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33
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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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42
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18 <meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" />
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33
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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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42
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36 """
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33
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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
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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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33
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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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42
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49 """
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33
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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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42
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72 self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
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33
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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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42
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80 """
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33
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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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42
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88 """
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33
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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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42
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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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33
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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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42
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127 stdouts = self.readLarge(templog)
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33
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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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42
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136 return s, stdouts, rval # sometimes s is an output
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33
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137
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138 def runPic(self, jar, cl):
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139 """
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42
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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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42
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146
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147 print runme,self.opts.outdir
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148
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149 s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir)
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150 return stdouts,rval
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151
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152 def samToBam(self,infile=None,outdir=None):
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153 """
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42
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154 use samtools view to convert sam to bam
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155 """
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33
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156 fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam')
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157 cl = ['samtools view -h -b -S -o ',tempbam,infile]
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158 tlog,stdouts,rval = self.runCL(cl,outdir)
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159 return tlog,tempbam,rval
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160
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161 def sortSam(self, infile=None,outfile=None,outdir=None):
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162 """
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42
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163 """
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33
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164 print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir)
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165 cl = ['samtools sort',infile,outfile]
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166 tlog,stdouts,rval = self.runCL(cl,outdir)
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167 return tlog
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168
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169 def cleanup(self):
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170 for fname in self.delme:
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171 try:
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172 os.unlink(fname)
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173 except:
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174 pass
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175
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176 def prettyPicout(self,transpose,maxrows):
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177 """organize picard outpouts into a report html page
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42
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178 """
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33
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179 res = []
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180 try:
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181 r = open(self.metricsOut,'r').readlines()
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182 except:
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42
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183 r = []
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33
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184 if len(r) > 0:
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185 res.append('<b>Picard on line resources</b><ul>\n')
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186 res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n')
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187 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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188 if transpose:
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42
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189 res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n')
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190 else:
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42
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191 res.append('<b>Picard output</b><hr/>\n')
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33
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192 res.append('<table cellpadding="3" >\n')
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193 dat = []
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194 heads = []
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195 lastr = len(r) - 1
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196 # special case for estimate library complexity hist
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197 thist = False
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198 for i,row in enumerate(r):
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199 if row.strip() > '':
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200 srow = row.split('\t')
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201 if row.startswith('#'):
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202 heads.append(row.strip()) # want strings
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203 else:
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204 dat.append(srow) # want lists
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205 if row.startswith('## HISTOGRAM'):
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206 thist = True
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207 if len(heads) > 0:
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208 hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)]
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209 res += hres
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210 heads = []
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211 if len(dat) > 0:
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212 if transpose and not thist:
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213 tdat = map(None,*dat) # transpose an arbitrary list of lists
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42
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214 tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)]
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33
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215 else:
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216 tdat = ['\t'.join(x).strip() for x in dat] # back to strings :(
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217 tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)]
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218 res += tdat
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219 dat = []
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42
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220 res.append('</table>\n')
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221 return res
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222
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223 def fixPicardOutputs(self,transpose,maxloglines):
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224 """
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42
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225 picard produces long hard to read tab header files
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226 make them available but present them transposed for readability
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227 """
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33
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228 logging.shutdown()
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229 self.cleanup() # remove temp files stored in delme
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230 rstyle="""<style type="text/css">
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42
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231 tr.d0 td {background-color: oldlace; color: black;}
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232 tr.d1 td {background-color: aliceblue; color: black;}
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233 </style>"""
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33
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234 res = [rstyle,]
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42
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235 res.append(galhtmlprefix % self.progname)
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236 res.append(galhtmlattr % (self.picname,timenow()))
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42
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237 flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')]
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33
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238 pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
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239 if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
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240 for p in pdflist:
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241 pbase = os.path.splitext(p)[0] # removes .pdf
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242 imghref = '%s.jpg' % pbase
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243 mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking!
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244 if mimghref in flist:
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245 imghref=mimghref # only one for thumbnail...it's a multi page pdf
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246 res.append('<table cellpadding="10"><tr><td>\n')
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42
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247 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))
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248 res.append('</tr></td></table>\n')
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33
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249 if len(flist) > 0:
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250 res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>')
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251 res.append('<table>\n')
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252 for i,f in enumerate(flist):
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253 fn = os.path.split(f)[-1]
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254 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn))
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42
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255 res.append('</table><p/>\n')
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33
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256 pres = self.prettyPicout(transpose,maxloglines)
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257 if len(pres) > 0:
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258 res += pres
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259 l = open(self.log_filename,'r').readlines()
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260 llen = len(l)
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42
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261 if llen > 0:
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262 res.append('<b>Picard Tool Run Log</b><hr/>\n')
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33
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263 rlog = ['<pre>',]
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264 if llen > maxloglines:
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265 n = min(50,int(maxloglines/2))
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266 rlog += l[:n]
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267 rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines))
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268 rlog += l[-n:]
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269 else:
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270 rlog += l
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271 rlog.append('</pre>')
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272 if llen > maxloglines:
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273 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))
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274 res += rlog
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275 else:
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276 res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename)
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42
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277 res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
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278 res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool')
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279 res.append(galhtmlpostfix)
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280 outf = open(self.opts.htmlout,'w')
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42
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281 outf.write(''.join(res))
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33
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282 outf.write('\n')
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283 outf.close()
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284
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285 def makePicInterval(self,inbed=None,outf=None):
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286 """
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42
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287 picard wants bait and target files to have the same header length as the incoming bam/sam
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288 a meaningful (ie accurate) representation will fail because of this - so this hack
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289 it would be far better to be able to supply the original bed untouched
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290 Additional checking added Ross Lazarus Dec 2011 to deal with two 'bug' reports on the list
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291 """
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33
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292 assert inbed <> None
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293 bed = open(inbed,'r').readlines()
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294 sbed = [x.split('\t') for x in bed] # lengths MUST be 5
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295 lens = [len(x) for x in sbed]
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296 strands = [x[3] for x in sbed if not x[3] in ['+','-']]
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297 maxl = max(lens)
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298 minl = min(lens)
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299 e = []
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300 if maxl <> minl:
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301 e.append("## Input error: Inconsistent field count in %s - please read the documentation on bait/target format requirements, fix and try again" % inbed)
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302 if maxl <> 5:
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303 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))
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304 if len(strands) > 0:
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305 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))
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306 if len(e) > 0: # write to stderr and quit
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307 print >> sys.stderr, '\n'.join(e)
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308 sys.exit(1)
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309 thead = os.path.join(self.opts.outdir,'tempSamHead.txt')
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310 if self.opts.datatype == 'sam':
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311 cl = ['samtools view -H -S',self.opts.input,'>',thead]
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312 else:
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313 cl = ['samtools view -H',self.opts.input,'>',thead]
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314 self.runCL(cl=cl,output_dir=self.opts.outdir)
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315 head = open(thead,'r').readlines()
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316 s = '## got %d rows of header\n' % (len(head))
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317 logging.info(s)
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318 o = open(outf,'w')
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319 o.write(''.join(head))
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320 o.write(''.join(bed))
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321 o.close()
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322 return outf
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323
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324 def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None):
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325 """
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42
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326 interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs!
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327 Do the work of removing all the error sequences
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328 pysam is cool
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329 infile = pysam.Samfile( "-", "r" )
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330 outfile = pysam.Samfile( "-", "w", template = infile )
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331 for s in infile: outfile.write(s)
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33
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332
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42
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333 errors from ValidateSameFile.jar look like
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334 WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing
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335 ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary.
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336 ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041
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33
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337
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42
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338 """
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33
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339 assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam
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340 assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path'
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341 removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2]
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342 remDict = dict(zip(removeNames,range(len(removeNames))))
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343 infile = pysam.Samfile(insam,'rb')
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344 info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict))
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345 if len(removeNames) > 0:
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346 outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file
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347 i = 0
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|
|
348 j = 0
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349 for row in infile:
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350 dropme = remDict.get(row.qname,None) # keep if None
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351 if not dropme:
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352 outfile.write(row)
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353 j += 1
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354 else: # discard
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355 i += 1
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356 info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam))
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357 outfile.close()
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358 infile.close()
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359 else: # we really want a nullop or a simple pointer copy
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360 infile.close()
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|
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361 if newsam:
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362 shutil.copy(insam,newsam)
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363 logging.info(info)
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364
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365
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366
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367 def __main__():
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368 doFix = False # tools returning htmlfile don't need this
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369 doTranspose = True # default
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42
|
370 maxloglines = 100 # default
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33
|
371 #Parse Command Line
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372 op = optparse.OptionParser()
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373 # All tools
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374 op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' )
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375 op.add_option('-e', '--inputext', default=None)
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376 op.add_option('-o', '--output', default=None)
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377 op.add_option('-n', '--title', default="Pick a Picard Tool")
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378 op.add_option('-t', '--htmlout', default=None)
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379 op.add_option('-d', '--outdir', default=None)
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42
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380 op.add_option('-x', '--maxjheap', default='3000m')
|
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33
|
381 op.add_option('-b', '--bisulphite', default='false')
|
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42
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382 op.add_option('-s', '--sortorder', default='query')
|
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33
|
383 op.add_option('','--tmpdir', default='/tmp')
|
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42
|
384 op.add_option('-j','--jar',default='')
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385 op.add_option('','--picard-cmd',default=None)
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33
|
386 # Many tools
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387 op.add_option( '', '--output-format', dest='output_format', help='Output format' )
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388 op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' )
|
|
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389 op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None )
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|
390 # CreateSequenceDictionary
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|
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391 op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None )
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|
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392 op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' )
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|
|
393 op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' )
|
|
|
394 op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' )
|
|
|
395 # MarkDuplicates
|
|
|
396 op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' )
|
|
|
397 op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' )
|
|
|
398 # CollectInsertSizeMetrics
|
|
|
399 op.add_option('', '--taillimit', default="0")
|
|
|
400 op.add_option('', '--histwidth', default="0")
|
|
|
401 op.add_option('', '--minpct', default="0.01")
|
|
|
402 op.add_option('', '--malevel', default='')
|
|
|
403 op.add_option('', '--deviations', default="0.0")
|
|
|
404 # CollectAlignmentSummaryMetrics
|
|
|
405 op.add_option('', '--maxinsert', default="20")
|
|
|
406 op.add_option('', '--adaptors', default='')
|
|
|
407 # FixMateInformation and validate
|
|
|
408 # CollectGcBiasMetrics
|
|
|
409 op.add_option('', '--windowsize', default='100')
|
|
42
|
410 op.add_option('', '--mingenomefrac', default='0.00001')
|
|
33
|
411 # AddOrReplaceReadGroups
|
|
|
412 op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' )
|
|
|
413 op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' )
|
|
|
414 op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' )
|
|
|
415 op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' )
|
|
|
416 op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' )
|
|
|
417 op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' )
|
|
|
418 op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' )
|
|
|
419 op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' )
|
|
|
420 # ReorderSam
|
|
|
421 op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' )
|
|
|
422 op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' )
|
|
|
423 # ReplaceSamHeader
|
|
|
424 op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' )
|
|
|
425
|
|
42
|
426 op.add_option('','--assumesorted', default='true')
|
|
33
|
427 op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*")
|
|
|
428 #estimatelibrarycomplexity
|
|
|
429 op.add_option('','--minid', default="5")
|
|
|
430 op.add_option('','--maxdiff', default="0.03")
|
|
|
431 op.add_option('','--minmeanq', default="20")
|
|
|
432 #hsmetrics
|
|
|
433 op.add_option('','--baitbed', default=None)
|
|
|
434 op.add_option('','--targetbed', default=None)
|
|
|
435 #validate
|
|
|
436 op.add_option('','--ignoreflags', action='append', type="string")
|
|
|
437 op.add_option('','--maxerrors', default=None)
|
|
|
438 op.add_option('','--datatype', default=None)
|
|
|
439 op.add_option('','--bamout', default=None)
|
|
|
440 op.add_option('','--samout', default=None)
|
|
|
441 #downsample
|
|
|
442 op.add_option('','--probability', default="1")
|
|
|
443 op.add_option('','--seed', default="1")
|
|
|
444
|
|
|
445 opts, args = op.parse_args()
|
|
|
446 opts.sortme = opts.assumesorted == 'false'
|
|
|
447 assert opts.input <> None
|
|
|
448 # need to add
|
|
|
449 # instance that does all the work
|
|
|
450 pic = PicardBase(opts,sys.argv[0])
|
|
|
451
|
|
|
452 tmp_dir = opts.outdir
|
|
|
453 haveTempout = False # we use this where sam output is an option
|
|
|
454 rval = 0
|
|
|
455 stdouts = 'Not run yet'
|
|
|
456 # set ref and dict files to use (create if necessary)
|
|
|
457 ref_file_name = opts.ref
|
|
|
458 if opts.ref_file <> None:
|
|
|
459 csd = 'CreateSequenceDictionary'
|
|
|
460 realjarpath = os.path.split(opts.jar)[0]
|
|
|
461 jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq
|
|
|
462 tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname)
|
|
|
463 ref_file_name = '%s.fasta' % tmp_ref_name
|
|
|
464 # build dict
|
|
|
465 dict_file_name = '%s.dict' % tmp_ref_name
|
|
|
466 os.symlink( opts.ref_file, ref_file_name )
|
|
|
467 cl = ['REFERENCE=%s' % ref_file_name]
|
|
|
468 cl.append('OUTPUT=%s' % dict_file_name)
|
|
|
469 cl.append('URI=%s' % os.path.basename( opts.ref_file ))
|
|
|
470 cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names)
|
|
|
471 if opts.species_name:
|
|
|
472 cl.append('SPECIES=%s' % opts.species_name)
|
|
|
473 if opts.build_name:
|
|
|
474 cl.append('GENOME_ASSEMBLY=%s' % opts.build_name)
|
|
|
475 pic.delme.append(dict_file_name)
|
|
|
476 pic.delme.append(ref_file_name)
|
|
|
477 pic.delme.append(tmp_ref_name)
|
|
|
478 stdouts,rval = pic.runPic(jarpath, cl)
|
|
|
479 # run relevant command(s)
|
|
|
480
|
|
|
481 # define temporary output
|
|
|
482 # if output is sam, it must have that extension, otherwise bam will be produced
|
|
|
483 # specify sam or bam file with extension
|
|
|
484 if opts.output_format == 'sam':
|
|
|
485 suff = '.sam'
|
|
|
486 else:
|
|
|
487 suff = ''
|
|
|
488 tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff )
|
|
|
489
|
|
|
490 cl = ['VALIDATION_STRINGENCY=LENIENT',]
|
|
|
491
|
|
|
492 if pic.picname == 'AddOrReplaceReadGroups':
|
|
|
493 # sort order to match Galaxy's default
|
|
|
494 cl.append('SORT_ORDER=coordinate')
|
|
|
495 # input
|
|
|
496 cl.append('INPUT=%s' % opts.input)
|
|
|
497 # outputs
|
|
|
498 cl.append('OUTPUT=%s' % tempout)
|
|
|
499 # required read groups
|
|
|
500 cl.append('RGLB="%s"' % opts.rg_library)
|
|
|
501 cl.append('RGPL="%s"' % opts.rg_platform)
|
|
|
502 cl.append('RGPU="%s"' % opts.rg_plat_unit)
|
|
|
503 cl.append('RGSM="%s"' % opts.rg_sample)
|
|
|
504 if opts.rg_id:
|
|
|
505 cl.append('RGID="%s"' % opts.rg_id)
|
|
|
506 # optional read groups
|
|
|
507 if opts.rg_seq_center:
|
|
|
508 cl.append('RGCN="%s"' % opts.rg_seq_center)
|
|
|
509 if opts.rg_desc:
|
|
|
510 cl.append('RGDS="%s"' % opts.rg_desc)
|
|
|
511 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
512 haveTempout = True
|
|
|
513
|
|
|
514 elif pic.picname == 'BamIndexStats':
|
|
|
515 tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir )
|
|
|
516 tmp_bam_name = '%s.bam' % tmp_name
|
|
|
517 tmp_bai_name = '%s.bai' % tmp_bam_name
|
|
|
518 os.symlink( opts.input, tmp_bam_name )
|
|
|
519 os.symlink( opts.bai_file, tmp_bai_name )
|
|
|
520 cl.append('INPUT=%s' % ( tmp_bam_name ))
|
|
|
521 pic.delme.append(tmp_bam_name)
|
|
|
522 pic.delme.append(tmp_bai_name)
|
|
|
523 pic.delme.append(tmp_name)
|
|
|
524 stdouts,rval = pic.runPic( opts.jar, cl )
|
|
|
525 f = open(pic.metricsOut,'a')
|
|
|
526 f.write(stdouts) # got this on stdout from runCl
|
|
|
527 f.write('\n')
|
|
|
528 f.close()
|
|
|
529 doTranspose = False # but not transposed
|
|
|
530
|
|
|
531 elif pic.picname == 'EstimateLibraryComplexity':
|
|
|
532 cl.append('I=%s' % opts.input)
|
|
|
533 cl.append('O=%s' % pic.metricsOut)
|
|
|
534 if float(opts.minid) > 0:
|
|
|
535 cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid)
|
|
|
536 if float(opts.maxdiff) > 0.0:
|
|
|
537 cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff)
|
|
|
538 if float(opts.minmeanq) > 0:
|
|
|
539 cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq)
|
|
|
540 if opts.readregex > '':
|
|
|
541 cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
|
|
|
542 if float(opts.optdupdist) > 0:
|
|
|
543 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
|
|
|
544 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
545
|
|
|
546 elif pic.picname == 'CollectAlignmentSummaryMetrics':
|
|
42
|
547 # Why do we do this fakefasta thing?
|
|
33
|
548 # Because we need NO fai to be available or picard barfs unless it matches the input data.
|
|
|
549 # why? Dunno Seems to work without complaining if the .bai file is AWOL....
|
|
|
550 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
|
|
|
551 try:
|
|
|
552 os.symlink(ref_file_name,fakefasta)
|
|
|
553 except:
|
|
|
554 s = '## unable to symlink %s to %s - different devices? Will shutil.copy'
|
|
|
555 info = s
|
|
|
556 shutil.copy(ref_file_name,fakefasta)
|
|
|
557 pic.delme.append(fakefasta)
|
|
|
558 cl.append('ASSUME_SORTED=true')
|
|
|
559 adaptlist = opts.adaptors.split(',')
|
|
|
560 adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist]
|
|
|
561 cl += adaptorseqs
|
|
|
562 cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite)
|
|
|
563 cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert)
|
|
|
564 cl.append('OUTPUT=%s' % pic.metricsOut)
|
|
|
565 cl.append('R=%s' % fakefasta)
|
|
|
566 cl.append('TMP_DIR=%s' % opts.tmpdir)
|
|
|
567 if not opts.assumesorted.lower() == 'true': # we need to sort input
|
|
|
568 sortedfile = '%s.sorted' % os.path.basename(opts.input)
|
|
42
|
569 if opts.datatype == 'sam': # need to work with a bam
|
|
33
|
570 tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir)
|
|
|
571 pic.delme.append(tempbam)
|
|
|
572 try:
|
|
|
573 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
|
|
|
574 except:
|
|
|
575 print '## exception on sorting sam file %s' % opts.input
|
|
|
576 else: # is already bam
|
|
|
577 try:
|
|
|
578 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
|
|
|
579 except : # bug - [bam_sort_core] not being ignored - TODO fixme
|
|
|
580 print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input)
|
|
|
581 cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile)))
|
|
|
582 pic.delme.append(os.path.join(opts.outdir,sortedfile))
|
|
|
583 else:
|
|
42
|
584 cl.append('INPUT=%s' % os.path.abspath(opts.input))
|
|
33
|
585 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
586
|
|
|
587
|
|
|
588 elif pic.picname == 'CollectGcBiasMetrics':
|
|
|
589 assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name
|
|
|
590 # 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.
|
|
42
|
591 # why? Dunno
|
|
33
|
592 fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
|
|
|
593 try:
|
|
|
594 os.symlink(ref_file_name,fakefasta)
|
|
|
595 except:
|
|
|
596 s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
|
|
|
597 info = s
|
|
|
598 shutil.copy(ref_file_name,fakefasta)
|
|
|
599 pic.delme.append(fakefasta)
|
|
|
600 x = 'rgPicardGCBiasMetrics'
|
|
|
601 pdfname = '%s.pdf' % x
|
|
|
602 jpgname = '%s.jpg' % x
|
|
|
603 tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out')
|
|
|
604 temppdf = os.path.join(opts.outdir,pdfname)
|
|
|
605 cl.append('R=%s' % fakefasta)
|
|
|
606 cl.append('WINDOW_SIZE=%s' % opts.windowsize)
|
|
|
607 cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac)
|
|
|
608 cl.append('INPUT=%s' % opts.input)
|
|
|
609 cl.append('OUTPUT=%s' % tempout)
|
|
|
610 cl.append('TMP_DIR=%s' % opts.tmpdir)
|
|
|
611 cl.append('CHART_OUTPUT=%s' % temppdf)
|
|
|
612 cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut)
|
|
|
613 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
614 if os.path.isfile(temppdf):
|
|
|
615 cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find
|
|
|
616 s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir)
|
|
|
617 else:
|
|
|
618 s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf
|
|
|
619 lf = open(pic.log_filename,'a')
|
|
|
620 lf.write(s)
|
|
|
621 lf.write('\n')
|
|
|
622 lf.close()
|
|
|
623
|
|
|
624 elif pic.picname == 'CollectInsertSizeMetrics':
|
|
|
625 """ <command interpreter="python">
|
|
42
|
626 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
|
|
|
627 --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
|
|
|
628 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
|
|
|
629 </command>
|
|
|
630 """
|
|
33
|
631 isPDF = 'InsertSizeHist.pdf'
|
|
|
632 pdfpath = os.path.join(opts.outdir,isPDF)
|
|
|
633 histpdf = 'InsertSizeHist.pdf'
|
|
|
634 cl.append('I=%s' % opts.input)
|
|
|
635 cl.append('O=%s' % pic.metricsOut)
|
|
|
636 cl.append('HISTOGRAM_FILE=%s' % histpdf)
|
|
|
637 #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56
|
|
42
|
638 # cl.append('TAIL_LIMIT=%s' % opts.taillimit)
|
|
|
639 if opts.histwidth <> '0':
|
|
33
|
640 cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth)
|
|
|
641 if float( opts.minpct) > 0.0:
|
|
|
642 cl.append('MINIMUM_PCT=%s' % opts.minpct)
|
|
|
643 if float(opts.deviations) > 0.0:
|
|
|
644 cl.append('DEVIATIONS=%s' % opts.deviations)
|
|
|
645 if opts.malevel:
|
|
|
646 malists = opts.malevel.split(',')
|
|
|
647 malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists]
|
|
|
648 cl += malist
|
|
|
649 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
42
|
650 if os.path.exists(pdfpath): # automake thumbnail - will be added to html
|
|
33
|
651 cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
|
|
|
652 pic.runCL(cl=cl2,output_dir=opts.outdir)
|
|
|
653 else:
|
|
|
654 s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
|
|
|
655 s += 'This <b>always happens if single ended data was provided</b> to this tool,\n'
|
|
|
656 s += 'so please double check that your input data really is paired-end NGS data.<br/>\n'
|
|
|
657 s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>'
|
|
|
658 logging.info(s)
|
|
|
659 if len(stdouts) > 0:
|
|
|
660 logging.info(stdouts)
|
|
|
661
|
|
|
662 elif pic.picname == 'MarkDuplicates':
|
|
|
663 # assume sorted even if header says otherwise
|
|
|
664 cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
|
|
|
665 # input
|
|
|
666 cl.append('INPUT=%s' % opts.input)
|
|
|
667 # outputs
|
|
42
|
668 cl.append('OUTPUT=%s' % opts.output)
|
|
33
|
669 cl.append('METRICS_FILE=%s' % pic.metricsOut )
|
|
|
670 # remove or mark duplicates
|
|
|
671 cl.append('REMOVE_DUPLICATES=%s' % opts.remdups)
|
|
|
672 # the regular expression to be used to parse reads in incoming SAM file
|
|
|
673 cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
|
|
|
674 # maximum offset between two duplicate clusters
|
|
|
675 cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
|
|
|
676 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
677
|
|
|
678 elif pic.picname == 'FixMateInformation':
|
|
|
679 cl.append('I=%s' % opts.input)
|
|
|
680 cl.append('O=%s' % tempout)
|
|
|
681 cl.append('SORT_ORDER=%s' % opts.sortorder)
|
|
|
682 stdouts,rval = pic.runPic(opts.jar,cl)
|
|
|
683 haveTempout = True
|
|
|
684
|
|
|
685 elif pic.picname == 'ReorderSam':
|
|
|
686 # input
|
|
|
687 cl.append('INPUT=%s' % opts.input)
|
|
|
688 # output
|
|
|
689 cl.append('OUTPUT=%s' % tempout)
|
|
|
690 # reference
|
|
|
691 cl.append('REFERENCE=%s' % ref_file_name)
|
|
|
692 # incomplete dict concordance
|
|
|
693 if opts.allow_inc_dict_concord == 'true':
|
|
|
694 cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true')
|
|
|
695 # contig length discordance
|
|
|
696 if opts.allow_contig_len_discord == 'true':
|
|
|
697 cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true')
|
|
|
698 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
699 haveTempout = True
|
|
|
700
|
|
|
701 elif pic.picname == 'ReplaceSamHeader':
|
|
|
702 cl.append('INPUT=%s' % opts.input)
|
|
|
703 cl.append('OUTPUT=%s' % tempout)
|
|
|
704 cl.append('HEADER=%s' % opts.header_file)
|
|
|
705 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
706 haveTempout = True
|
|
|
707
|
|
|
708 elif pic.picname == 'CalculateHsMetrics':
|
|
|
709 maxloglines = 100
|
|
|
710 baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait')
|
|
|
711 targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target')
|
|
|
712 baitf = pic.makePicInterval(opts.baitbed,baitfname)
|
|
|
713 if opts.targetbed == opts.baitbed: # same file sometimes
|
|
|
714 targetf = baitf
|
|
|
715 else:
|
|
42
|
716 targetf = pic.makePicInterval(opts.targetbed,targetfname)
|
|
33
|
717 cl.append('BAIT_INTERVALS=%s' % baitf)
|
|
|
718 cl.append('TARGET_INTERVALS=%s' % targetf)
|
|
|
719 cl.append('INPUT=%s' % os.path.abspath(opts.input))
|
|
|
720 cl.append('OUTPUT=%s' % pic.metricsOut)
|
|
|
721 cl.append('TMP_DIR=%s' % opts.tmpdir)
|
|
|
722 stdouts,rval = pic.runPic(opts.jar,cl)
|
|
|
723
|
|
|
724 elif pic.picname == 'ValidateSamFile':
|
|
|
725 import pysam
|
|
|
726 doTranspose = False
|
|
|
727 sortedfile = os.path.join(opts.outdir,'rgValidate.sorted')
|
|
|
728 stf = open(pic.log_filename,'w')
|
|
|
729 tlog = None
|
|
42
|
730 if opts.datatype == 'sam': # need to work with a bam
|
|
33
|
731 tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
|
|
|
732 try:
|
|
|
733 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
|
|
|
734 except:
|
|
|
735 print '## exception on sorting sam file %s' % opts.input
|
|
|
736 else: # is already bam
|
|
|
737 try:
|
|
|
738 tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
|
|
|
739 except: # bug - [bam_sort_core] not being ignored - TODO fixme
|
|
|
740 print '## exception on sorting bam file %s' % opts.input
|
|
|
741 if tlog:
|
|
|
742 print '##tlog=',tlog
|
|
|
743 stf.write(tlog)
|
|
|
744 stf.write('\n')
|
|
42
|
745 sortedfile = '%s.bam' % sortedfile # samtools does that
|
|
33
|
746 cl.append('O=%s' % pic.metricsOut)
|
|
|
747 cl.append('TMP_DIR=%s' % opts.tmpdir)
|
|
|
748 cl.append('I=%s' % sortedfile)
|
|
|
749 opts.maxerrors = '99999999'
|
|
|
750 cl.append('MAX_OUTPUT=%s' % opts.maxerrors)
|
|
|
751 if opts.ignoreflags[0] <> 'None': # picard error values to ignore
|
|
|
752 igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None']
|
|
|
753 cl.append(' '.join(igs))
|
|
|
754 if opts.bisulphite.lower() <> 'false':
|
|
|
755 cl.append('IS_BISULFITE_SEQUENCED=true')
|
|
|
756 if opts.ref <> None or opts.ref_file <> None:
|
|
42
|
757 cl.append('R=%s' % ref_file_name)
|
|
33
|
758 stdouts,rval = pic.runPic(opts.jar,cl)
|
|
|
759 if opts.datatype == 'sam':
|
|
|
760 pic.delme.append(tempbam)
|
|
|
761 newsam = opts.output
|
|
|
762 outformat = 'bam'
|
|
|
763 pe = open(pic.metricsOut,'r').readlines()
|
|
|
764 pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat)
|
|
|
765 pic.delme.append(sortedfile) # not wanted
|
|
|
766 stf.close()
|
|
|
767 pic.cleanup()
|
|
42
|
768
|
|
|
769 ####liubo added CleanSam tool####
|
|
|
770 elif pic.picname == 'CleanSam':
|
|
|
771 # input
|
|
|
772 cl.append('INPUT=%s' % opts.input)
|
|
|
773 # output
|
|
|
774 cl.append('OUTPUT=%s' % tempout)
|
|
|
775 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
776 haveTempout = True
|
|
|
777
|
|
|
778 elif pic.picname == 'SortSam':
|
|
|
779 cl.append('I=%s' % opts.input)
|
|
|
780 cl.append('O=%s' % tempout)
|
|
|
781 cl.append('SORT_ORDER=%s' % opts.sortorder)
|
|
|
782 stdouts,rval = pic.runPic(opts.jar,cl)
|
|
|
783 haveTempout = True
|
|
|
784
|
|
|
785 elif pic.picname == 'BuildBamIndex':
|
|
|
786 cl.append('I=%s' % opts.input)
|
|
|
787 cl.append('O=%s' % tempout)
|
|
|
788 stdouts,rval = pic.runPic(opts.jar,cl)
|
|
|
789 haveTempout = True
|
|
|
790
|
|
|
791 elif pic.picname == 'SamFormatConverter':
|
|
|
792 cl.append('INPUT=%s' % opts.input)
|
|
|
793 cl.append('OUTPUT=%s' % tempout)
|
|
|
794 pic.runPic(opts.jar, cl)
|
|
|
795 haveTempout = True
|
|
33
|
796 elif pic.picname == "DownsampleSam":
|
|
|
797 cl.append('I=%s' % opts.input)
|
|
|
798 mystring = opts.output
|
|
|
799 mystringsam = mystring + ".sam"
|
|
|
800 cl.append('O=%s' % mystringsam)
|
|
|
801 if float(opts.probability) > 0:
|
|
|
802 cl.append('PROBABILITY=%s' % opts.probability)
|
|
|
803 if float(opts.seed) > 0:
|
|
|
804 cl.append('RANDOM_SEED=%s' % opts.seed)
|
|
|
805 stdouts,rval = pic.runPic(opts.jar, cl)
|
|
|
806 myoutput = mystringsam.replace(".sam", "")
|
|
|
807 os.rename(mystringsam,myoutput)
|
|
42
|
808
|
|
|
809
|
|
33
|
810 else:
|
|
|
811 print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname
|
|
|
812 sys.exit(1)
|
|
|
813 if haveTempout:
|
|
42
|
814 # Some Picard tools produced a potentially intermediate bam file.
|
|
33
|
815 # Either just move to final location or create sam
|
|
|
816 if os.path.exists(tempout):
|
|
|
817 shutil.move(tempout, os.path.abspath(opts.output))
|
|
|
818 if opts.htmlout <> None or doFix: # return a pretty html page
|
|
|
819 pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)
|
|
|
820 if rval <> 0:
|
|
|
821 print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts)
|
|
|
822 # signal failure
|
|
|
823 if __name__=="__main__": __main__()
|
