ctat_trinity_rnaseq: ctat_trinity

annotate ctat_trinity_wrapper.py @ 3:777b35c8ee3e draft default tip

Trying newer trinity

author	trinity_ctat
date	Mon, 25 Jun 2018 16:38:28 -0400
parents	6a3722879525
children

rev	line source
0 6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	1 #!/usr/bin/env python
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	2
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	3 '''
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	4 trinity_runner.py
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	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:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	6 ~ Required args ~
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	7 Input files - single or paired (left and right)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	8 File type (fasta, fastq)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	9 Max memory - this I need to derive somehow from the dynamic runner using Galaxy slots
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	10
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	11 ~ Optional args ~
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	12 Output directory - this allows users to run the same job over in case it walltime'd out or failed for recoverable reasons.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	13
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	14 --
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	15 Created Tuesday, 7 March 2017.
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	16 Carrie Ganote
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	17
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	18 Licensed to Indiana University under Creative Commons 3.0
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	19 '''
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	20 import subprocess32
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	21 import argparse
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	22 import logging as log
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	23 import sys
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	24 import os
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	25 import errno
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	26 from datetime import datetime
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	27
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	28 TRINITY_OUT_DIR = "trinity_out_dir"
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	29
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	30 def main(*args):
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	31 parser = argparse.ArgumentParser(description="")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	32 parser.add_argument("-o","--output", help="Name of output directory")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	33 parser.add_argument("-q","--seqType", help="Type of reads; fa or fq")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	34 parser.add_argument("-m","--max_memory", help="How much memory to allocate? Or maybe how many cpus?")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	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")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	36 parser.add_argument("-s","--single", help="Single read file input")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	37 parser.add_argument("-l","--left", help="Left read file from paired inputs")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	38 parser.add_argument("-r","--right", help="Right read file from paired inputs")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	39 parser.add_argument("-v","--verbose", help="Enable debugging messages to be displayed", action='store_true')
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	40 parser.add_argument("-g","--log", help="Log file")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	41 parser.add_argument("-t","--timing", help="Timing file, if it exists", default=None)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	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.")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	43 parser.add_argument("-u","--user", help="Username to run job under")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	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.")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	45 parser.add_argument("-c","--CPU", help="CPUs, either a hard coded numer or from Galaxy slots")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	46 # parser.add_argument("-","--", help="")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	47 args = parser.parse_args()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	48
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	49 if args.verbose:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	50 log.basicConfig(format='%(message)s',level=log.DEBUG)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	51 cmd = ["Trinity"]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	52
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	53 ### Add rerun ability ###########################################
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	54 # This variable tells us later whether to copy the files back to the job working directory
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	55 copyback = False
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	56 if args.dir and args.user and args.fullpath:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	57 cleandir = args.dir
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	58 chars = "\\`*_{}[]()>#+-.!$&;\| "
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	59 for c in chars:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	60 if c in cleandir:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	61 cleandir = cleandir.replace(c, "_")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	62 rerunPath = "%s/%s/%s" % (args.fullpath, args.user, cleandir)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	63 print "Rerunpath is ",rerunPath
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	64 try:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	65 os.makedirs(rerunPath)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	66 print "Created dir ",rerunPath
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	67 except OSError as exc:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	68 if exc.errno == errno.EEXIST and os.path.isdir(rerunPath):
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	69 pass
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	70 else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	71 raise
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	72 copyback = os.getcwd()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	73 outdir = copyback + "/" + TRINITY_OUT_DIR
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	74 try:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	75 os.makedirs(outdir)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	76 print "Created dir ",outdir
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	77 except OSError as exc:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	78 if exc.errno == errno.EEXIST and os.path.isdir(outdir):
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	79 pass
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	80 else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	81 raise
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	82 os.chdir(rerunPath)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	83
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	84 ### Add information for reads ###################################
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	85 if args.left and args.right:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	86 cmd += ["--left",args.left,"--right", args.right]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	87 elif args.single:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	88 cmd += ["--single",args.single]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	89 else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	90 raise Exception ("Need input files in order to run Trinity!")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	91
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	92 ### Add seqtype ##################################################
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	93 if args.seqType:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	94 cmd += ["--seqType",args.seqType]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	95 else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	96 raise Exception ("Please specify a file type for your reads!")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	97
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	98 ### Memory and CPU management ####################################
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	99 if args.mem_per_cpu and not args.max_memory:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	100 if args.CPU:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	101 memry = int(args.CPU) * int(args.mem_per_cpu)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	102 memstr = "%dG" % (memry)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	103 cmd += ["--max_memory",memstr]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	104 else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	105 memry = 2 * int(args.mem_per_cpu)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	106 memstr = "%dG" % (memry)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	107 cmd += ["--max_memory",memstr]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	108 elif args.max_memory and not args.mem_per_cpu:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	109 cmd += ["--max_memory",args.max_memory]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	110 else:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	111 raise Exception ("Please pick Memory per cpu, or max mem, but not both.")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	112 if args.CPU:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	113 cmd += ["--CPU", args.CPU]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	114
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	115 ### Enough args, let's run it ####################################
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	116 print "About to write to %s" % args.log
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	117 out = open(args.log, 'w')
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	118 totalattempts = attempts = 2
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	119 ec = 1
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	120 finish = 1
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	121 out.write("Command is:\n%s\n" % (" ".join(cmd)))
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	122
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	123 ### There is definitely some value in running the job more than once, especially if it dies for stupid reasons.. ###
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	124 while ec != 0 and attempts > 0 and finish != 0:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	125
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	126 dt = datetime.now()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	127 dtstr = dt.strftime("%d/%m/%y %H:%M")
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	128 out.write("Beginning attempt %d of Trinity job at %s\n" % (totalattempts - attempts +1, dtstr) )
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	129 attempts -= 1
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	130 ec = subprocess32.call(cmd, shell=False, stdin=None, stdout=out, stderr=out, timeout=None)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	131 out.write("Trinity exited with status %d\n" % ec)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	132
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	133 greplog = open("greplog", 'w')
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	134 cmds = ["grep", 'All commands completed successfully', args.log]
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	135 finish = subprocess32.call(cmds,shell=False, stdin=None, stdout=greplog, stderr=greplog, timeout=None)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	136 greplog.close()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	137 out.write("Finished and found the success command with grep code %d\n" % finish)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	138
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	139 if ec == 0 and args.timing is not None:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	140 if copyback is not False:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	141 cwd = os.getcwd()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	142 dest = copyback + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	143 src = cwd + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	144 print "copying trinity outputs from %s to %s" % (src, dest)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	145 os.symlink(src, dest)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	146
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	147 #copy the timing file into the log
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	148 try:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	149 handle = open (args.timing, 'r')
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	150 for line in handle:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	151 out.write(line)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	152 handle.close()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	153 except (OSError, IOError) as e:
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	154 print "Oops, no timing file found? ",e
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	155
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	156
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	157 out.close()
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	158 exit (ec)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	159
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	160 if __name__ == "__main__":
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	161 main(*sys.argv)
6a3722879525 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	162

Mercurial > repos > trinity_ctat > ctat_trinity_rnaseq

annotate ctat_trinity_wrapper.py @ 3:777b35c8ee3e draft default tip