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prueba.py.1
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prueba.py.1
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#-------------------------------------------------------------------------------
# EXPRESSION:
#-------------------------------------------------------------------------------
# If any programs from the expression part:
if soft_data.expression_progs & steps:
# OUTPUT folder:
os.mkdir(folders_dict["EXPRESSION_FOLDER"])
#-------------------------------------------------------------------------------
if "CUFFDIFF" in steps:
if "BOWTIE2" in steps:
# if bowtie already selected by the user
slurm_id = prepareAndSubmit("cuffdiff",
"expression/cuffdiff.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env)
slurm_ids.append( slurm_id )
else:
slurm_id = prepareAndSubmit("bowtie2",
"ass_map/bowtie2.cmd",
dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env)
slurm_ids.append( slurm_id )
expr_dep.append(slurm_id)
slurm_id = prepareAndSubmit("cuffdiff",
"expression/cuffdiff.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env)
slurm_ids.append( slurm_id )
#-------------------------------------------------------------------------------
if "CUFFLINKS" in steps:
if "BOWTIE2" in steps:
# if bowtie already selected by the user
slurm_id = prepareAndSubmit("cufflinks",
"expression/cufflinks.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env,
folders_dict["STAT_FOLDER"] +
"expression_stats")
slurm_ids.append( slurm_id )
else:
slurm_id = prepareAndSubmit("bowtie2",
"ass_map/bowtie2.cmd",
dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env)
slurm_ids.append( slurm_id )
expr_dep.append(slurm_id)
slurm_id = prepareAndSubmit("cufflinks",
"expression/cufflinks.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env,
folders_dict["STAT_FOLDER"] +
"expression_stats")
slurm_ids.append( slurm_id )
#-------------------------------------------------------------------------------
if "RSEM" in steps:
slurm_id = prepareAndSubmit("RSEM",
"expression/RSEM.cmd",
dep,
folders_dict["OUT_FOLDER"],
1, 16, "72:00:00", env,
folders_dict["STAT_FOLDER"] +
"expression_stats")
slurm_ids.append(slurm_id)
#-------------------------------------------------------------------------------
if "EXPRESS" in steps:
if "BOWTIE2" in steps:
slurm_id = prepareAndSubmit("express",
"expression/express.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 1, "72:00:00", env,
folders_dict["STAT_FOLDER"] +
"expression_stats")
slurm_ids.append(slurm_id)
else:
# Perform bowtie and post processing
slurm_id = prepareAndSubmit("bowtie2",
"ass_map/bowtie2.cmd",
dep,
folders_dict["OUT_FOLDER"],
1, 16, "24:00:00", env)
slurm_ids.append( slurm_id )
expr_dep.append(slurm_id)
# Bam postprocessing
slurm_id = prepareAndSubmit("bam_postprocess",
"ass_map/bam_postproc.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 16, "24:00:00", env)
slurm_ids.append( slurm_id )
expr_dep.append(slurm_id)
slurm_id = prepareAndSubmit("express",
"expression/express.cmd",
expr_dep,
folders_dict["OUT_FOLDER"],
1, 1, "72:00:00", env,
folders_dict["STAT_FOLDER"] +
"expression_stats")
slurm_ids.append(slurm_id)
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------