def fix_fastqc(self, rep=[], flist=[], runlog=[]):
""" add some of our stuff to the html
"""
bodyindex = len(rep) - 1 # hope they don't change this
footrow = bodyindex - 1
footer = rep[footrow]
rep = rep[:footrow] + rep[footrow + 1:]
res = [
'<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n'
]
flist.sort()
for i, f in enumerate(flist):
if not (os.path.isdir(f)):
fn = os.path.split(f)[-1]
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' %
(fn, getFileString(fn, self.opts.outputdir)))
res.append('</table>\n')
res.append(
'<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n'
)
res.append(
'FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>'
)
res.append(footer)
fixed = rep[:bodyindex] + res + rep[bodyindex:]
return fixed # with our additions
def write_html_report(self):
"""
write the report as html
"""
out_folder = self.opts.outdir
my_template = Template(
filename=os.path.join(self.tool_folder, self.__class__.HTML_REPORT_TEMPLATE),
strict_undefined=True)
if os.path.exists(os.path.abspath(out_folder)):
files = [os.path.join(out_folder, x) for x in os.listdir(out_folder)
if not x.startswith('.')]
files.sort(key=lambda f: os.path.getmtime(f))
file_info = [(os.path.split(f)[-1], getFileString(os.path.split(f)[-1], self.opts.outdir))
for f in files]
else:
file_info = []
template_parameters = {
'program_name': str(self.program_name),
'timestamp' : str(timenow()),
'file_info': file_info,
'log_data' : open(self.tlogname).read().replace('\n', '\n<BR />'),
'command_string': str(self.cl)
}
f = open(self.opts.htmlout, 'w')
f.write(my_template.render(**template_parameters))
f.close()
def makehtml(self):
"""
write the report as html
"""
logdat = open(self.tlogname,'r').readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname,timenow()))
res.append('<b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b><hr/>')
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(flist) > 0: # show what's left
flist = [x for x in flist if not (x.startswith('.') or x == 'None')]
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir,x)),x) for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
res.append('<div><b>Output files.</b><hr/>\n')
res.append('<table>\n')
for i,f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn,self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fs))
res.append('</table></div>\n')
res.append('<b>Log of activity</b><hr/>\n')
res.append('\n%s' % '<br/>'.join(logdat))
res.append('<hr/>Note: The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
res.append('generated all outputs reported here. These third party tools were')
res.append('orchestrated by the Galaxy rgEstLibComplexity wrapper and this command line from the Galaxy form:<br/>\n%s' % (self.cl))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout,'w')
f.write('\n'.join(res))
f.close()
def fix_fastqc(self, rep=[], flist=[], runlog=[]):
""" add some of our stuff to the html
"""
bs = '</body></html>\n' # hope they don't change this
try:
bodyindex = rep.index(bs) # hope they don't change this
except:
bodyindex = len(rep) - 1
res = []
res.append('<table>\n')
flist.sort()
for i, f in enumerate(flist):
if not (os.path.isdir(f)):
fn = os.path.split(f)[-1]
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' %
(fn, getFileString(fn, self.opts.outputdir)))
res.append('</table><p/>\n')
res.append(
'<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n'
)
res.append(
'FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n'
)
fixed = rep[:bodyindex] + res + rep[bodyindex:]
return fixed # with our additions
def write_html_report(self):
"""
write the report as html
"""
out_folder = self.opts.outdir
my_template = Template(filename=os.path.join(
self.tool_folder, self.__class__.HTML_REPORT_TEMPLATE),
strict_undefined=True)
if os.path.exists(os.path.abspath(out_folder)):
files = [
os.path.join(out_folder, x) for x in os.listdir(out_folder)
if not x.startswith('.')
]
files.sort(key=lambda f: os.path.getmtime(f))
file_info = [
(os.path.split(f)[-1],
getFileString(os.path.split(f)[-1], self.opts.outdir))
for f in files
]
else:
file_info = []
template_parameters = {
'program_name': str(self.program_name),
'timestamp': str(timenow()),
'file_info': file_info,
'log_data': open(self.tlogname).read().replace('\n', '\n<BR />'),
'command_string': str(self.cl)
}
f = open(self.opts.htmlout, 'w')
f.write(my_template.render(**template_parameters))
f.close()
def makehtml(self):
"""
write the report as html
"""
logdat = open(self.tlogname, 'r').readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname, timenow()))
res.append(
'<b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b><hr/>'
)
imghref = '%s.jpg' % os.path.splitext(self.isPDF)[0] # removes .pdf
res.append('<table cellpadding="10"><tr><td>\n')
res.append(
'<a href="%s"><img src="%s" alt="%s" hspace="10" align="middle"></a>\n'
% (self.isPDF, imghref, imghref))
res.append('</tr><td></table>\n')
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(
flist
) > 0: # we should clean everything up - picard doesn't tell us what it did in cleansam unfortunately
flist = [
x for x in flist if not (x.startswith('.') or x == 'None')
]
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir, x)), x)
for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
res.append('<div><b>Output files.</b><hr/>\n')
res.append('<table>\n')
for i, f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn, self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' %
(fn, fs))
res.append('</table></div>\n')
res.append('<b>Log of activity</b><hr/>\n')
res.append('\n%s' % '<br/>'.join(logdat))
res.append(
'<hr/>Note: The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n'
)
res.append(
'generated all outputs reported here. These third party tools were'
)
res.append(
'orchestrated by the Galaxy rgInsertSize wrapper and this command line from the Galaxy form:<br/>\n%s'
% (self.cl))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout, 'w')
f.write('\n'.join(res))
f.close()
def writehtml(self):
"""
write the report as html
"""
logdat = open(self.tlogname,'r').readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname,timenow()))
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(flist) > 0: # show what's left
flist = [x for x in flist if not (x.startswith('.') or x == 'None')]
pdfs = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir,x)),x) for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
if len(pdfs) > 0:
cells = []
pdfs.sort()
res.append('<div><table cellpadding="5" cellspacing="10">\n')
for p in pdfs:
pfname = os.path.split(p)[-1]
pfroot = os.path.splitext(pfname)[0]
imghref = '%s.jpg' % pfroot # thumbnail name from mogrify
cl = ['mogrify', '-resize x300 -write %s %s' % (imghref,pfname),]
self.run(cl)
s = '<a href="%s"><img src="%s" title="%s" hspace="10" align="middle"></a>' % (pfname,imghref,pfname)
cells.append('<td>%s</br>%s</td>' % (pfroot,s))
ncells = len(cells)
for i in range(ncells):
if i % 2 == 1:
res.append('<tr>%s%s</tr>\n' % (cells[i-1],cells[i]))
if ncells % 2 == 0: # last one
res.append('<tr colspan="2">%s</tr>\n' % (cells[-1]))
res.append('</table></div>\n')
res.append('<div><b>Output files.</b><hr/>\n')
res.append('<table>\n')
for i,f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn,self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fs))
res.append('</table></div>\n')
res.append('<b>Your job produced the following log of activity - check here for a record of what was done and any unexpected events</b><hr/>')
res.append('\n%s' % '<br/>'.join(logdat))
res.append('<hr/>Note: The freely available <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Main_Page">GATK</a> \n')
res.append('did all the work reportexampleBAM.bam ed here. GATK is an independent non-Galaxy community resource, whose third party tools were')
res.append('orchestrated by the Galaxy rgGATKRecalibrate wrapper and this command line from the Galaxy form:<br/>\n%s' % (self.cl))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout,'w')
f.write('\n'.join(res))
f.close()
def writehtml(self):
"""
write the report as html
"""
logdat = open(self.tlogname,'r').readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname,timenow()))
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(flist) > 0: # show what's left
flist = [x for x in flist if not (x.startswith('.') or x == 'None')]
pdfs = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir,x)),x) for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
if len(pdfs) > 0:
cells = []
pdfs.sort()
res.append('<div><table cellpadding="5" cellspacing="10">\n')
for p in pdfs:
pfname = os.path.split(p)[-1]
pfroot = os.path.splitext(pfname)[0]
imghref = '%s.jpg' % pfroot # thumbnail name from mogrify
cl = ['mogrify', '-resize x300 -write %s %s' % (imghref,pfname),]
self.run(cl)
s = '<a href="%s"><img src="%s" alt="%s" hspace="10" align="middle"></a>' % (pfname,imghref,pfname)
cells.append('<td>%s</br>%s</td>' % (pfroot,s))
ncells = len(cells)
for i in range(ncells):
if i % 2 == 1:
res.append('<tr>%s%s</tr>\n' % (cells[i-1],cells[i]))
if ncells % 2 == 0: # last one
res.append('<tr colspan="2">%s</tr>\n' % (cells[-1]))
res.append('</table></div>\n')
res.append('<div><b>Output files.</b><hr/>\n')
res.append('<table>\n')
for i,f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn,self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fs))
res.append('</table></div>\n')
res.append('<b>Your job produced the following log of activity - check here for a record of what was done and any unexpected events</b><hr/>')
res.append('\n%s' % '<br/>'.join(logdat))
res.append('<hr/>Note: The freely available <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Main_Page">GATK</a> \n')
res.append('did all the work reportexampleBAM.bam ed here. GATK is an independent non-Galaxy community resource, whose third party tools were')
res.append('orchestrated by the Galaxy rgGATKRecalibrate wrapper and this command line from the Galaxy form:<br/>\n%s' % (self.cl))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout,'w')
f.write('\n'.join(res))
f.close()
def writehtml(self):
"""
write the report as html
note complications needed to write pre and post reports - they have to be separated since gatk insists on giving them all the same names
but at least allows a separate output directory...
"""
logdat = open(self.tlogname, 'r').readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname, timenow()))
res.append(
'<font size="-2">Note: The freely available <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Main_Page">GATK</a>'
)
res.append(
'did all the calculations arranged here in your Galaxy history')
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(flist) > 0: # show what's left after cleanup
flist = [
x for x in flist if not (x.startswith('.') or x == 'None')
]
pdfs = [
x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'
]
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir, x)), x)
for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
if len(pdfs) > 0:
res = self.writeImages(pdfs, res)
res.append('<div><b>Output files.</b><hr/>\n')
res.append('<table>\n')
for i, f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn, self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' %
(fn, fs))
res.append('</table></div>\n')
res.append(
'<b>Your job produced the following log of activity - check here for a record of what was done and any unexpected events</b><hr/>'
)
res.append('\n%s' % '<br/>'.join(logdat))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout, 'w')
f.write('\n'.join(res))
f.close()
def fix_fastqc(self,rep=[],flist=[],runlog=[]):
""" add some of our stuff to the html
"""
bodyindex = len(rep) -1 # hope they don't change this
footrow = bodyindex - 1
footer = rep[footrow]
rep = rep[:footrow] + rep[footrow+1:]
res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n']
flist.sort()
for i,f in enumerate(flist):
if not(os.path.isdir(f)):
fn = os.path.split(f)[-1]
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir)))
res.append('</table>\n')
res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n')
res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>')
res.append(footer)
fixed = rep[:bodyindex] + res + rep[bodyindex:]
return fixed # with our additions
def fix_fastqc(self,rep=[],flist=[],runlog=[]):
""" add some of our stuff to the html
"""
bs = '</body></html>\n' # hope they don't change this
try:
bodyindex = rep.index(bs) # hope they don't change this
except:
bodyindex = len(rep) - 1
res = []
res.append('<table>\n')
flist.sort()
for i,f in enumerate(flist):
if not(os.path.isdir(f)):
fn = os.path.split(f)[-1]
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir)))
res.append('</table><p/>\n')
res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n')
res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n')
fixed = rep[:bodyindex] + res + rep[bodyindex:]
return fixed # with our additions
def writehtml(self):
"""
write the report as html
note complications needed to write pre and post reports - they have to be separated since gatk insists on giving them all the same names
but at least allows a separate output directory...
"""
logdat = open(self.tlogname, "r").readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname, timenow()))
res.append(
'<font size="-2">Note: The freely available <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Main_Page">GATK</a>'
)
res.append("did all the calculations arranged here in your Galaxy history")
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(flist) > 0: # show what's left after cleanup
flist = [x for x in flist if not (x.startswith(".") or x == "None")]
pdfs = [x for x in flist if os.path.splitext(x)[-1].lower() == ".pdf"]
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir, x)), x) for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
if len(pdfs) > 0:
res = self.writeImages(pdfs, res)
res.append("<div><b>Output files.</b><hr/>\n")
res.append("<table>\n")
for i, f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn, self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn, fs))
res.append("</table></div>\n")
res.append(
"<b>Your job produced the following log of activity - check here for a record of what was done and any unexpected events</b><hr/>"
)
res.append("\n%s" % "<br/>".join(logdat))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout, "w")
f.write("\n".join(res))
f.close()
def makehtml(self):
"""
write the report as html
"""
logdat = open(self.tlogname,'r').readlines()
res = []
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname,timenow()))
res.append('<b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b><hr/>')
imghref = '%s.jpg' % os.path.splitext(self.isPDF)[0] # removes .pdf
res.append('<table cellpadding="10"><tr><td>\n')
res.append('<a href="%s"><img src="%s" alt="%s" hspace="10" align="middle"></a>\n' % (self.isPDF,imghref,imghref))
res.append('</tr><td></table>\n')
try:
flist = os.listdir(self.opts.outdir)
except:
flist = []
if len(flist) > 0: # we should clean everything up - picard doesn't tell us what it did in cleansam unfortunately
flist = [x for x in flist if not (x.startswith('.') or x == 'None')]
tlist = [(os.path.getmtime(os.path.join(self.opts.outdir,x)),x) for x in flist]
tlist.sort()
flist = [x[1] for x in tlist]
res.append('<div><b>Output files.</b><hr/>\n')
res.append('<table>\n')
for i,f in enumerate(flist):
fn = os.path.split(f)[-1]
fs = getFileString(fn,self.opts.outdir)
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fs))
res.append('</table></div>\n')
res.append('<b>Log of activity</b><hr/>\n')
res.append('\n%s' % '<br/>'.join(logdat))
res.append('<hr/>Note: The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
res.append('generated all outputs reported here. These third party tools were')
res.append('orchestrated by the Galaxy rgInsertSize wrapper and this command line from the Galaxy form:<br/>\n%s' % (self.cl))
res.append(galhtmlpostfix)
f = open(self.opts.htmlout,'w')
f.write('\n'.join(res))
f.close()