# HG changeset patch
# User devteam
# Date 1392162191 18000
# Node ID b0585923decc42a4f066229266c4e81048ab5e32
# Parent c2f6ec2fee7e3ac3bcc669c87475296e4eb958c0
Uploaded
diff -r c2f6ec2fee7e -r b0585923decc picard_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_wrapper.py Tue Feb 11 18:43:11 2014 -0500
@@ -0,0 +1,808 @@
+#!/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 = """
+
+
+
+
+"""
+galhtmlattr = """Galaxy tool %s run at %s
\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
+
+ print runme,self.opts.outdir
+
+ 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('Picard on line resources Picard output (transposed to make it easier to see) Picard output \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 = ['%s %s %s %s
\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=""""""
+ 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('\n')
+ res.append('
\n')
+ if len(flist) > 0:
+ res.append('The following output files were created (click the filename to view/download a copy): \n')
+ for i,f in enumerate(flist):
+ fn = os.path.split(f)[-1]
+ res.append('%s
\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('Picard Tool Run Log ',]
+ 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(' ')
+ if llen > maxloglines:
+ rlog.append('\n## WARNING - %d log lines truncated - %s contains entire output ' % (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('Picard software \n')
+ res.append( 'generated all outputs reported here running as a Galaxy 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)
+
+ 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':
+ """
+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"
+
+"""
+ 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 %salways happens if single ended data was provided to this tool,\n'
+ s += 'so please double check that your input data really is paired-end NGS data.