Mercurial > repos > devteam > picard1106
changeset 135:1790970e47fe draft
Uploaded
| author | devteam |
|---|---|
| date | Wed, 26 Feb 2014 17:29:45 -0500 |
| parents | 522c7184b0f2 |
| children | aab4fc9d443d |
| files | picard_wrapper.py |
| diffstat | 1 files changed, 879 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_wrapper.py Wed Feb 26 17:29:45 2014 -0500 @@ -0,0 +1,879 @@ +#!/usr/bin/env python +""" +Originally written by Kelly Vincent +pretty output and additional picard wrappers by Ross Lazarus for rgenetics +Runs all available wrapped Picard tools. +usage: picard_wrapper.py [options] +code Ross wrote licensed under the LGPL +see http://www.gnu.org/copyleft/lesser.html +""" + +import optparse, os, sys, subprocess, tempfile, shutil, time, logging + +galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +""" +galhtmlattr = """Galaxy tool %s run at %s</b><br/>""" +galhtmlpostfix = """</div></body></html>\n""" + + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + + +def timenow(): + """return current time as a string +""" + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + + +class PicardBase(): + """ +simple base class with some utilities for Picard +adapted and merged with Kelly Vincent's code april 2011 Ross +lots of changes... +""" + + def __init__(self, opts=None,arg0=None): + """ common stuff needed at init for a picard tool +""" + assert opts <> None, 'PicardBase needs opts at init' + self.opts = opts + if self.opts.outdir == None: + self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir + assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in' + self.picname = self.baseName(opts.jar) + if self.picname.startswith('picard'): + self.picname = opts.picard_cmd # special case for some tools like replaceheader? + self.progname = self.baseName(arg0) + self.version = '0.002' + self.delme = [] # list of files to destroy + self.title = opts.title + self.inputfile = opts.input + try: + os.makedirs(opts.outdir) + except: + pass + try: + os.makedirs(opts.tmpdir) + except: + pass + self.log_filename = os.path.join(self.opts.outdir,'%s.log' % self.picname) + self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname) + self.setLogging(logfname=self.log_filename) + + def baseName(self,name=None): + return os.path.splitext(os.path.basename(name))[0] + + def setLogging(self,logfname="picard_wrapper.log"): + """setup a logger +""" + logging.basicConfig(level=logging.INFO, + filename=logfname, + filemode='a') + + + def readLarge(self,fname=None): + """ read a potentially huge file. +""" + try: + # get stderr, allowing for case where it's very large + tmp = open( fname, 'rb' ) + s = '' + buffsize = 1048576 + try: + while True: + more = tmp.read( buffsize ) + if len(more) > 0: + s += more + else: + break + except OverflowError: + pass + tmp.close() + except Exception, e: + stop_err( 'Read Large Exception : %s' % str( e ) ) + return s + + def runCL(self,cl=None,output_dir=None): + """ construct and run a command line +we have galaxy's temp path as opt.temp_dir so don't really need isolation +sometimes stdout is needed as the output - ugly hacks to deal with potentially vast artifacts +""" + assert cl <> None, 'PicardBase runCL needs a command line as cl' + if output_dir == None: + output_dir = self.opts.outdir + if type(cl) == type([]): + cl = ' '.join(cl) + fd,templog = tempfile.mkstemp(dir=output_dir,suffix='rgtempRun.txt') + tlf = open(templog,'wb') + fd,temperr = tempfile.mkstemp(dir=output_dir,suffix='rgtempErr.txt') + tef = open(temperr,'wb') + process = subprocess.Popen(cl, shell=True, stderr=tef, stdout=tlf, cwd=output_dir) + rval = process.wait() + tlf.close() + tef.close() + stderrs = self.readLarge(temperr) + stdouts = self.readLarge(templog) + if rval > 0: + s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs) + stdouts = '%s\n%s' % (stdouts,stderrs) + else: + s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval) + logging.info(s) + os.unlink(templog) # always + os.unlink(temperr) # always + return s, stdouts, rval # sometimes s is an output + + def runPic(self, jar, cl): + """ +cl should be everything after the jar file name in the command +""" + runme = ['java -Xmx%s' % self.opts.maxjheap] + runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir) + runme.append('-jar %s' % jar) + runme += cl + s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir) + return stdouts,rval + + def samToBam(self,infile=None,outdir=None): + """ +use samtools view to convert sam to bam +""" + fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam') + cl = ['samtools view -h -b -S -o ',tempbam,infile] + tlog,stdouts,rval = self.runCL(cl,outdir) + return tlog,tempbam,rval + + def sortSam(self, infile=None,outfile=None,outdir=None): + """ +""" + print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir) + cl = ['samtools sort',infile,outfile] + tlog,stdouts,rval = self.runCL(cl,outdir) + return tlog + + def cleanup(self): + for fname in self.delme: + try: + os.unlink(fname) + except: + pass + + def prettyPicout(self,transpose,maxrows): + """organize picard outpouts into a report html page +""" + res = [] + try: + r = open(self.metricsOut,'r').readlines() + except: + r = [] + if len(r) > 0: + res.append('<b>Picard on line resources</b><ul>\n') + res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n') + res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n') + if transpose: + res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n') + else: + res.append('<b>Picard output</b><hr/>\n') + res.append('<table cellpadding="3" >\n') + dat = [] + heads = [] + lastr = len(r) - 1 + # special case for estimate library complexity hist + thist = False + for i,row in enumerate(r): + if row.strip() > '': + srow = row.split('\t') + if row.startswith('#'): + heads.append(row.strip()) # want strings + else: + dat.append(srow) # want lists + if row.startswith('## HISTOGRAM'): + thist = True + if len(heads) > 0: + hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)] + res += hres + heads = [] + if len(dat) > 0: + if transpose and not thist: + tdat = map(None,*dat) # transpose an arbitrary list of lists + tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)] + else: + tdat = ['\t'.join(x).strip() for x in dat] # back to strings :( + tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)] + res += tdat + dat = [] + res.append('</table>\n') + return res + + def fixPicardOutputs(self,transpose,maxloglines): + """ +picard produces long hard to read tab header files +make them available but present them transposed for readability +""" + logging.shutdown() + self.cleanup() # remove temp files stored in delme + rstyle="""<style type="text/css"> +tr.d0 td {background-color: oldlace; color: black;} +tr.d1 td {background-color: aliceblue; color: black;} +</style>""" + res = [rstyle,] + res.append(galhtmlprefix % self.progname) + res.append(galhtmlattr % (self.picname,timenow())) + flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')] + pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'] + if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs + for p in pdflist: + pbase = os.path.splitext(p)[0] # removes .pdf + imghref = '%s.jpg' % pbase + mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking! + if mimghref in flist: + imghref=mimghref # only one for thumbnail...it's a multi page pdf + res.append('<table cellpadding="10"><tr><td>\n') + res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) + res.append('</tr></td></table>\n') + if len(flist) > 0: + res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>') + res.append('<table>\n') + for i,f in enumerate(flist): + fn = os.path.split(f)[-1] + res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn)) + res.append('</table><p/>\n') + pres = self.prettyPicout(transpose,maxloglines) + if len(pres) > 0: + res += pres + l = open(self.log_filename,'r').readlines() + llen = len(l) + if llen > 0: + res.append('<b>Picard Tool Run Log</b><hr/>\n') + rlog = ['<pre>',] + if llen > maxloglines: + n = min(50,int(maxloglines/2)) + rlog += l[:n] + rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines)) + rlog += l[-n:] + else: + rlog += l + rlog.append('</pre>') + if llen > maxloglines: + rlog.append('\n<b>## WARNING - %d log lines truncated - <a href="%s">%s</a> contains entire output</b>' % (llen - maxloglines,self.log_filename,self.log_filename)) + res += rlog + else: + res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename) + res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n') + res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool') + res.append(galhtmlpostfix) + outf = open(self.opts.htmlout,'w') + outf.write(''.join(res)) + outf.write('\n') + outf.close() + + def makePicInterval(self,inbed=None,outf=None): + """ +picard wants bait and target files to have the same header length as the incoming bam/sam +a meaningful (ie accurate) representation will fail because of this - so this hack +it would be far better to be able to supply the original bed untouched +Additional checking added Ross Lazarus Dec 2011 to deal with two 'bug' reports on the list +""" + assert inbed <> None + bed = open(inbed,'r').readlines() + sbed = [x.split('\t') for x in bed] # lengths MUST be 5 + lens = [len(x) for x in sbed] + strands = [x[3] for x in sbed if not x[3] in ['+','-']] + maxl = max(lens) + minl = min(lens) + e = [] + if maxl <> minl: + e.append("## Input error: Inconsistent field count in %s - please read the documentation on bait/target format requirements, fix and try again" % inbed) + if maxl <> 5: + e.append("## Input error: %d fields found in %s, 5 required - please read the warning and documentation on bait/target format requirements, fix and try again" % (maxl,inbed)) + if len(strands) > 0: + e.append("## Input error: Fourth column in %s is not the required strand (+ or -) - please read the warning and documentation on bait/target format requirements, fix and try again" % (inbed)) + if len(e) > 0: # write to stderr and quit + print >> sys.stderr, '\n'.join(e) + sys.exit(1) + thead = os.path.join(self.opts.outdir,'tempSamHead.txt') + if self.opts.datatype == 'sam': + cl = ['samtools view -H -S',self.opts.input,'>',thead] + else: + cl = ['samtools view -H',self.opts.input,'>',thead] + self.runCL(cl=cl,output_dir=self.opts.outdir) + head = open(thead,'r').readlines() + s = '## got %d rows of header\n' % (len(head)) + logging.info(s) + o = open(outf,'w') + o.write(''.join(head)) + o.write(''.join(bed)) + o.close() + return outf + + def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None): + """ +interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs! +Do the work of removing all the error sequences +pysam is cool +infile = pysam.Samfile( "-", "r" ) +outfile = pysam.Samfile( "-", "w", template = infile ) +for s in infile: outfile.write(s) + +errors from ValidateSameFile.jar look like +WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing +ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary. +ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041 + +""" + assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam + assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path' + removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2] + remDict = dict(zip(removeNames,range(len(removeNames)))) + infile = pysam.Samfile(insam,'rb') + info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict)) + if len(removeNames) > 0: + outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file + i = 0 + j = 0 + for row in infile: + dropme = remDict.get(row.qname,None) # keep if None + if not dropme: + outfile.write(row) + j += 1 + else: # discard + i += 1 + info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam)) + outfile.close() + infile.close() + else: # we really want a nullop or a simple pointer copy + infile.close() + if newsam: + shutil.copy(insam,newsam) + logging.info(info) + + + +def __main__(): + doFix = False # tools returning htmlfile don't need this + doTranspose = True # default + maxloglines = 100 # default + #Parse Command Line + op = optparse.OptionParser() + # All tools + op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' ) + op.add_option('-e', '--inputext', default=None) + op.add_option('-o', '--output', default=None) + op.add_option('-n', '--title', default="Pick a Picard Tool") + op.add_option('-t', '--htmlout', default=None) + op.add_option('-d', '--outdir', default=None) + op.add_option('-x', '--maxjheap', default='3000m') + op.add_option('-b', '--bisulphite', default='false') + op.add_option('-s', '--sortorder', default='query') + op.add_option('','--tmpdir', default='/tmp') + op.add_option('-j','--jar',default='') + op.add_option('','--picard-cmd',default=None) + # Many tools + op.add_option( '', '--output-format', dest='output_format', help='Output format' ) + op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' ) + op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None ) + # CreateSequenceDictionary + op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None ) + op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' ) + op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' ) + op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' ) + # MarkDuplicates + op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' ) + op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' ) + # CollectInsertSizeMetrics + op.add_option('', '--taillimit', default="0") + op.add_option('', '--histwidth', default="0") + op.add_option('', '--minpct', default="0.01") + op.add_option('', '--malevel', default='') + op.add_option('', '--deviations', default="0.0") + # CollectAlignmentSummaryMetrics + op.add_option('', '--maxinsert', default="20") + op.add_option('', '--adaptors', default='') + # FixMateInformation and validate + # CollectGcBiasMetrics + op.add_option('', '--windowsize', default='100') + op.add_option('', '--mingenomefrac', default='0.00001') + # AddOrReplaceReadGroups + op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' ) + op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' ) + op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' ) + op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' ) + op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' ) + op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' ) + op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' ) + op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' ) + # ReorderSam + op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' ) + op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' ) + # ReplaceSamHeader + op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' ) + + op.add_option('','--assumesorted', default='true') + op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*") + #estimatelibrarycomplexity + op.add_option('','--minid', default="5") + op.add_option('','--maxdiff', default="0.03") + op.add_option('','--minmeanq', default="20") + #hsmetrics + op.add_option('','--baitbed', default=None) + op.add_option('','--targetbed', default=None) + #validate + op.add_option('','--ignoreflags', action='append', type="string") + op.add_option('','--maxerrors', default=None) + op.add_option('','--datatype', default=None) + op.add_option('','--bamout', default=None) + op.add_option('','--samout', default=None) + #downsample + op.add_option('','--probability', default="1") + op.add_option('','--seed', default="1") + #meanqualitybycycle + op.add_option('','--pfreadsonly', default='false') + op.add_option('','--alignedreadsonly', default='false') + #collectrnaseqmetrics + op.add_option('','--ignoreseq', action='append', type="string") + op.add_option('','--minlength', default=None) + op.add_option('','--refflat', default=None) + op.add_option('','--strandspecificity', default=None) + op.add_option('','--ribosomalintervals', default='null') + op.add_option('','--rrnafragmentpercentage', default=None) + + opts, args = op.parse_args() + opts.sortme = opts.assumesorted == 'false' + assert opts.input <> None + # need to add + # instance that does all the work + pic = PicardBase(opts,sys.argv[0]) + + tmp_dir = opts.outdir + haveTempout = False # we use this where sam output is an option + rval = 0 + stdouts = 'Not run yet' + # set ref and dict files to use (create if necessary) + ref_file_name = opts.ref + if opts.ref_file <> None: + csd = 'CreateSequenceDictionary' + realjarpath = os.path.split(opts.jar)[0] + jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq + tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname) + ref_file_name = '%s.fasta' % tmp_ref_name + # build dict + dict_file_name = '%s.dict' % tmp_ref_name + os.symlink( opts.ref_file, ref_file_name ) + cl = ['REFERENCE=%s' % ref_file_name] + cl.append('OUTPUT=%s' % dict_file_name) + cl.append('URI=%s' % os.path.basename( opts.ref_file )) + cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names) + if opts.species_name: + cl.append('SPECIES=%s' % opts.species_name) + if opts.build_name: + cl.append('GENOME_ASSEMBLY=%s' % opts.build_name) + pic.delme.append(dict_file_name) + pic.delme.append(ref_file_name) + pic.delme.append(tmp_ref_name) + stdouts,rval = pic.runPic(jarpath, cl) + # run relevant command(s) + + # define temporary output + # if output is sam, it must have that extension, otherwise bam will be produced + # specify sam or bam file with extension + if opts.output_format == 'sam': + suff = '.sam' + else: + suff = '' + tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff ) + + cl = ['VALIDATION_STRINGENCY=LENIENT',] + + if pic.picname == 'AddOrReplaceReadGroups': + # sort order to match Galaxy's default + cl.append('SORT_ORDER=coordinate') + # input + cl.append('INPUT=%s' % opts.input) + # outputs + cl.append('OUTPUT=%s' % tempout) + # required read groups + cl.append('RGLB="%s"' % opts.rg_library) + cl.append('RGPL="%s"' % opts.rg_platform) + cl.append('RGPU="%s"' % opts.rg_plat_unit) + cl.append('RGSM="%s"' % opts.rg_sample) + if opts.rg_id: + cl.append('RGID="%s"' % opts.rg_id) + # optional read groups + if opts.rg_seq_center: + cl.append('RGCN="%s"' % opts.rg_seq_center) + if opts.rg_desc: + cl.append('RGDS="%s"' % opts.rg_desc) + stdouts,rval = pic.runPic(opts.jar, cl) + haveTempout = True + + elif pic.picname == 'BamIndexStats': + tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir ) + tmp_bam_name = '%s.bam' % tmp_name + tmp_bai_name = '%s.bai' % tmp_bam_name + os.symlink( opts.input, tmp_bam_name ) + os.symlink( opts.bai_file, tmp_bai_name ) + cl.append('INPUT=%s' % ( tmp_bam_name )) + pic.delme.append(tmp_bam_name) + pic.delme.append(tmp_bai_name) + pic.delme.append(tmp_name) + stdouts,rval = pic.runPic( opts.jar, cl ) + f = open(pic.metricsOut,'a') + f.write(stdouts) # got this on stdout from runCl + f.write('\n') + f.close() + doTranspose = False # but not transposed + + elif pic.picname == 'EstimateLibraryComplexity': + cl.append('I=%s' % opts.input) + cl.append('O=%s' % pic.metricsOut) + if float(opts.minid) > 0: + cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid) + if float(opts.maxdiff) > 0.0: + cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff) + if float(opts.minmeanq) > 0: + cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq) + if opts.readregex > '': + cl.append('READ_NAME_REGEX="%s"' % opts.readregex) + if float(opts.optdupdist) > 0: + cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) + stdouts,rval = pic.runPic(opts.jar, cl) + + elif pic.picname == 'CollectAlignmentSummaryMetrics': + # Why do we do this fakefasta thing? + # Because we need NO fai to be available or picard barfs unless it matches the input data. + # why? Dunno Seems to work without complaining if the .bai file is AWOL.... + fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) + try: + os.symlink(ref_file_name,fakefasta) + except: + s = '## unable to symlink %s to %s - different devices? Will shutil.copy' + info = s + shutil.copy(ref_file_name,fakefasta) + pic.delme.append(fakefasta) + cl.append('ASSUME_SORTED=true') + adaptlist = opts.adaptors.split(',') + adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist] + cl += adaptorseqs + cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite) + cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert) + cl.append('OUTPUT=%s' % pic.metricsOut) + cl.append('R=%s' % fakefasta) + cl.append('TMP_DIR=%s' % opts.tmpdir) + if not opts.assumesorted.lower() == 'true': # we need to sort input + sortedfile = '%s.sorted' % os.path.basename(opts.input) + if opts.datatype == 'sam': # need to work with a bam + tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir) + pic.delme.append(tempbam) + try: + tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) + except: + print '## exception on sorting sam file %s' % opts.input + else: # is already bam + try: + tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) + except : # bug - [bam_sort_core] not being ignored - TODO fixme + print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input) + cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile))) + pic.delme.append(os.path.join(opts.outdir,sortedfile)) + else: + cl.append('INPUT=%s' % os.path.abspath(opts.input)) + stdouts,rval = pic.runPic(opts.jar, cl) + + + elif pic.picname == 'CollectGcBiasMetrics': + assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name + # sigh. Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data. + # why? Dunno + fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) + try: + os.symlink(ref_file_name,fakefasta) + except: + s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' + info = s + shutil.copy(ref_file_name,fakefasta) + pic.delme.append(fakefasta) + x = 'rgPicardGCBiasMetrics' + pdfname = '%s.pdf' % x + jpgname = '%s.jpg' % x + tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out') + temppdf = os.path.join(opts.outdir,pdfname) + cl.append('R=%s' % fakefasta) + cl.append('WINDOW_SIZE=%s' % opts.windowsize) + cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac) + cl.append('INPUT=%s' % opts.input) + cl.append('OUTPUT=%s' % tempout) + cl.append('TMP_DIR=%s' % opts.tmpdir) + cl.append('CHART_OUTPUT=%s' % temppdf) + cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut) + stdouts,rval = pic.runPic(opts.jar, cl) + if os.path.isfile(temppdf): + cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find + s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir) + else: + s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf + lf = open(pic.log_filename,'a') + lf.write(s) + lf.write('\n') + lf.close() + + elif pic.picname == 'CollectInsertSizeMetrics': + """ <command interpreter="python"> +picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" +--histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" +-j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" +</command> +""" + isPDF = 'InsertSizeHist.pdf' + pdfpath = os.path.join(opts.outdir,isPDF) + histpdf = 'InsertSizeHist.pdf' + cl.append('I=%s' % opts.input) + cl.append('O=%s' % pic.metricsOut) + cl.append('HISTOGRAM_FILE=%s' % histpdf) + #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56 + # cl.append('TAIL_LIMIT=%s' % opts.taillimit) + if opts.histwidth <> '0': + cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth) + if float( opts.minpct) > 0.0: + cl.append('MINIMUM_PCT=%s' % opts.minpct) + if float(opts.deviations) > 0.0: + cl.append('DEVIATIONS=%s' % opts.deviations) + if opts.malevel: + malists = opts.malevel.split(',') + malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists] + cl += malist + stdouts,rval = pic.runPic(opts.jar, cl) + if os.path.exists(pdfpath): # automake thumbnail - will be added to html + cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] + pic.runCL(cl=cl2,output_dir=opts.outdir) + else: + s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath + s += 'This <b>always happens if single ended data was provided</b> to this tool,\n' + s += 'so please double check that your input data really is paired-end NGS data.<br/>\n' + s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>' + logging.info(s) + if len(stdouts) > 0: + logging.info(stdouts) + + elif pic.picname == 'MarkDuplicates': + # assume sorted even if header says otherwise + cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) + # input + cl.append('INPUT=%s' % opts.input) + # outputs + cl.append('OUTPUT=%s' % opts.output) + cl.append('METRICS_FILE=%s' % pic.metricsOut ) + # remove or mark duplicates + cl.append('REMOVE_DUPLICATES=%s' % opts.remdups) + # the regular expression to be used to parse reads in incoming SAM file + cl.append('READ_NAME_REGEX="%s"' % opts.readregex) + # maximum offset between two duplicate clusters + cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) + stdouts,rval = pic.runPic(opts.jar, cl) + + elif pic.picname == 'FixMateInformation': + cl.append('I=%s' % opts.input) + cl.append('O=%s' % tempout) + cl.append('SORT_ORDER=%s' % opts.sortorder) + stdouts,rval = pic.runPic(opts.jar,cl) + haveTempout = True + + elif pic.picname == 'ReorderSam': + # input + cl.append('INPUT=%s' % opts.input) + # output + cl.append('OUTPUT=%s' % tempout) + # reference + cl.append('REFERENCE=%s' % ref_file_name) + # incomplete dict concordance + if opts.allow_inc_dict_concord == 'true': + cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true') + # contig length discordance + if opts.allow_contig_len_discord == 'true': + cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true') + stdouts,rval = pic.runPic(opts.jar, cl) + haveTempout = True + + elif pic.picname == 'ReplaceSamHeader': + cl.append('INPUT=%s' % opts.input) + cl.append('OUTPUT=%s' % tempout) + cl.append('HEADER=%s' % opts.header_file) + stdouts,rval = pic.runPic(opts.jar, cl) + haveTempout = True + + elif pic.picname == 'CalculateHsMetrics': + maxloglines = 100 + baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait') + targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target') + baitf = pic.makePicInterval(opts.baitbed,baitfname) + if opts.targetbed == opts.baitbed: # same file sometimes + targetf = baitf + else: + targetf = pic.makePicInterval(opts.targetbed,targetfname) + cl.append('BAIT_INTERVALS=%s' % baitf) + cl.append('TARGET_INTERVALS=%s' % targetf) + cl.append('INPUT=%s' % os.path.abspath(opts.input)) + cl.append('OUTPUT=%s' % pic.metricsOut) + cl.append('TMP_DIR=%s' % opts.tmpdir) + stdouts,rval = pic.runPic(opts.jar,cl) + + elif pic.picname == 'ValidateSamFile': + import pysam + doTranspose = False + sortedfile = os.path.join(opts.outdir,'rgValidate.sorted') + stf = open(pic.log_filename,'w') + tlog = None + if opts.datatype == 'sam': # need to work with a bam + tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) + try: + tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) + except: + print '## exception on sorting sam file %s' % opts.input + else: # is already bam + try: + tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) + except: # bug - [bam_sort_core] not being ignored - TODO fixme + print '## exception on sorting bam file %s' % opts.input + if tlog: + print '##tlog=',tlog + stf.write(tlog) + stf.write('\n') + sortedfile = '%s.bam' % sortedfile # samtools does that + cl.append('O=%s' % pic.metricsOut) + cl.append('TMP_DIR=%s' % opts.tmpdir) + cl.append('I=%s' % sortedfile) + opts.maxerrors = '99999999' + cl.append('MAX_OUTPUT=%s' % opts.maxerrors) + if opts.ignoreflags[0] <> 'None': # picard error values to ignore + igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None'] + cl.append(' '.join(igs)) + if opts.bisulphite.lower() <> 'false': + cl.append('IS_BISULFITE_SEQUENCED=true') + if opts.ref <> None or opts.ref_file <> None: + cl.append('R=%s' % ref_file_name) + stdouts,rval = pic.runPic(opts.jar,cl) + if opts.datatype == 'sam': + pic.delme.append(tempbam) + newsam = opts.output + outformat = 'bam' + pe = open(pic.metricsOut,'r').readlines() + pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat) + pic.delme.append(sortedfile) # not wanted + stf.close() + pic.cleanup() + +####liubo added CleanSam tool#### + elif pic.picname == 'CleanSam': + # input + cl.append('INPUT=%s' % opts.input) + # output + cl.append('OUTPUT=%s' % tempout) + stdouts,rval = pic.runPic(opts.jar, cl) + haveTempout = True + + elif pic.picname == 'SortSam': + cl.append('I=%s' % opts.input) + cl.append('O=%s' % tempout) + cl.append('SORT_ORDER=%s' % opts.sortorder) + stdouts,rval = pic.runPic(opts.jar,cl) + haveTempout = True + + elif pic.picname == 'BuildBamIndex': + cl.append('I=%s' % opts.input) + cl.append('O=%s' % tempout) + stdouts,rval = pic.runPic(opts.jar,cl) + haveTempout = True + + elif pic.picname == 'SamFormatConverter': + cl.append('INPUT=%s' % opts.input) + cl.append('OUTPUT=%s' % tempout) + pic.runPic(opts.jar, cl) + haveTempout = True + elif pic.picname == "DownsampleSam": + cl.append('I=%s' % opts.input) + mystring = opts.output + mystringsam = mystring + ".sam" + cl.append('O=%s' % mystringsam) + if float(opts.probability) > 0: + cl.append('PROBABILITY=%s' % opts.probability) + if float(opts.seed) > 0: + cl.append('RANDOM_SEED=%s' % opts.seed) + stdouts,rval = pic.runPic(opts.jar, cl) + myoutput = mystringsam.replace(".sam", "") + os.rename(mystringsam,myoutput) + + elif pic.picname == 'MeanQualityByCycle': + isPDF = 'MeanQualityByCycle.pdf' + pdfpath = os.path.join(opts.outdir,isPDF) + histpdf = isPDF + cl.append('I=%s' % opts.input) + cl.append('O=%s' % pic.metricsOut) + cl.append('CHART_OUTPUT=%s' % histpdf) + cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) + cl.append('ALIGNED_READS_ONLY=%s' % (opts.alignedreadsonly)) + cl.append('PF_READS_ONLY=%s' % (opts.pfreadsonly)) + stdouts,rval = pic.runPic(opts.jar, cl) + if os.path.exists(pdfpath): # automake thumbnail - will be added to html + cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] + pic.runCL(cl=cl2,output_dir=opts.outdir) + else: + s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath + logging.info(s) + if len(stdouts) > 0: + logging.info(stdouts) + + elif pic.picname == 'CollectRnaSeqMetrics': + isPDF = pic.picname + '.pdf' + pdfpath = os.path.join(opts.outdir,isPDF) + histpdf = isPDF + cl.append('I=%s' % opts.input) + cl.append('O=%s' % pic.metricsOut) + cl.append('CHART_OUTPUT=%s' % histpdf) + cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) + cl.append('MINIMUM_LENGTH=%s' % (opts.minlength)) + cl.append('REF_FLAT=%s' % (opts.refflat)) + cl.append('STRAND_SPECIFICITY=%s' % (opts.strandspecificity)) + cl.append('RIBOSOMAL_INTERVALS=%s' % (opts.ribosomalintervals)) + cl.append('RRNA_FRAGMENT_PERCENTAGE=%s' % (opts.rrnafragmentpercentage)) + if opts.ignoreseq: # picard error values to ignore + igs = ['IGNORE_SEQUENCE=%s' % x for x in opts.ignoreseq if x <> 'None'] + cl.append(' '.join(igs)) + if opts.malevel: + malists = opts.malevel.split(',') + malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists] + cl += malist + stdouts,rval = pic.runPic(opts.jar, cl) + if os.path.exists(pdfpath): # automake thumbnail - will be added to html + cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] + pic.runCL(cl=cl2,output_dir=opts.outdir) + else: + s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath + logging.info(s) + if len(stdouts) > 0: + logging.info(stdouts) + + else: + print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname + sys.exit(1) + if haveTempout: + # Some Picard tools produced a potentially intermediate bam file. + # Either just move to final location or create sam + if os.path.exists(tempout): + shutil.move(tempout, os.path.abspath(opts.output)) + if opts.htmlout <> None or doFix: # return a pretty html page + pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines) + if rval <> 0: + print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts) + # signal failure +if __name__=="__main__": __main__()