
#===================================
if os.path.exists(dataset4):
itl.add_variable('dataset4File', dataset4)
itl.add_variable('dataset4Label', 'cluster')
itl.add_variable('dataset4Separator','comma')
itl.add_variable('dataset4Type','colorstrip')
itl.add_variable('dataset4StripWidth','200')
itl.add_variable('dataset4PreventOverlap','1')
itl.add_variable('dataset4ColoringType','both')
#itl.add_variable('dataset1BarSizeMax','1')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print ''
print 'Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server'
good_upload = itl.upload()
if good_upload == False:
print 'There was an error:'+itl.comm.upload_output
sys.exit(1)
#Read the tree ID
print 'Tree ID: '+str(itl.comm.tree_id)
#Read the iTOL API return statement
print 'iTOL output: '+str(itl.comm.upload_output)
#Website to be redirected to iTOL tree
print 'Tree Web Page URL: '+itl.get_webpage()
# Warnings associated with the upload
print 'Warnings: '+str(itl.comm.warnings)
#Export to pdf
print 'Exporting to pdf'
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('displayMode',"circular")
itol_exporter.set_export_param_value('showBS',"0")
itol_exporter.set_export_param_value('fontSize',fontsize)
itol_exporter.set_export_param_value('alignLabels',"1")
itol_exporter.set_export_param_value('datasetList','dataset1,dataset2,dataset3,dataset4')
epsfile = outpath + os.sep + pfamid + '-itol.eps'
pdffile = outpath + os.sep + pfamid + '-itol.pdf'
jpgfile = outpath + os.sep + pfamid + '-itol.jpg'
svgfile = outpath + os.sep + pfamid + '-itol.svg'
itol_exporter.export(epsfile)
itol_exporter.export(svgfile)
os.system("epstopdf %s" % epsfile )
os.system("convert %s %s" % (epsfile, jpgfile) )
print 'exported tree to ', pdffile
input_dict['mem_str'] = mem_str
input_dict['write_out'] = False
angst_inputs = [input_dict]
# run angst one more time at that scaling
input_dict['write_out'] = True
input_dict['start_time'] = start_time
RunAnGST(input_dict)
#######CHANGED FOR THE ANGST SERVER######
# Run iTOL API and Upload species and gene trees
sys.path.append('/home/albertyw/itol/')
import Itol
import os
species_tree_location = input_info.species_tree_filename
itol_species_tree = Itol.Itol()
itol_species_tree.add_variable('treeFile', species_tree_location)
itol_species_tree.upload()
species_tree_webpage = itol_species_tree.get_webpage()
gene_tree_location = input_info.boots_file
itol_gene_tree = Itol.Itol()
itol_gene_tree.add_variable('treeFile', gene_tree_location)
itol_gene_tree.upload()
gene_tree_webpage = itol_gene_tree.get_webpage()
itol_file_location = os.path.dirname(
input_info.species_tree_filename) + '/itol'
itol_file = open(itol_file_location, 'w')
itol_file.write(species_tree_webpage + "\n" + gene_tree_webpage)
itol_file.close()
def makeITOLcall(tree, XITOL, HIST, com):
handle = open(com["-o"] + ".TreeLabeled", "w")
handle.write(tree.format("newick"))
handle.close()
buffITOL = XITOL.to_csv(header=False, sep="\t")
handle = open(com["-o"] + "_tableXitol.txt", "w")
handle.write(buffITOL)
handle.close()
buffHIST = HIST.to_csv()
handle = open(com["-o"] + "_tableHistXitol.txt", "w")
handle.write(buffHIST)
handle.close()
#handle=open(com["-o"]+"_CollapseList.txt","w")
#handle.write(Collapse)
#handle.close()
#SSS=SignFeature2Itol(SN)
#handle=open(com["-o"]+"_tableSignNodeXitol.txt","w")
#handle.write(SSS)
#handle.close()
test = Itol.Itol()
test.add_variable('treeFile', com["-o"] + ".TreeLabeled")
test.add_variable('treeName', com["-o"])
test.add_variable('treeFormat', "newick")
#test.add_variable('preCollapsedFile',com["-o"]+"_CollapseList.txt")
test.add_variable('showInternalIDs', '1')
test.add_variable('colorDefinitionFile', com["-o"] + "_tableXitol.txt")
test.add_variable('dataset1File', com["-o"] + "_tableHistXitol.txt")
test.add_variable('dataset1Label', 'Counts')
test.add_variable('dataset1Separator', 'comma')
test.add_variable('dataset1Type', 'multibar')
test.print_variables()
good_upload = test.upload()
if good_upload == False:
print 'There was an error:' + test.comm.upload_output
link = test.get_webpage()
itol_exporter = test.get_itol_export()
itol_exporter.set_export_param_value('format', 'svg')
itol_exporter.set_export_param_value('rangesCover', 'clades')
itol_exporter.set_export_param_value('showInternalLabels', '1')
itol_exporter.set_export_param_value('colorBranches', '1')
itol_exporter.set_export_param_value('datasetList', 'dataset1')
itol_exporter.export(com["-o"] + "BetaEtree.svg")
import re
import sys
print "try to add link from tree to table and then add to html file"
SCRIPT = """
<style>
text:hover
{
opacity: 1;
}
</style>
"""
def addHref(matchobj):
name = matchobj.group()[1:-1]
return '><a xlink:href="#' + name + '">' + name + '</a><'
def addOpacity(matchobj):
name = matchobj.group()[:]
return "opacity=0 " + name
def addStyle(matchobj):
name = matchobj.group()[:]
return name + SCRIPT
f = open(com["-o"] + "BetaEtree.svg", "r").read()
f = re.sub("</style>", addStyle, f)
f = re.sub(">L[0-9]*<", addHref, f)
#f=re.sub('fill="black">[0-9_. A-z-]+</text>',addOpacity,f)
f = re.sub('<path fill="white" .+\r', "", f)
link = "<a href='" + link + "'>Click here to modify image</a>"
B = link + f
F = open(com["-o"] + ".html", "r").read()
B = re.sub('<img src=".+" alt="some_text">', B, F)
F = open(com["-o"] + ".html", "w")
F.write(B)
F.close()