/
idba_ud_wrapper.py
92 lines (61 loc) · 2.63 KB
/
idba_ud_wrapper.py
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#!/usr/bin/python
#PYTHON SCRIPT
#written by: Richard Wolfe
#
#to run type: python idba_ud_wrapper.py -r <joined reads> -o <outputfile>
#
# if error: /usr/bin/python^M: bad interpreter: No such file or directory
# -there is a windows endl after shebang
# -open in vi
# once in vi type:
# :set ff=unix<return>
# :x<return>
#
#
#
#
#
# -r --merged_reads <string> (required)
# -o --output_dir <string> (required)
#
# Example command to run :
#
import sys #for exit command and maxint
import argparse #to get command line args
#needed to install argparse module because using python 2.6
#and argparse comes with python 2.7
# sudo easy_install argparse
import os #to run system commands
import resource #to keep track of memory usage
print "Script started ..."
#create an argument parser object
#description will be printed when help is used
parser = argparse.ArgumentParser(description='A script to run AMPHORA2')
#add the available arguments -h and --help are added by default
#if the input file does not exist then program will exit
#if output file does not exit it will be created
# args.input is the input file Note: cant write to this file because read only
# args.output is the output file
# args.m is the minimum seq length
#parser.add_argument('-f', '--forward_reads', type=argparse.FileType('rU'), help='forward reads file',required=True)
parser.add_argument('-r', '--merged_reads', help='name of merged forward and reverse reads file', required=True)
parser.add_argument('-o', '--output_dir', help='name of output directory', required=True)
#get the args
args = parser.parse_args()
#additional argument tests
#get full paths
#forward_file_name = os.path.basename(args.forward_reads.name)
#reverse_file_name = os.path.basename(args.reverse_reads.name)
#close the files so there are no problems
#args.forward_reads.close()
#args.reverse_reads.close()
# idba_ud -r R1R2_All_trimmed.fa -o idba_assembled_output
cmd = 'idba_ud -r ' + args.merged_reads + ' -o ' + args.output_dir
print 'executing cmd = ', cmd
retvalue = os.system(cmd) #returns 0 if no error in command
if retvalue != 0: #if command failed
print "ERROR command did not return 0 and failed"
sys.exit(1) #return 0 if sucess
#print "Maximum amount of memory used (in MB) = " , resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1000
print "Maximum amount of memory used (in MB) = " , resource.getrusage(resource.RUSAGE_BOTH).ru_maxrss / 1000
print "Script finished..."