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