def run_D_to_J(STEPS, LIB, ACC, STAR, OUT_REF2, PROC, STAR_OPT, PREFIX, JAVA,
PICARD, REF, GATK, PLOIDY, UseUnifiedGenotyperForBaseRecal,
BAMTOOLS, PYTHON, QUEUE, PATHNAME, DICO_CHR):
if 'd' in STEPS:
to_return = utils.run_step_D_RNAseq(LIB, ACC, STAR, OUT_REF2, PROC,
STAR_OPT, PREFIX, QUEUE)
if 'e' in STEPS:
to_return = utils.run_step_E_RNAseq(LIB, ACC, PREFIX, JAVA, PICARD,
QUEUE)
if 'f' in STEPS:
to_return = utils.run_step_F_RNAseq(ACC, JAVA, PICARD, PREFIX, QUEUE)
if 'g' in STEPS:
to_return = utils.run_step_G_RNAseq(JAVA, PICARD, ACC, REF, PREFIX,
QUEUE)
if 'h' in STEPS:
to_return = utils.run_step_H_RNAseq(JAVA, GATK, ACC, REF, PREFIX,
QUEUE)
if 'i' in STEPS:
to_return = utils.run_step_I_RNAseq(ACC, JAVA, GATK, REF, PLOIDY,
PREFIX,
UseUnifiedGenotyperForBaseRecal,
QUEUE)
if 'j' in STEPS:
to_return = utils.run_step_E(ACC, PYTHON, REF, DICO_CHR, PREFIX, QUEUE,
PATHNAME)
if to_return == 0:
return 0
else:
return to_return
def run_analysis(LIB_DIC, ACC_ID, PLOIDY, OPTIONS, LOCA_PROGRAMS, CONFIG,
DICO_CHR, QUEUE, PATHNAME, PARSEUNMAPPED):
TMP = tempfile.NamedTemporaryFile().name.split('/')[-1]
REF = CONFIG.get('Reference', 'genome')
SAMTOOLS = LOCA_PROGRAMS.get('Programs', 'samtools')
BWA = LOCA_PROGRAMS.get('Programs', 'bwa')
JAVA = LOCA_PROGRAMS.get('Programs', 'java')
PICARD = LOCA_PROGRAMS.get('Programs', 'picard')
GATK = LOCA_PROGRAMS.get('Programs', 'gatk')
UseUnifiedGenotyperForBaseRecal = 'no'
PYTHON = LOCA_PROGRAMS.get('Programs', 'python')
PLOTBAMSTAT = LOCA_PROGRAMS.get('Programs', 'plotbamstats')
PREFIX = OPTIONS.prefix
if CONFIG.has_section('Variant'):
if CONFIG.has_option('Variant', 'UseUnifiedGenotyperForBaseRecal'):
UseUnifiedGenotyperForBaseRecal = CONFIG.get(
'Variant', 'UseUnifiedGenotyperForBaseRecal')
if 'a' in OPTIONS.steps:
#1 Mapping
#2 Merging
to_return = utils.run_step_A(ACC_ID, LIB_DIC, BWA, REF, TMP, JAVA,
PICARD, SAMTOOLS, PREFIX, QUEUE,
PARSEUNMAPPED, PLOTBAMSTAT)
if 'b' in OPTIONS.steps:
#3 removing duplicates
to_return = utils.run_step_B(JAVA, PICARD, ACC_ID, TMP, PREFIX, QUEUE)
if 'c' in OPTIONS.steps:
#4 indel realignment
to_return = utils.run_step_C(ACC_ID, JAVA, GATK, REF, CONFIG, PREFIX,
QUEUE)
if 'd' in OPTIONS.steps:
#5 Base recalibration
to_return = utils.run_step_D(CONFIG, ACC_ID,
UseUnifiedGenotyperForBaseRecal, JAVA,
GATK, REF, PLOIDY, PREFIX, QUEUE)
if 'e' in OPTIONS.steps:
#6 GVCF generation
to_return = utils.run_step_E(ACC_ID, PYTHON, REF, DICO_CHR, PREFIX,
QUEUE, PATHNAME)
if to_return == 0:
return 0
else:
return to_return