Mercurial > repos > cmonjeau > mapsembler2

comparison mapsembler2.py @ 2:5aea5b993ae8

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fix .dat unknown extension for kissreads
author cmonjeau
date Fri, 11 Sep 2015 10:04:40 +0000
parents f905f982ee3d
children c62c5fd56ebf
comparison
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1:f7458a23cebe 2:5aea5b993ae8
10 10
11 Mapsember2 is available after compiling sources : 11 Mapsember2 is available after compiling sources :
12 12
13 http://www.irisa.fr/symbiose/people/ppeterlongo/mapsembler2_2.2.3.zip 13 http://www.irisa.fr/symbiose/people/ppeterlongo/mapsembler2_2.2.3.zip
14 14
15 or with the galaxy_mapsembler2 package in the GenOuest toolshed 15 or with the package_mapsembler2_2_2_3 package in the GUGGO toolshed and main toolshed
16 16
17 17
18 """ 18 """
19 19
20 def __main__(): 20 def __main__():
47 cmd_line.extend(["-s", options.input_starters]) 47 cmd_line.extend(["-s", options.input_starters])
48 48
49 #inputs 49 #inputs
50 cmd_line.append("-r") 50 cmd_line.append("-r")
51 51
52 #cmd_line.append(inputs) 52 inputs_tab = []
53 cmd_line.append(' '.join(options.input_files.split(","))) 53
54 for input in options.input_files.split(","):
55 os.symlink(input, os.path.basename(input)+'.'+options.extension_format)
56 inputs_tab.append(os.path.basename(input)+'.'+options.extension_format)
57
58 cmd_line.append(' '.join(inputs_tab))
54 59
55 # add parameters into the command line 60 # add parameters into the command line
56 cmd_line.extend(["-t", options.output_extension, "-k", options.kmer, "-c", options.coverage, "-d", options.substitutions, "-g", options.genome_size, "-f", options.process_search, "-x", options.max_length, "-y", options.max_depth]) 61 cmd_line.extend(["-t", options.output_extension, "-k", options.kmer, "-c", options.coverage, "-d", options.substitutions, "-g", options.genome_size, "-f", options.process_search, "-x", options.max_length, "-y", options.max_depth])
57 62
58 # open the output log file 63 # open the output log file
59 log = open(options.output, "w") 64 log = open(options.output, "w")
60 log.write("[COMMAND LINE] "+' '.join(cmd_line)) 65 log.write("[COMMAND LINE] "+' '.join(cmd_line))
61 66
62 process=subprocess.Popen(cmd_line, 67 process=subprocess.call(cmd_line)
63 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
64
65 stdoutput, stderror = process.communicate()
66 68
67 # results recuperation
68 log.write(stdoutput)
69 log.write(stderror)
70
71 # close log file 69 # close log file
72 log.close() 70 log.close()
73 71
74 # move results files inside the job_outputs dir 72 # move results files inside the job_outputs dir
75 os.mkdir("job_outputs") 73 os.mkdir("job_outputs")