#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def bwa1(sample, bwa1_flag):
'''BWA aligner for read1 of paired_end reads.
input:
.fastq
output:
.sam
citation:
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
link:
http://bio-bwa.sourceforge.net/bwa.shtml
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
BWA_INDEX:
RAW_DATA_DIR:
GATK_READ_GROUP_INFO:
COMPRESSION:
'''
SAMPLE1 = sample + "_1"
spawn_job(jobname = 'bwa1', SAMPLE = SAMPLE1, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 32, memory = "30gb", script = "/bwa_drmaa_RNA.sh", args_list = [p.BWA_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.BWA_VERSION, p.BWA_INDEX, SAMPLE1, p.RAW_DATA_DIR, p.GATK_READ_GROUP_INFO, p.COMPRESSION])
job_status(jobname = 'bwa1', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = SAMPLE1 + "/" + SAMPLE1 + ".sam", FLAG_PATH = p.FLAG_PATH)
return
[docs]def bwa2(sample, bwa2_flag):
'''BWA aligner for read2 of paired_end reads.
input:
.fastq
output:
.sam
citation:
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
link:
http://bio-bwa.sourceforge.net/bwa.shtml
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
BWA_INDEX:
RAW_DATA_DIR:
GATK_READ_GROUP_INFO:
COMPRESSION:
'''
SAMPLE2 = sample + "_2"
spawn_job(jobname = 'bwa2', SAMPLE = SAMPLE2, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 32, memory = "30gb", script = "/bwa_drmaa_RNA.sh", args_list = [p.BWA_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.BWA_VERSION, p.BWA_INDEX, SAMPLE2, p.RAW_DATA_DIR, p.GATK_READ_GROUP_INFO, p.COMPRESSION])
job_status(jobname = 'bwa2', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = SAMPLE2 + "/" + SAMPLE2 + ".sam", FLAG_PATH = p.FLAG_PATH)
return
[docs]def bwa_RNA(sample, bwa_flag):
'''BWA aligner for single end reads.
input:
.fastq
output:
.sam
citation:
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
link:
http://bio-bwa.sourceforge.net/bwa.shtml
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
BWA_INDEX:
RAW_DATA_DIR:
GATK_READ_GROUP_INFO:
COMPRESSION:
'''
spawn_job(jobname = 'bwa', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 32, memory = "30gb", script = "/bwa_drmaa_RNA.sh", args_list = [p.BWA_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.BWA_VERSION, p.BWA_INDEX, sample, p.RAW_DATA_DIR, p.GATK_READ_GROUP_INFO, p.COMPRESSION])
job_status(jobname = 'bwa', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + ".sam", FLAG_PATH = p.FLAG_PATH)
return
[docs]def bwa_mem(sample,bwa_mem_flag):
'''BWA aligner with BWA-MEM algorithm.
input:
.fastq
output:
.sam
citation:
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
link:
http://bio-bwa.sourceforge.net/bwa.shtml
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
GENOME:
RAW_DATA_DIR:
BWA_OPTIONS:
COMPRESSION:
'''
spawn_job(jobname = 'bwa_mem', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 32, memory = "30gb", script = "/bwa_drmaa_" + p.ENDS + "_DNA.sh", args_list = [p.BWA_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.BWA_VERSION, p.BWA_INDEX, sample, p.RAW_DATA_DIR, p.BWA_OPTIONS, p.COMPRESSION])
job_status(jobname = 'bwa_mem', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + "_sorted.bam", FLAG_PATH = p.FLAG_PATH)
return
[docs]def bwa_mem_pipe(sample,bwa_mem_pipe_flag):
'''BWA aligner with BWA-MEM algorithm.
input:
.fastq
output:
.sam
citation:
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
link:
http://bio-bwa.sourceforge.net/bwa.shtml
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
GENOME:
RAW_DATA_DIR:
BWA_OPTIONS:
COMPRESSION:
SAMBAMBA_VERSION:
SAMBLASTER_VERSION:
SAMBAMBA_OPTIONS:
'''
spawn_job(jobname = 'bwa_mem_pipe', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 32, memory = "30gb", script = "/bwa_drmaa_" + p.ENDS + "_DNA_piped.sh", args_list = [p.BWA_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.BWA_VERSION, p.BWA_INDEX, sample, p.RAW_DATA_DIR, p.BWA_OPTIONS, p.COMPRESSION, p.SAMBAMBA_VERSION, p.SAMBLASTER_VERSION, p.SAMBAMBA_OPTIONS])
job_status(jobname = 'bwa_mem_pipe', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + "_sorted.bam", FLAG_PATH = p.FLAG_PATH)
return
#(resultspath + "/" + outputfilename)
if __name__ == '__main__':
bwa1(sample, bwa1_flag)
bwa2(sample, bwa2_flag)
bwa_RNA(sample, bwa_flag)
bwa_mem(sample,bwa_mem_flag)
bwa_mem_pipe(sample, bwa_mem_pipe_flag)
sys.exit(0)