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annotate trinity_wrapper.py @ 0:f571ca145e9d draft

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Initial commit with concatenate and trinity tools. Still testing.
author trinity_ctat
date Mon, 11 Sep 2017 16:42:11 -0400
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0
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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1 #!/usr/bin/env python
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2
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3 '''
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4 trinity_runner.py
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5 This program is used as a wrapper for Trinity to allow an automatic rerun of failed jobs. It takes arguments for a typical Trinity run:
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6 ~ Required args ~
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7 Input files - single or paired (left and right)
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8 File type (fasta, fastq)
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9 Max memory - this I need to derive somehow from the dynamic runner using Galaxy slots
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10
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11 ~ Optional args ~
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12 Output directory - this allows users to run the same job over in case it walltime'd out or failed for recoverable reasons.
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13
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14 --
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15 Created Tuesday, 7 March 2017.
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16 Carrie Ganote
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17
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18 Licensed to Indiana University under Creative Commons 3.0
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19 '''
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20 import subprocess32
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21 import argparse
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22 import logging as log
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23 import sys
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24 import os
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25 import errno
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26 from datetime import datetime
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27
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28 TRINITY_OUT_DIR = "trinity_out_dir"
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29
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30 def main(*args):
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31 parser = argparse.ArgumentParser(description="")
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32 parser.add_argument("-o","--output", help="Name of output directory")
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33 parser.add_argument("-q","--seqType", help="Type of reads; fa or fq")
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34 parser.add_argument("-m","--max_memory", help="How much memory to allocate? Or maybe how many cpus?")
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35 parser.add_argument("-p","--mem_per_cpu", help="Memory PER CPU, in GB, in case we want to multiply mem x cpu at runtime")
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36 parser.add_argument("-s","--single", help="Single read file input")
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37 parser.add_argument("-l","--left", help="Left read file from paired inputs")
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38 parser.add_argument("-r","--right", help="Right read file from paired inputs")
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39 parser.add_argument("-v","--verbose", help="Enable debugging messages to be displayed", action='store_true')
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40 parser.add_argument("-g","--log", help="Log file")
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41 parser.add_argument("-t","--timing", help="Timing file, if it exists", default=None)
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42 parser.add_argument("-d","--dir", help="if supplying a rerunnable job, this is the (hopefully unique) name of the directory to run it in.")
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43 parser.add_argument("-u","--user", help="Username to run job under")
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44 parser.add_argument("-f","--fullpath", help="if supplying a rerunnable job, this is the full path (except the user and dir names) to run the job in.")
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45 parser.add_argument("-c","--CPU", help="CPUs, either a hard coded numer or from Galaxy slots")
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46 # parser.add_argument("-","--", help="")
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47 args = parser.parse_args()
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48
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49 if args.verbose:
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50 log.basicConfig(format='%(message)s',level=log.DEBUG)
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51 cmd = ["Trinity"]
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52
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53 ### Add rerun ability ###########################################
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54 # This variable tells us later whether to copy the files back to the job working directory
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55 copyback = False
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56 if args.dir and args.user and args.fullpath:
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57 cleandir = args.dir
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58 chars = "\\`*_{}[]()>#+-.!$&;| "
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59 for c in chars:
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60 if c in cleandir:
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61 cleandir = cleandir.replace(c, "_")
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62 rerunPath = "%s/%s/%s" % (args.fullpath, args.user, cleandir)
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63 print "Rerunpath is ",rerunPath
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64 try:
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65 os.makedirs(rerunPath)
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66 print "Created dir ",rerunPath
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67 except OSError as exc:
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68 if exc.errno == errno.EEXIST and os.path.isdir(rerunPath):
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69 pass
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70 else:
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71 raise
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72 copyback = os.getcwd()
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73 outdir = copyback + "/" + TRINITY_OUT_DIR
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74 try:
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75 os.makedirs(outdir)
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76 print "Created dir ",outdir
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77 except OSError as exc:
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78 if exc.errno == errno.EEXIST and os.path.isdir(outdir):
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79 pass
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80 else:
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81 raise
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82 os.chdir(rerunPath)
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83
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84 ### Add information for reads ###################################
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85 if args.left and args.right:
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86 cmd += ["--left",args.left,"--right", args.right]
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87 elif args.single:
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88 cmd += ["--single",args.single]
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89 else:
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90 raise Exception ("Need input files in order to run Trinity!")
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91
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92 ### Add seqtype ##################################################
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93 if args.seqType:
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94 cmd += ["--seqType",args.seqType]
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95 else:
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96 raise Exception ("Please specify a file type for your reads!")
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97
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98 ### Memory and CPU management ####################################
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99 if args.mem_per_cpu and not args.max_memory:
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100 if args.CPU:
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101 memry = int(args.CPU) * int(args.mem_per_cpu)
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102 memstr = "%dG" % (memry)
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103 cmd += ["--max_memory",memstr]
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104 else:
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105 memry = 2 * int(args.mem_per_cpu)
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106 memstr = "%dG" % (memry)
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107 cmd += ["--max_memory",memstr]
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108 elif args.max_memory and not args.mem_per_cpu:
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109 cmd += ["--max_memory",args.max_memory]
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110 else:
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111 raise Exception ("Please pick Memory per cpu, or max mem, but not both.")
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112 if args.CPU:
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113 cmd += ["--CPU", args.CPU]
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114
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115 ### Enough args, let's run it ####################################
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116 print "About to write to %s" % args.log
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117 out = open(args.log, 'w')
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118 totalattempts = attempts = 2
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119 ec = 1
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120 finish = 1
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121 out.write("Command is:\n%s\n" % (" ".join(cmd)))
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122
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123 ### There is definitely some value in running the job more than once, especially if it dies for stupid reasons.. ###
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124 while ec != 0 and attempts > 0 and finish != 0:
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125
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126 dt = datetime.now()
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127 dtstr = dt.strftime("%d/%m/%y %H:%M")
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128 out.write("Beginning attempt %d of Trinity job at %s\n" % (totalattempts - attempts +1, dtstr) )
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129 attempts -= 1
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130 ec = subprocess32.call(cmd, shell=False, stdin=None, stdout=out, stderr=out, timeout=None)
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131 out.write("Trinity exited with status %d\n" % ec)
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132
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133 greplog = open("greplog", 'w')
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134 cmds = ["grep", 'All commands completed successfully', args.log]
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135 finish = subprocess32.call(cmds,shell=False, stdin=None, stdout=greplog, stderr=greplog, timeout=None)
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136 greplog.close()
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137 out.write("Finished and found the success command with grep code %d\n" % finish)
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138
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139 if ec == 0 and args.timing is not None:
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140 if copyback is not False:
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141 cwd = os.getcwd()
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142 dest = copyback + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
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143 src = cwd + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
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144 print "copying trinity outputs from %s to %s" % (src, dest)
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145 os.symlink(src, dest)
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146
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147 #copy the timing file into the log
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148 try:
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149 handle = open (args.timing, 'r')
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150 for line in handle:
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151 out.write(line)
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152 handle.close()
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153 except (OSError, IOError) as e:
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154 print "Oops, no timing file found? ",e
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155
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156
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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157 out.close()
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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158 exit (ec)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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159
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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160 if __name__ == "__main__":
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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161 main(*sys.argv)
f571ca145e9d Initial commit with concatenate and trinity tools. Still testing.
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162