Commit 95b82a69 authored by Mikaël Salson's avatar Mikaël Salson Committed by Mathieu Giraud
Browse files

task.py: reindent after previous commit

parent 54593dd6
......@@ -183,32 +183,32 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
vidjil_log_file = open(out_log, 'w')
try:
## commande complete
cmd = defs.DIR_VIDJIL + '/vidjil ' + ' -o ' + out_folder + " -b " + output_filename
cmd += ' ' + vidjil_cmd + ' '+ seq_file
## execute la commande vidjil
print "=== Launching Vidjil ==="
print cmd
print "========================"
sys.stdout.flush()
## commande complete
cmd = defs.DIR_VIDJIL + '/vidjil ' + ' -o ' + out_folder + " -b " + output_filename
cmd += ' ' + vidjil_cmd + ' '+ seq_file
## execute la commande vidjil
print "=== Launching Vidjil ==="
print cmd
print "========================"
sys.stdout.flush()
p = Popen(cmd, shell=True, stdin=PIPE, stdout=vidjil_log_file, stderr=STDOUT, close_fds=True)
p = Popen(cmd, shell=True, stdin=PIPE, stdout=vidjil_log_file, stderr=STDOUT, close_fds=True)
(stdoutdata, stderrdata) = p.communicate()
(stdoutdata, stderrdata) = p.communicate()
print "Output log in " + out_log
sys.stdout.flush()
db.commit()
print "Output log in " + out_log
sys.stdout.flush()
db.commit()
## Get result file
if grep_reads:
out_results = out_folder + '/seq/clone.fa-1'
else:
out_results = out_folder + '/' + output_filename + '.vidjil'
## Get result file
if grep_reads:
out_results = out_folder + '/seq/clone.fa-1'
else:
out_results = out_folder + '/' + output_filename + '.vidjil'
print "===>", out_results
results_filepath = os.path.abspath(out_results)
print "===>", out_results
results_filepath = os.path.abspath(out_results)
stream = open(results_filepath, 'rb')
except:
......@@ -320,29 +320,29 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False
## commande complete
try:
mixcr = defs.DIR_MIXCR + 'mixcr'
cmd = mixcr + ' align --save-reads -t 1 -r ' + align_report + ' ' + args_1 + ' ' + seq_file + ' ' + out_alignments
cmd += ' && '
cmd += mixcr + ' assemble -t 1 -r ' + assembly_report + ' ' + args_2 + ' ' + out_alignments + ' ' + out_clones
cmd += ' && rm ' + out_alignments
cmd += ' && '
cmd += mixcr + ' exportClones --format vidjil -germline -id -name -reads -sequence -top -seg -s ' + args_3 + ' ' + out_clones + ' ' + out_results
## execute la commande MiXCR
print "=== Launching MiXCR ==="
print cmd
print "========================"
sys.stdout.flush()
mixcr = defs.DIR_MIXCR + 'mixcr'
cmd = mixcr + ' align --save-reads -t 1 -r ' + align_report + ' ' + args_1 + ' ' + seq_file + ' ' + out_alignments
cmd += ' && '
cmd += mixcr + ' assemble -t 1 -r ' + assembly_report + ' ' + args_2 + ' ' + out_alignments + ' ' + out_clones
cmd += ' && rm ' + out_alignments
cmd += ' && '
cmd += mixcr + ' exportClones --format vidjil -germline -id -name -reads -sequence -top -seg -s ' + args_3 + ' ' + out_clones + ' ' + out_results
## execute la commande MiXCR
print "=== Launching MiXCR ==="
print cmd
print "========================"
sys.stdout.flush()
p = Popen(cmd, shell=True, stdin=PIPE, stdout=log_file, stderr=STDOUT, close_fds=True)
p.wait()
p = Popen(cmd, shell=True, stdin=PIPE, stdout=log_file, stderr=STDOUT, close_fds=True)
p.wait()
print "Output log in " + out_log
sys.stdout.flush()
print "Output log in " + out_log
sys.stdout.flush()
## Get result file
print "===>", out_results
results_filepath = os.path.abspath(out_results)
## Get result file
print "===>", out_results
results_filepath = os.path.abspath(out_results)
stream = open(results_filepath, 'rb')
stream.close()
except:
......@@ -493,20 +493,20 @@ def run_fuse(id_file, id_config, id_data, sample_set_id, clean_before=True, clea
sequence_file_list += str(row.results_file.sequence_file_id) + "_"
try:
fuse_cmd = db.config[id_config].fuse_command
cmd = "python "+defs.DIR_FUSE+"/fuse.py -o "+ output_file + " " + fuse_cmd + " " + files
fuse_cmd = db.config[id_config].fuse_command
cmd = "python "+defs.DIR_FUSE+"/fuse.py -o "+ output_file + " " + fuse_cmd + " " + files
print "=== fuse.py ==="
print cmd
print "==============="
sys.stdout.flush()
print "=== fuse.py ==="
print cmd
print "==============="
sys.stdout.flush()
p = Popen(cmd, shell=True, stdin=PIPE, stdout=fuse_log_file, stderr=STDOUT, close_fds=True)
(stdoutdata, stderrdata) = p.communicate()
print "Output log in "+out_folder+'/'+output_filename+'.fuse.log'
p = Popen(cmd, shell=True, stdin=PIPE, stdout=fuse_log_file, stderr=STDOUT, close_fds=True)
(stdoutdata, stderrdata) = p.communicate()
print "Output log in "+out_folder+'/'+output_filename+'.fuse.log'
fuse_filepath = os.path.abspath(output_file)
fuse_filepath = os.path.abspath(output_file)
stream = open(fuse_filepath, 'rb')
except:
......@@ -577,9 +577,9 @@ def custom_fuse(file_list):
files += os.path.abspath(defs.DIR_RESULTS + db.results_file[id].data_file) + " "
try:
cmd = "python "+ os.path.abspath(defs.DIR_FUSE) +"/fuse.py -o "+output_file+" -t 100 "+files
proc_srvr = xmlrpclib.ServerProxy("http://%s:%d" % (defs.FUSE_SERVER, defs.PORT_FUSE_SERVER))
fuse_filepath = proc_srvr.fuse(cmd, out_folder, output_filename)
cmd = "python "+ os.path.abspath(defs.DIR_FUSE) +"/fuse.py -o "+output_file+" -t 100 "+files
proc_srvr = xmlrpclib.ServerProxy("http://%s:%d" % (defs.FUSE_SERVER, defs.PORT_FUSE_SERVER))
fuse_filepath = proc_srvr.fuse(cmd, out_folder, output_filename)
f = open(fuse_filepath, 'rb')
data = gluon.contrib.simplejson.loads(f.read())
......@@ -688,26 +688,26 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
pre_process = db.pre_process[pre_process_id]
try:
cmd = pre_process.command.replace( "&file1&", defs.DIR_SEQUENCES + sequence_file.data_file)
if sequence_file.data_file2:
cmd = cmd.replace( "&file2&", defs.DIR_SEQUENCES + sequence_file.data_file2)
cmd = cmd.replace( "&result&", output_file)
cmd = cmd.replace("&pear&", defs.DIR_PEAR)
print "=== Pre-process %s ===" % pre_process_id
print cmd
print "==============="
sys.stdout.flush()
cmd = pre_process.command.replace( "&file1&", defs.DIR_SEQUENCES + sequence_file.data_file)
if sequence_file.data_file2:
cmd = cmd.replace( "&file2&", defs.DIR_SEQUENCES + sequence_file.data_file2)
cmd = cmd.replace( "&result&", output_file)
cmd = cmd.replace("&pear&", defs.DIR_PEAR)
print "=== Pre-process %s ===" % pre_process_id
print cmd
print "==============="
sys.stdout.flush()
out_log = out_folder+'/'+output_filename+'.pre.log'
log_file = open(out_log, 'w')
os.chdir(defs.DIR_FUSE)
p = Popen(cmd, shell=True, stdin=PIPE, stdout=log_file, stderr=log_file, close_fds=True)
(stdoutdata, stderrdata) = p.communicate()
print "Output log in " + out_log
out_log = out_folder+'/'+output_filename+'.pre.log'
log_file = open(out_log, 'w')
os.chdir(defs.DIR_FUSE)
p = Popen(cmd, shell=True, stdin=PIPE, stdout=log_file, stderr=log_file, close_fds=True)
(stdoutdata, stderrdata) = p.communicate()
print "Output log in " + out_log
filepath = os.path.abspath(output_file)
filepath = os.path.abspath(output_file)
stream = open(filepath, 'rb')
except:
......
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