call variations from wheat DNA_seq

文件格式是如下，就是SRA编号，一行一个SRA。fastq文件是在ncbi上下载的SRA格式。小麦基因组单条染色体往往大于500Mb，所以要使用part版本的。mapping使用的bwa mem，call variantion使用的是sentieon
SRR5873706
SRR5873707

#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'wheatomics'



import subprocess

with open('dna_input.txt', 'r') as f:
    sra_input = ''
    ref_fasta = '/data2/Fshare/FastaAndIndex/IWGSC_v1.0_bwa/161010_Chinese_Spring_v1.0_pseudomolecules_parts.fasta'
    sample = 'mutant'

    for line in f:
        sra = line.strip().split()[0]
        print sra + '.sra'
        # sra to fastq.gz
        proc = subprocess.Popen(['fastq-dump', '--split-3', '--helicos', '--gzip',  sra + '.sra'], shell=False)
        proc.wait()
        # Mapping each set of input fastq with BWA-MEM, sorting
        proc = subprocess.Popen('bwa mem -M -R \'@RG\tID:' + sra + '\tSM:' + sample + '\tPL:ILLUMINA\'' +
                                 ' -t 12 -K 10000000 ' + ref_fasta + ' ' + sra.split('.')[0] + '_1.fastq.gz' + ' ' + sra.split('.')[0] + '_2.fastq.gz' +
                                 ' | ' + 'sentieon util sort -r ' + ref_fasta + ' -o ' + sra + 'sorted.bam' + ' -t 10 --sam2bam -i -', shell=True)
        proc.wait()
        # delete all the fastq.gz
        proc = subprocess.Popen(['shred', '-u', '-z', sra.split('.')[0] + '_1.fastq.gz'], shell=False)
        proc.wait()
        proc = subprocess.Popen(['shred', '-u', '-z', sra.split('.')[0] + '_2.fastq.gz'], shell=False)
        proc.wait()
        # get all bam file and put them into next step
        sra_input = sra_input + ' -i ' + sra + 'sorted.bam'
        proc.wait()
    print sra_input
    # Remove Duplicate Reads on the multiple sorted BAM files
    proc = subprocess.Popen(['sentieon', 'driver',  '-t', '10', sra_input, '--algo', 'LocusCollector', '--fun', 'score_info', 'score.txt'], shell= False)
    proc.wait()

    proc = subprocess.Popen(['sentieon', 'driver', '-t', '10', sra_input, '--algo', 'Dedup', '--rmdup', '--score_info',
                             'score.txt', '--metrics', 'dedup_metrics.txt', 'deduped.bam'], shell=False)
    proc.wait()
    # Indel realigner
    proc = subprocess.Popen(['sentieon', 'driver', '-r', ref_fasta, '-t', '10', '-i', 'deduped.bam', '--algo', 'Realigner',
                             'realigned.bam'], shell=False)
    proc.wait()
    # Base recalibration
    proc = subprocess.Popen(['shred', '-u', '-z', 'deduped.bam'], shell=False)
    proc.wait()


    proc = subprocess.Popen(['sentieon', 'driver', '-r', ref_fasta, '-t', '10', '-i', 'realigned.bam', '--algo',
                             'QualCal', 'recal_data.table'], shell=False)
    proc.wait()

    proc = subprocess.Popen(['sentieon', 'driver', '-r', ref_fasta, '-t', '10', '-i', 'realigned.bam', '-q',
                             'recal_data.table', '--algo', 'QualCal', 'recal_data.table.post'], shell=False)
    proc.wait()

    proc = subprocess.Popen(['sentieon', 'driver', '-t', '10', '--algo', 'QualCal', '--plot', '--before',
                             'recal_data.table', '--after', 'recal_data.table.post', 'recal.csv'], shell= False)
    proc.wait()

    proc = subprocess.Popen(['sentieon', 'plot', 'bqsr', '-o', 'recal_plots.pdf', 'recal.csv'], shell=False)
    proc.wait()
    # HC Variant caller
    proc = subprocess.Popen(['sentieon', 'driver', '-r', ref_fasta, '-t', '10', '-i', 'realigned.bam', '-q',
                             'recal_data.table', '--algo', 'Haplotyper', '--emit_mode', 'gvcf', '--emit_conf',
                             '10', '--call_conf', '30', sample + '-hc.g.vcf.gz'], shell=False)
    proc.wait()

    proc = subprocess.Popen(['shred', '-u', '-z', 'realigned.bam'], shell=False)
    proc.wait()

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