annotate picard_wrapper.py @ 3:bf1c3f9f8282

Fix for FastqToSam MAX_Q usage detection.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 03 May 2013 17:13:01 -0400
parents 1cd7f3b42609
children
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1 #!/usr/bin/env python
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2 """
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3 Originally written by Kelly Vincent
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4 pretty output and additional picard wrappers by Ross Lazarus for rgenetics
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5 Runs all available wrapped Picard tools.
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6 usage: picard_wrapper.py [options]
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7 code Ross wrote licensed under the LGPL
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8 see http://www.gnu.org/copyleft/lesser.html
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9 """
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10
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11 import optparse, os, sys, subprocess, tempfile, shutil, time, logging
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12
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13 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
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14 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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15 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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16 <head>
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17 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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18 <meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" />
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19 <title></title>
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20 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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21 </head>
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22 <body>
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23 <div class="document">
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24 """
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25 galhtmlattr = """Galaxy tool %s run at %s</b><br/>"""
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26 galhtmlpostfix = """</div></body></html>\n"""
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27
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28
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29 def stop_err( msg ):
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30 sys.stderr.write( '%s\n' % msg )
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31 sys.exit()
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32
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33
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34 def timenow():
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35 """return current time as a string
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36 """
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37 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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38
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39
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40 class PicardBase():
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41 """
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42 simple base class with some utilities for Picard
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43 adapted and merged with Kelly Vincent's code april 2011 Ross
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44 lots of changes...
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45 """
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46
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47 def __init__(self, opts=None,arg0=None):
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48 """ common stuff needed at init for a picard tool
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49 """
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50 assert opts <> None, 'PicardBase needs opts at init'
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51 self.opts = opts
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52 if self.opts.outdir == None:
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53 self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir
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54 assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in'
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55 self.picname = self.baseName(opts.jar)
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56 if self.picname.startswith('picard'):
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57 self.picname = opts.picard_cmd # special case for some tools like replaceheader?
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58 self.progname = self.baseName(arg0)
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59 self.version = '0.002'
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60 self.delme = [] # list of files to destroy
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61 self.title = opts.title
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62 self.inputfile = opts.input
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63 try:
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64 os.makedirs(opts.outdir)
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65 except:
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66 pass
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67 try:
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68 os.makedirs(opts.tmpdir)
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69 except:
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70 pass
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71 self.log_filename = os.path.join(self.opts.outdir,'%s.log' % self.picname)
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72 self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
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73 self.setLogging(logfname=self.log_filename)
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74
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75 def baseName(self,name=None):
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76 return os.path.splitext(os.path.basename(name))[0]
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77
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78 def setLogging(self,logfname="picard_wrapper.log"):
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79 """setup a logger
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80 """
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81 logging.basicConfig(level=logging.INFO,
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82 filename=logfname,
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83 filemode='a')
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84
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85
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86 def readLarge(self,fname=None):
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87 """ read a potentially huge file.
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88 """
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89 try:
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90 # get stderr, allowing for case where it's very large
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91 tmp = open( fname, 'rb' )
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92 s = ''
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93 buffsize = 1048576
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94 try:
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95 while True:
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96 more = tmp.read( buffsize )
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97 if len(more) > 0:
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98 s += more
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99 else:
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100 break
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101 except OverflowError:
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102 pass
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103 tmp.close()
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104 except Exception, e:
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105 stop_err( 'Read Large Exception : %s' % str( e ) )
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106 return s
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107
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108 def runCL(self,cl=None,output_dir=None):
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109 """ construct and run a command line
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110 we have galaxy's temp path as opt.temp_dir so don't really need isolation
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111 sometimes stdout is needed as the output - ugly hacks to deal with potentially vast artifacts
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112 """
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113 assert cl <> None, 'PicardBase runCL needs a command line as cl'
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114 if output_dir == None:
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115 output_dir = self.opts.outdir
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116 if type(cl) == type([]):
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117 cl = ' '.join(cl)
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118 fd,templog = tempfile.mkstemp(dir=output_dir,suffix='rgtempRun.txt')
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119 tlf = open(templog,'wb')
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120 fd,temperr = tempfile.mkstemp(dir=output_dir,suffix='rgtempErr.txt')
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121 tef = open(temperr,'wb')
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122 process = subprocess.Popen(cl, shell=True, stderr=tef, stdout=tlf, cwd=output_dir)
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123 rval = process.wait()
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124 tlf.close()
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125 tef.close()
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126 stderrs = self.readLarge(temperr)
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127 stdouts = self.readLarge(templog)
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128 if rval > 0:
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129 s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs)
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130 stdouts = '%s\n%s' % (stdouts,stderrs)
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131 else:
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132 s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval)
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133 logging.info(s)
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134 os.unlink(templog) # always
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135 os.unlink(temperr) # always
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136 return s, stdouts, rval # sometimes s is an output
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137
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138 def runPic(self, jar, cl):
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139 """
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140 cl should be everything after the jar file name in the command
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141 """
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142 runme = ['java -Xmx%s' % self.opts.maxjheap]
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143 runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir)
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144 runme.append('-jar %s' % jar)
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145 runme += cl
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146 s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir)
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147 return stdouts,rval
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148
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149 def samToBam(self,infile=None,outdir=None):
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150 """
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151 use samtools view to convert sam to bam
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152 """
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153 fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam')
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154 cl = ['samtools view -h -b -S -o ',tempbam,infile]
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155 tlog,stdouts,rval = self.runCL(cl,outdir)
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156 return tlog,tempbam,rval
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157
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158 def sortSam(self, infile=None,outfile=None,outdir=None):
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159 """
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160 """
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161 print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir)
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162 cl = ['samtools sort',infile,outfile]
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163 tlog,stdouts,rval = self.runCL(cl,outdir)
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164 return tlog
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165
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166 def cleanup(self):
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167 for fname in self.delme:
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168 try:
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169 os.unlink(fname)
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170 except:
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171 pass
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172
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173 def prettyPicout(self,transpose,maxrows):
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174 """organize picard outpouts into a report html page
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175 """
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176 res = []
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177 try:
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178 r = open(self.metricsOut,'r').readlines()
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179 except:
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180 r = []
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181 if len(r) > 0:
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182 res.append('<b>Picard on line resources</b><ul>\n')
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183 res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n')
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184 res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n')
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185 if transpose:
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186 res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n')
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187 else:
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188 res.append('<b>Picard output</b><hr/>\n')
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189 res.append('<table cellpadding="3" >\n')
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190 dat = []
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191 heads = []
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192 lastr = len(r) - 1
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193 # special case for estimate library complexity hist
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194 thist = False
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195 for i,row in enumerate(r):
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196 if row.strip() > '':
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197 srow = row.split('\t')
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198 if row.startswith('#'):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
199 heads.append(row.strip()) # want strings
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
200 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
201 dat.append(srow) # want lists
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
202 if row.startswith('## HISTOGRAM'):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
203 thist = True
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
204 if len(heads) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
205 hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
206 res += hres
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
207 heads = []
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
208 if len(dat) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
209 if transpose and not thist:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
210 tdat = map(None,*dat) # transpose an arbitrary list of lists
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
211 tdat = ['<tr class="d%d"><td>%s</td><td>%s&nbsp;</td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
212 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
213 tdat = ['\t'.join(x).strip() for x in dat] # back to strings :(
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
214 tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
215 res += tdat
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
216 dat = []
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
217 res.append('</table>\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
218 return res
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
219
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
220 def fixPicardOutputs(self,transpose,maxloglines):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
221 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
222 picard produces long hard to read tab header files
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
223 make them available but present them transposed for readability
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
224 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
225 logging.shutdown()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
226 self.cleanup() # remove temp files stored in delme
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
227 rstyle="""<style type="text/css">
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
228 tr.d0 td {background-color: oldlace; color: black;}
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
229 tr.d1 td {background-color: aliceblue; color: black;}
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
230 </style>"""
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
231 res = [rstyle,]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
232 res.append(galhtmlprefix % self.progname)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
233 res.append(galhtmlattr % (self.picname,timenow()))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
234 flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
235 pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
236 if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
237 for p in pdflist:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
238 pbase = os.path.splitext(p)[0] # removes .pdf
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
239 imghref = '%s.jpg' % pbase
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
240 mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking!
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
241 if mimghref in flist:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
242 imghref=mimghref # only one for thumbnail...it's a multi page pdf
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
243 res.append('<table cellpadding="10"><tr><td>\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
244 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))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
245 res.append('</tr></td></table>\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
246 if len(flist) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
247 res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
248 res.append('<table>\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
249 for i,f in enumerate(flist):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
250 fn = os.path.split(f)[-1]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
251 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
252 res.append('</table><p/>\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
253 pres = self.prettyPicout(transpose,maxloglines)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
254 if len(pres) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
255 res += pres
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
256 l = open(self.log_filename,'r').readlines()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
257 llen = len(l)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
258 if llen > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
259 res.append('<b>Picard Tool Run Log</b><hr/>\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
260 rlog = ['<pre>',]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
261 if llen > maxloglines:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
262 n = min(50,int(maxloglines/2))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
263 rlog += l[:n]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
264 rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
265 rlog += l[-n:]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
266 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
267 rlog += l
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
268 rlog.append('</pre>')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
269 if llen > maxloglines:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
270 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))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
271 res += rlog
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
272 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
273 res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
274 res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
275 res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
276 res.append(galhtmlpostfix)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
277 outf = open(self.opts.htmlout,'w')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
278 outf.write(''.join(res))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
279 outf.write('\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
280 outf.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
281
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
282 def makePicInterval(self,inbed=None,outf=None):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
283 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
284 picard wants bait and target files to have the same header length as the incoming bam/sam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
285 a meaningful (ie accurate) representation will fail because of this - so this hack
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
286 it would be far better to be able to supply the original bed untouched
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
287 Additional checking added Ross Lazarus Dec 2011 to deal with two 'bug' reports on the list
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
288 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
289 assert inbed <> None
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
290 bed = open(inbed,'r').readlines()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
291 sbed = [x.split('\t') for x in bed] # lengths MUST be 5
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
292 lens = [len(x) for x in sbed]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
293 strands = [x[3] for x in sbed if not x[3] in ['+','-']]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
294 maxl = max(lens)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
295 minl = min(lens)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
296 e = []
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
297 if maxl <> minl:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
298 e.append("## Input error: Inconsistent field count in %s - please read the documentation on bait/target format requirements, fix and try again" % inbed)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
299 if maxl <> 5:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
300 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))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
301 if len(strands) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
302 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))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
303 if len(e) > 0: # write to stderr and quit
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
304 print >> sys.stderr, '\n'.join(e)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
305 sys.exit(1)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
306 thead = os.path.join(self.opts.outdir,'tempSamHead.txt')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
307 if self.opts.datatype == 'sam':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
308 cl = ['samtools view -H -S',self.opts.input,'>',thead]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
309 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
310 cl = ['samtools view -H',self.opts.input,'>',thead]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
311 self.runCL(cl=cl,output_dir=self.opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
312 head = open(thead,'r').readlines()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
313 s = '## got %d rows of header\n' % (len(head))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
314 logging.info(s)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
315 o = open(outf,'w')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
316 o.write(''.join(head))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
317 o.write(''.join(bed))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
318 o.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
319 return outf
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
320
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
321 def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
322 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
323 interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs!
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
324 Do the work of removing all the error sequences
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
325 pysam is cool
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
326 infile = pysam.Samfile( "-", "r" )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
327 outfile = pysam.Samfile( "-", "w", template = infile )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
328 for s in infile: outfile.write(s)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
329
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
330 errors from ValidateSameFile.jar look like
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
331 WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
332 ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
333 ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
334
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
335 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
336 assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
337 assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
338 removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
339 remDict = dict(zip(removeNames,range(len(removeNames))))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
340 infile = pysam.Samfile(insam,'rb')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
341 info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
342 if len(removeNames) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
343 outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
344 i = 0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
345 j = 0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
346 for row in infile:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
347 dropme = remDict.get(row.qname,None) # keep if None
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
348 if not dropme:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
349 outfile.write(row)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
350 j += 1
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
351 else: # discard
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
352 i += 1
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
353 info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
354 outfile.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
355 infile.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
356 else: # we really want a nullop or a simple pointer copy
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
357 infile.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
358 if newsam:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
359 shutil.copy(insam,newsam)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
360 logging.info(info)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
361
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
362
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
363
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
364 def __main__():
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
365 doFix = False # tools returning htmlfile don't need this
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
366 doTranspose = True # default
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
367 maxloglines = 100 # default
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
368 #Parse Command Line
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
369 op = optparse.OptionParser()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
370 # All tools
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
371 op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
372 op.add_option('-e', '--inputext', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
373 op.add_option('-o', '--output', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
374 op.add_option('-n', '--title', default="Pick a Picard Tool")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
375 op.add_option('-t', '--htmlout', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
376 op.add_option('-d', '--outdir', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
377 op.add_option('-x', '--maxjheap', default='4g')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
378 op.add_option('-b', '--bisulphite', default='false')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
379 op.add_option('-s', '--sortorder', default='query')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
380 op.add_option('','--tmpdir', default='/tmp')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
381 op.add_option('-j','--jar',default='')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
382 op.add_option('','--picard-cmd',default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
383 # Many tools
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
384 op.add_option( '', '--output-format', dest='output_format', help='Output format' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
385 op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
386 op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
387 # CreateSequenceDictionary
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
388 op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
389 op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
390 op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
391 op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
392 # MarkDuplicates
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
393 op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
394 op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
395 # CollectInsertSizeMetrics
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
396 op.add_option('', '--taillimit', default="0")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
397 op.add_option('', '--histwidth', default="0")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
398 op.add_option('', '--minpct', default="0.01")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
399 op.add_option('', '--malevel', default='')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
400 op.add_option('', '--deviations', default="0.0")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
401 # CollectAlignmentSummaryMetrics
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
402 op.add_option('', '--maxinsert', default="20")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
403 op.add_option('', '--adaptors', default='')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
404 # FixMateInformation and validate
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
405 # CollectGcBiasMetrics
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
406 op.add_option('', '--windowsize', default='100')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
407 op.add_option('', '--mingenomefrac', default='0.00001')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
408 # AddOrReplaceReadGroups
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
409 op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
410 op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
411 op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
412 op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
413 op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
414 op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
415 op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
416 op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
417 # ReorderSam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
418 op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
419 op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
420 # ReplaceSamHeader
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
421 op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
422
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
423 op.add_option('','--assumesorted', default='true')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
424 op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
425 #estimatelibrarycomplexity
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
426 op.add_option('','--minid', default="5")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
427 op.add_option('','--maxdiff', default="0.03")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
428 op.add_option('','--minmeanq', default="20")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
429 #hsmetrics
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
430 op.add_option('','--baitbed', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
431 op.add_option('','--targetbed', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
432 #validate
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
433 op.add_option('','--ignoreflags', action='append', type="string")
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
434 op.add_option('','--maxerrors', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
435 op.add_option('','--datatype', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
436 op.add_option('','--bamout', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
437 op.add_option('','--samout', default=None)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
438
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
439 opts, args = op.parse_args()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
440 opts.sortme = opts.assumesorted == 'false'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
441 assert opts.input <> None
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
442 # need to add
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
443 # instance that does all the work
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
444 pic = PicardBase(opts,sys.argv[0])
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
445
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
446 tmp_dir = opts.outdir
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
447 haveTempout = False # we use this where sam output is an option
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
448 rval = 0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
449 stdouts = 'Not run yet'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
450 # set ref and dict files to use (create if necessary)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
451 ref_file_name = opts.ref
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
452 if opts.ref_file <> None:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
453 csd = 'CreateSequenceDictionary'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
454 realjarpath = os.path.split(opts.jar)[0]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
455 jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
456 tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
457 ref_file_name = '%s.fasta' % tmp_ref_name
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
458 # build dict
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
459 dict_file_name = '%s.dict' % tmp_ref_name
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
460 os.symlink( opts.ref_file, ref_file_name )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
461 cl = ['REFERENCE=%s' % ref_file_name]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
462 cl.append('OUTPUT=%s' % dict_file_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
463 cl.append('URI=%s' % os.path.basename( opts.ref_file ))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
464 cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
465 if opts.species_name:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
466 cl.append('SPECIES=%s' % opts.species_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
467 if opts.build_name:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
468 cl.append('GENOME_ASSEMBLY=%s' % opts.build_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
469 pic.delme.append(dict_file_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
470 pic.delme.append(ref_file_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
471 pic.delme.append(tmp_ref_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
472 stdouts,rval = pic.runPic(jarpath, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
473 # run relevant command(s)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
474
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
475 # define temporary output
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
476 # if output is sam, it must have that extension, otherwise bam will be produced
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
477 # specify sam or bam file with extension
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
478 if opts.output_format == 'sam':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
479 suff = '.sam'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
480 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
481 suff = ''
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
482 tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
483
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
484 cl = ['VALIDATION_STRINGENCY=LENIENT',]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
485
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
486 if pic.picname == 'AddOrReplaceReadGroups':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
487 # sort order to match Galaxy's default
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
488 cl.append('SORT_ORDER=coordinate')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
489 # input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
490 cl.append('INPUT=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
491 # outputs
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
492 cl.append('OUTPUT=%s' % tempout)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
493 # required read groups
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
494 cl.append('RGLB="%s"' % opts.rg_library)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
495 cl.append('RGPL="%s"' % opts.rg_platform)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
496 cl.append('RGPU="%s"' % opts.rg_plat_unit)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
497 cl.append('RGSM="%s"' % opts.rg_sample)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
498 if opts.rg_id:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
499 cl.append('RGID="%s"' % opts.rg_id)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
500 # optional read groups
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
501 if opts.rg_seq_center:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
502 cl.append('RGCN="%s"' % opts.rg_seq_center)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
503 if opts.rg_desc:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
504 cl.append('RGDS="%s"' % opts.rg_desc)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
505 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
506 haveTempout = True
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
507
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
508 elif pic.picname == 'BamIndexStats':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
509 tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
510 tmp_bam_name = '%s.bam' % tmp_name
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
511 tmp_bai_name = '%s.bai' % tmp_bam_name
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
512 os.symlink( opts.input, tmp_bam_name )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
513 os.symlink( opts.bai_file, tmp_bai_name )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
514 cl.append('INPUT=%s' % ( tmp_bam_name ))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
515 pic.delme.append(tmp_bam_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
516 pic.delme.append(tmp_bai_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
517 pic.delme.append(tmp_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
518 stdouts,rval = pic.runPic( opts.jar, cl )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
519 f = open(pic.metricsOut,'a')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
520 f.write(stdouts) # got this on stdout from runCl
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
521 f.write('\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
522 f.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
523 doTranspose = False # but not transposed
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
524
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
525 elif pic.picname == 'EstimateLibraryComplexity':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
526 cl.append('I=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
527 cl.append('O=%s' % pic.metricsOut)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
528 if float(opts.minid) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
529 cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
530 if float(opts.maxdiff) > 0.0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
531 cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
532 if float(opts.minmeanq) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
533 cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
534 if opts.readregex > '':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
535 cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
536 if float(opts.optdupdist) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
537 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
538 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
539
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
540 elif pic.picname == 'CollectAlignmentSummaryMetrics':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
541 # Why do we do this fakefasta thing?
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
542 # Because we need NO fai to be available or picard barfs unless it matches the input data.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
543 # why? Dunno Seems to work without complaining if the .bai file is AWOL....
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
544 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
545 try:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
546 os.symlink(ref_file_name,fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
547 except:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
548 s = '## unable to symlink %s to %s - different devices? Will shutil.copy'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
549 info = s
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
550 shutil.copy(ref_file_name,fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
551 pic.delme.append(fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
552 cl.append('ASSUME_SORTED=true')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
553 adaptlist = opts.adaptors.split(',')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
554 adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
555 cl += adaptorseqs
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
556 cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
557 cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
558 cl.append('OUTPUT=%s' % pic.metricsOut)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
559 cl.append('R=%s' % fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
560 cl.append('TMP_DIR=%s' % opts.tmpdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
561 if not opts.assumesorted.lower() == 'true': # we need to sort input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
562 sortedfile = '%s.sorted' % os.path.basename(opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
563 if opts.datatype == 'sam': # need to work with a bam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
564 tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
565 pic.delme.append(tempbam)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
566 try:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
567 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
568 except:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
569 print '## exception on sorting sam file %s' % opts.input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
570 else: # is already bam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
571 try:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
572 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
573 except : # bug - [bam_sort_core] not being ignored - TODO fixme
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
574 print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
575 cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile)))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
576 pic.delme.append(os.path.join(opts.outdir,sortedfile))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
577 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
578 cl.append('INPUT=%s' % os.path.abspath(opts.input))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
579 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
580
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
581
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
582 elif pic.picname == 'CollectGcBiasMetrics':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
583 assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
584 # 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.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
585 # why? Dunno
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
586 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
587 try:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
588 os.symlink(ref_file_name,fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
589 except:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
590 s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
591 info = s
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
592 shutil.copy(ref_file_name,fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
593 pic.delme.append(fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
594 x = 'rgPicardGCBiasMetrics'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
595 pdfname = '%s.pdf' % x
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
596 jpgname = '%s.jpg' % x
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
597 tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
598 temppdf = os.path.join(opts.outdir,pdfname)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
599 cl.append('R=%s' % fakefasta)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
600 cl.append('WINDOW_SIZE=%s' % opts.windowsize)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
601 cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
602 cl.append('INPUT=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
603 cl.append('OUTPUT=%s' % tempout)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
604 cl.append('TMP_DIR=%s' % opts.tmpdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
605 cl.append('CHART_OUTPUT=%s' % temppdf)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
606 cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
607 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
608 if os.path.isfile(temppdf):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
609 cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
610 s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
611 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
612 s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
613 lf = open(pic.log_filename,'a')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
614 lf.write(s)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
615 lf.write('\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
616 lf.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
617
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
618 elif pic.picname == 'CollectInsertSizeMetrics':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
619 """ <command interpreter="python">
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
620 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
621 --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
622 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
623 </command>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
624 """
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
625 isPDF = 'InsertSizeHist.pdf'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
626 pdfpath = os.path.join(opts.outdir,isPDF)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
627 histpdf = 'InsertSizeHist.pdf'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
628 cl.append('I=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
629 cl.append('O=%s' % pic.metricsOut)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
630 cl.append('HISTOGRAM_FILE=%s' % histpdf)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
631 #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
632 # cl.append('TAIL_LIMIT=%s' % opts.taillimit)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
633 if opts.histwidth <> '0':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
634 cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
635 if float( opts.minpct) > 0.0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
636 cl.append('MINIMUM_PCT=%s' % opts.minpct)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
637 if float(opts.deviations) > 0.0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
638 cl.append('DEVIATIONS=%s' % opts.deviations)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
639 if opts.malevel:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
640 malists = opts.malevel.split(',')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
641 malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
642 cl += malist
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
643 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
644 if os.path.exists(pdfpath): # automake thumbnail - will be added to html
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
645 cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
646 pic.runCL(cl=cl2,output_dir=opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
647 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
648 s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
649 s += 'This <b>always happens if single ended data was provided</b> to this tool,\n'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
650 s += 'so please double check that your input data really is paired-end NGS data.<br/>\n'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
651 s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
652 logging.info(s)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
653 if len(stdouts) > 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
654 logging.info(stdouts)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
655
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
656 elif pic.picname == 'MarkDuplicates':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
657 # assume sorted even if header says otherwise
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
658 cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
659 # input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
660 cl.append('INPUT=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
661 # outputs
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
662 cl.append('OUTPUT=%s' % opts.output)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
663 cl.append('METRICS_FILE=%s' % pic.metricsOut )
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
664 # remove or mark duplicates
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
665 cl.append('REMOVE_DUPLICATES=%s' % opts.remdups)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
666 # the regular expression to be used to parse reads in incoming SAM file
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
667 cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
668 # maximum offset between two duplicate clusters
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
669 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
670 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
671
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
672 elif pic.picname == 'FixMateInformation':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
673 cl.append('I=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
674 cl.append('O=%s' % tempout)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
675 cl.append('SORT_ORDER=%s' % opts.sortorder)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
676 stdouts,rval = pic.runPic(opts.jar,cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
677 haveTempout = True
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
678
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
679 elif pic.picname == 'ReorderSam':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
680 # input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
681 cl.append('INPUT=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
682 # output
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
683 cl.append('OUTPUT=%s' % tempout)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
684 # reference
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
685 cl.append('REFERENCE=%s' % ref_file_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
686 # incomplete dict concordance
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
687 if opts.allow_inc_dict_concord == 'true':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
688 cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
689 # contig length discordance
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
690 if opts.allow_contig_len_discord == 'true':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
691 cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
692 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
693 haveTempout = True
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
694
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
695 elif pic.picname == 'ReplaceSamHeader':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
696 cl.append('INPUT=%s' % opts.input)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
697 cl.append('OUTPUT=%s' % tempout)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
698 cl.append('HEADER=%s' % opts.header_file)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
699 stdouts,rval = pic.runPic(opts.jar, cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
700 haveTempout = True
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
701
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
702 elif pic.picname == 'CalculateHsMetrics':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
703 maxloglines = 100
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
704 baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
705 targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
706 baitf = pic.makePicInterval(opts.baitbed,baitfname)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
707 if opts.targetbed == opts.baitbed: # same file sometimes
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
708 targetf = baitf
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
709 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
710 targetf = pic.makePicInterval(opts.targetbed,targetfname)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
711 cl.append('BAIT_INTERVALS=%s' % baitf)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
712 cl.append('TARGET_INTERVALS=%s' % targetf)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
713 cl.append('INPUT=%s' % os.path.abspath(opts.input))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
714 cl.append('OUTPUT=%s' % pic.metricsOut)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
715 cl.append('TMP_DIR=%s' % opts.tmpdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
716 stdouts,rval = pic.runPic(opts.jar,cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
717
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
718 elif pic.picname == 'ValidateSamFile':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
719 import pysam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
720 doTranspose = False
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
721 sortedfile = os.path.join(opts.outdir,'rgValidate.sorted')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
722 stf = open(pic.log_filename,'w')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
723 tlog = None
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
724 if opts.datatype == 'sam': # need to work with a bam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
725 tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
726 try:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
727 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
728 except:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
729 print '## exception on sorting sam file %s' % opts.input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
730 else: # is already bam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
731 try:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
732 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
733 except: # bug - [bam_sort_core] not being ignored - TODO fixme
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
734 print '## exception on sorting bam file %s' % opts.input
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
735 if tlog:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
736 print '##tlog=',tlog
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
737 stf.write(tlog)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
738 stf.write('\n')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
739 sortedfile = '%s.bam' % sortedfile # samtools does that
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
740 cl.append('O=%s' % pic.metricsOut)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
741 cl.append('TMP_DIR=%s' % opts.tmpdir)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
742 cl.append('I=%s' % sortedfile)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
743 opts.maxerrors = '99999999'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
744 cl.append('MAX_OUTPUT=%s' % opts.maxerrors)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
745 if opts.ignoreflags[0] <> 'None': # picard error values to ignore
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
746 igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None']
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
747 cl.append(' '.join(igs))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
748 if opts.bisulphite.lower() <> 'false':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
749 cl.append('IS_BISULFITE_SEQUENCED=true')
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
750 if opts.ref <> None or opts.ref_file <> None:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
751 cl.append('R=%s' % ref_file_name)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
752 stdouts,rval = pic.runPic(opts.jar,cl)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
753 if opts.datatype == 'sam':
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
754 pic.delme.append(tempbam)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
755 newsam = opts.output
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
756 outformat = 'bam'
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
757 pe = open(pic.metricsOut,'r').readlines()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
758 pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
759 pic.delme.append(sortedfile) # not wanted
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
760 stf.close()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
761 pic.cleanup()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
762 else:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
763 print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
764 sys.exit(1)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
765 if haveTempout:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
766 # Some Picard tools produced a potentially intermediate bam file.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
767 # Either just move to final location or create sam
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
768 if os.path.exists(tempout):
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
769 shutil.move(tempout, os.path.abspath(opts.output))
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
770 if opts.htmlout <> None or doFix: # return a pretty html page
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
771 pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
772 if rval <> 0:
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
773 print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts)
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
774 # signal failure
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
775 if __name__=="__main__": __main__()
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
776