Commit 9b8778f9 authored by HERBERT Ryan's avatar HERBERT Ryan

task.py adjusting mixcr cmd, added mixcr report outputs

parent f4aa5518
......@@ -222,19 +222,22 @@ def run_mixcr(id_file, id_config, id_data, id_fuse, clean_before=False, clean_af
os.makedirs(out_folder)
out_log = out_folder + output_filename+'.mixcr.log'
report = out_folder + output_filename + '.mixcr.report'
log_file = open(out_log, 'w')
out_alignments = out_folder + output_filename + '.align.vdjca'
out_clones = out_folder + output_filename + '.clones.clns'
out_results = out_folder + output_filename + '.mixcr'
out_results_file = output_filename + '.mixcr'
out_results = out_folder + out_results_file
## commande complete
mixcr = defs.DIR_MIXCR + 'mixcr'
cmd = mixcr + ' align --save-reads -t 1'
cmd = mixcr + ' align --save-reads -t 3 -r ' + report + '.aln'
#+ output_filename
# TODO reduce threads
cmd += ' ' + seq_file + ' ' + out_alignments
cmd += ' && ' + mixcr + ' assemble -t 1 ' + out_alignments + ' ' + out_clones
cmd += ' && ' + mixcr + ' exportClones -t 1 ' + arg_cmd + ' ' + out_clones + ' ' + out_results
cmd += ' && ' + mixcr + ' assemble -t 3 -r ' + report + '.asmbl ' + out_alignments + ' ' + out_clones
cmd += ' && ' + mixcr + ' exportClones -t 3 --format vidjil -germline -id -name -reads -sequence -top -seg -s ' + out_clones + ' ' + out_results
## execute la commande MiXCR
print "=== Launching MiXCR ==="
......
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