def bowtie2_se(fastq, ref_index_prefix, multimapping, nth, mem_gb, out_dir):
basename = os.path.basename(strip_ext_fastq(fastq))
prefix = os.path.join(out_dir, basename)
tmp_bam = '{}.bam'.format(prefix)
run_shell_cmd(
'bowtie2 {multimapping} --mm --threads {nth} -x {ref} '
'-U {fastq} | samtools view -1 -S /dev/stdin > {tmp_bam}'.format(
multimapping='-k {mm}'.format(mm=multimapping +
1) if multimapping else '',
nth=nth,
ref=ref_index_prefix,
fastq=fastq,
tmp_bam=tmp_bam,
))
bam = samtools_sort(tmp_bam, nth, mem_gb, out_dir)
rm_f(tmp_bam)
return bam
def run_preseq(bam_w_dups, prefix, nth=1, mem_gb=None):
'''
Runs preseq. Look at preseq data output to get PBC/NRF.
'''
# First sort because this file no longer exists...
sort_bam = samtools_sort(bam_w_dups, nth, mem_gb)
logging.info('Running preseq...')
preseq_data = '{0}.preseq.dat'.format(prefix)
preseq_log = '{0}.preseq.log'.format(prefix)
run_shell_cmd('preseq lc_extrap -P -B -o {preseq_data} {sort_bam} '
'-seed 1 -v 2> {preseq_log}'.format(
preseq_data=preseq_data,
sort_bam=sort_bam,
preseq_log=preseq_log,
))
rm_f(sort_bam)
return preseq_data, preseq_log
def bwa_se(fastq, ref_index_prefix, nth, mem_gb, out_dir):
basename = os.path.basename(strip_ext_fastq(fastq))
prefix = os.path.join(out_dir, basename)
tmp_bam = '{}.bam'.format(prefix)
sai = bwa_aln(fastq, ref_index_prefix, nth, out_dir)
run_shell_cmd(
'bwa samse {ref} {sai} {fastq} | '
'samtools view -bS /dev/stdin {res_param} > {tmp_bam}'.format(
ref=ref_index_prefix,
sai=sai,
fastq=fastq,
res_param=get_samtools_res_param('view', nth=nth),
tmp_bam=tmp_bam,
))
rm_f(sai)
bam = samtools_sort(tmp_bam, nth, mem_gb)
rm_f(tmp_bam)
return bam
def bowtie2_pe(fastq1, fastq2, ref_index_prefix, multimapping, local, nth,
mem_gb, out_dir):
basename = os.path.basename(strip_ext_fastq(fastq1))
prefix = os.path.join(out_dir, basename)
tmp_bam = '{}.bam'.format(prefix)
run_shell_cmd(
'bowtie2 {multimapping} -X2000 {mode_param} --mm --threads {nth} -x {ref} '
'-1 {fastq1} -2 {fastq2} | samtools view -1 -S /dev/stdin > {tmp_bam}'.
format(
multimapping='-k {mm}'.format(mm=multimapping +
1) if multimapping else '',
mode_param='--local ' if local else '',
nth=nth,
ref=ref_index_prefix,
fastq1=fastq1,
fastq2=fastq2,
tmp_bam=tmp_bam,
))
bam = samtools_sort(tmp_bam, nth, mem_gb, out_dir)
rm_f(tmp_bam)
return bam
