def genome_align(args):
""" Use Bowtie2 to map reads to representative genomes """
# Bowtie2
bam_path = os.path.join(args['outdir'], 'snps/temp/genomes.bam')
command = '%s --no-unal ' % args['bowtie2']
command += '-x %s ' % '/'.join([args['outdir'], 'snps/temp/genomes'
]) # index
if args['max_reads']:
command += '-u %s ' % args['max_reads'] # max num of reads
if args['trim']: command += '--trim3 %s ' % args['trim'] # trim 3'
command += '--%s ' % args['speed'] # speed/sensitivity
command += '--threads %s ' % args['threads'] # threads
command += '-f ' if args['file_type'] == 'fasta' else '-q ' # input type
command += '-1 %s -2 %s ' % (
args['m1'],
args['m2']) if args['m2'] else '-U %s ' % args['m1'] # input reads
# Pipe to samtools
command += '| %s view -b - ' % args['samtools'] # convert to bam
command += '| %s sort -f - %s ' % (args['samtools'], bam_path) # sort bam
# Run command
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# Check for errors
utility.check_exit_code(process, command)
print(" finished aligning")
print(" checking bamfile integrity")
utility.check_bamfile(args, bam_path)
def genome_align(args):
""" Use Bowtie2 to map reads to representative genomes from each genome cluster
"""
# Build command
# bowtie2
command = '%s --no-unal ' % args['bowtie2']
# index
command += '-x %s ' % '/'.join([args['outdir'], 'snps/temp/genomes'])
# specify reads
if args['max_reads']: command += '-u %s ' % args['max_reads']
# trim reads
if args['trim']: command += '--trim3 %s ' % args['trim']
# speed/sensitivity
command += '--%s ' % args['speed']
# threads
command += '--threads %s ' % args['threads']
# file type
if args['file_type'] == 'fasta': command += '-f '
else: command += '-q '
# input file
if (args['m1'] and args['m2']): command += '-1 %s -2 %s ' % (args['m1'], args['m2'])
else: command += '-U %s' % args['m1']
# convert to bam
command += '| %s view -b - ' % args['samtools']
# sort bam
bam_path = os.path.join(args['outdir'], 'snps/temp/genomes.bam')
command += '| %s sort -f - %s ' % (args['samtools'], bam_path)
# Run command
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
# Check for errors
utility.check_exit_code(process, command)
utility.check_bamfile(args, bam_path)
def pangenome_align(args):
""" Use Bowtie2 to map reads to all specified genome species """
# Build command
command = '%s --no-unal ' % args['bowtie2']
# index
command += '-x %s ' % '/'.join([args['outdir'], 'genes/temp/pangenomes'])
# specify reads
if args['max_reads']: command += '-u %s ' % args['max_reads']
# trim reads
if args['trim']: command += '--trim3 %s ' % args['trim']
# speed/sensitivity
command += '--%s-local ' % args['speed']
# threads
command += '--threads %s ' % args['threads']
# file type
if args['file_type'] == 'fasta': command += '-f '
else: command += '-q '
# input file
if (args['m1'] and args['m2']): command += '-1 %s -2 %s ' % (args['m1'], args['m2'])
else: command += '-U %s ' % args['m1']
# output unsorted bam
bampath = '/'.join([args['outdir'], 'genes/temp/pangenomes.bam'])
command += '| %s view -b - > %s' % (args['samtools'], bampath)
# Run command
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
# Check for errors
utility.check_exit_code(process, command)
print(" finished aligning")
print(" checking bamfile integrity")
utility.check_bamfile(args, bampath)
def pangenome_align(args):
""" Use Bowtie2 to map reads to all specified genome clusters """
# Build command
command = '%s --no-unal ' % args['bowtie2']
# index
command += '-x %s ' % '/'.join([args['outdir'], 'genes/temp/pangenomes'])
# specify reads
if args['max_reads']: command += '-u %s ' % args['max_reads']
# trim reads
if args['trim']: command += '--trim3 %s ' % args['trim']
# speed/sensitivity
command += '--%s-local ' % args['speed']
# threads
command += '--threads %s ' % args['threads']
# file type
if args['file_type'] == 'fasta': command += '-f '
else: command += '-q '
# input file
if (args['m1'] and args['m2']): command += '-1 %s -2 %s ' % (args['m1'], args['m2'])
else: command += '-U %s' % args['m1']
# output unsorted bam
bampath = '/'.join([args['outdir'], 'genes/temp/pangenome.bam'])
command += '| %s view -b - > %s' % (args['samtools'], bampath)
# Run command
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
# Check for errors
utility.check_exit_code(process, command)
utility.check_bamfile(args, bampath)
def genome_align(args):
""" Use Bowtie2 to map reads to representative genomes """
# Bowtie2
bam_path = os.path.join(args['outdir'], 'snps/temp/genomes.bam')
command = '%s --no-unal ' % args['bowtie2']
if args['bowtie-db']:
command += '-x %s ' % '/'.join([args['bowtie-db'], 'genomes']) # index
else:
command += '-x %s ' % '/'.join([args['outdir'], 'snps/temp/genomes'
]) # index
if args['max_reads']:
command += '-u %s ' % args['max_reads'] # max num of reads
if args['trim']: command += '--trim3 %s ' % args['trim'] # trim 3'
command += '--%s' % args['speed'] # alignment speed
command += '-local ' if args[
'mode'] == 'local' else ' ' # global/local alignment
command += '--threads %s ' % args['threads']
command += '-f ' if args['file_type'] == 'fasta' else '-q ' # input type
if args['m2']: # -1 and -2 contain paired reads
command += '-1 %s -2 %s ' % (args['m1'], args['m2'])
elif args['interleaved']: # -1 contains paired reads
command += '--interleaved %s ' % args['m1']
else: # -1 contains unpaired reads
command += '-U %s ' % args['m1']
# Pipe to samtools
command += '| %s view -b - ' % args['samtools'] # convert to bam
command += '--threads %s ' % args['threads']
command += '| %s sort - ' % args['samtools']
command += '--threads %s ' % args['threads']
command += '-o %s ' % bam_path
# Run command
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# Check for errors
utility.check_exit_code(process, command)
print(" finished aligning")
print(" checking bamfile integrity")
utility.check_bamfile(args, bam_path)