def build_pangenome_db(args, genome_clusters):
""" Build FASTA and BT2 database from pangene cluster centroids """
import Bio.SeqIO
# fasta database
outdir = '/'.join([args['outdir'], 'genes/temp'])
pangenome_fasta = open('/'.join([outdir, 'pangenomes.fa']), 'w')
pangenome_map = open('/'.join([outdir, 'pangenome.map']), 'w')
db_stats = {'total_length':0, 'total_seqs':0, 'genome_clusters':0}
for species_id in genome_clusters:
db_stats['genome_clusters'] += 1
inpath = '/'.join([args['db'], 'genome_clusters', species_id, 'pangenome.fa.gz'])
infile = utility.iopen(inpath)
for r in Bio.SeqIO.parse(infile, 'fasta'):
genome_id = '.'.join(r.id.split('.')[0:2])
if not args['tax_mask'] or genome_id not in args['tax_mask']:
pangenome_fasta.write('>%s\n%s\n' % (r.id, str(r.seq)))
pangenome_map.write('%s\t%s\n' % (r.id, species_id))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
pangenome_fasta.close()
pangenome_map.close()
# print out database stats
print(" total species: %s" % db_stats['genome_clusters'])
print(" total genes: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([outdir, 'pangenomes.fa'])
outpath = '/'.join([outdir, 'pangenomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
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 build_pangenome_db(args, genome_clusters):
""" Build FASTA and BT2 database from pangene cluster centroids """
import Bio.SeqIO
# fasta database
outdir = '/'.join([args['outdir'], 'genes/temp'])
pangenome_fasta = open('/'.join([outdir, 'pangenomes.fa']), 'w')
pangenome_map = open('/'.join([outdir, 'pangenome.map']), 'w')
db_stats = {'total_length':0, 'total_seqs':0, 'genome_clusters':0}
for species_id in genome_clusters:
db_stats['genome_clusters'] += 1
inpath = '/'.join([args['db'], 'genome_clusters', species_id, 'pangenome.fa.gz'])
infile = gzip.open(inpath)
for r in Bio.SeqIO.parse(infile, 'fasta'):
genome_id = '.'.join(r.id.split('.')[0:2])
if not args['tax_mask'] or genome_id not in args['tax_mask']:
pangenome_fasta.write('>%s\n%s\n' % (r.id, str(r.seq)))
pangenome_map.write('%s\t%s\n' % (r.id, species_id))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
pangenome_fasta.close()
pangenome_map.close()
# print out database stats
print(" total species: %s" % db_stats['genome_clusters'])
print(" total genes: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([outdir, 'pangenomes.fa'])
outpath = '/'.join([outdir, 'pangenomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def pileup(args):
""" Filter alignments by % id, use samtools to create pileup, filter low quality bases, and write results to VCF file """
# Build command
# percent id filtering
bam_path = os.path.join(args['outdir'], 'snps/temp/genomes.bam')
command = 'python %s %s %s %s %s | ' % (args['stream_bam'], bam_path,
'/dev/stdout', args['mapid'],
args['readq'])
# mpileup
command += '%s mpileup -uv -A -d 10000 --skip-indels ' % args['samtools']
# quality filtering
if not args['baq']: command += '-B '
# quality filtering
if args['redo_baq']: command += '-E '
# adjust MQ
if args['adjust_mq']: command += '-C 50 '
# quality filtering
command += '-q %s -Q %s ' % (args['mapq'], args['baseq'])
# reference fna file
command += '-f %s ' % ('%s/snps/temp/genomes.fa' % args['outdir'])
# input bam file
command += '- '
# output vcf file
command += '> %s ' % ('%s/snps/temp/genomes.vcf' % args['outdir'])
# Run command
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def map_reads_hsblast(args):
""" Use hs-blastn to map reads in fasta file to marker database """
# stream sequences
command = 'python %s' % args['stream_seqs']
command += ' -1 %s' % args['m1'] # fasta/fastq
if args['m2']: command += ' -2 %s' % args['m2'] # mate
if args['max_reads']:
command += ' -n %s' % args['max_reads'] # number of reads
if args['read_length']:
command += ' -l %s' % args['read_length'] # read length
command += ' 2> %s/species/temp/read_count.txt' % args[
'outdir'] # tmpfile to store # of reads, bp sampled
# hs-blastn
command += ' | %s align' % args['hs-blastn']
command += ' -word_size %s' % args['word_size']
command += ' -query /dev/stdin'
command += ' -db %s/marker_genes/phyeco.fa' % args['db']
command += ' -outfmt 6'
command += ' -num_threads %s' % args['threads']
command += ' -out %s/species/temp/alignments.m8' % args['outdir']
command += ' -evalue 1e-3'
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def build_pangenome_db(args, species):
""" Build FASTA and BT2 database from pangene species centroids """
import Bio.SeqIO
# fasta database
outdir = '/'.join([args['outdir'], 'genes/temp'])
pangenome_fasta = open('/'.join([outdir, 'pangenomes.fa']), 'w')
pangenome_map = open('/'.join([outdir, 'pangenomes.map']), 'w')
db_stats = {'total_length':0, 'total_seqs':0, 'species':0}
for sp in species.values():
db_stats['species'] += 1
infile = utility.iopen(sp.paths['centroids.ffn'])
for r in Bio.SeqIO.parse(infile, 'fasta'):
pangenome_fasta.write('>%s\n%s\n' % (r.id, str(r.seq).upper()))
pangenome_map.write('%s\t%s\n' % (r.id, sp.id))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
infile.close()
pangenome_fasta.close()
pangenome_map.close()
# print out database stats
print(" total species: %s" % db_stats['species'])
print(" total genes: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([outdir, 'pangenomes.fa'])
outpath = '/'.join([outdir, 'pangenomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def pileup(args):
""" Filter alignments by % id, use samtools to create pileup, filter low quality bases """
# Stream bam, filter alignments
command = 'python %s ' % args['stream_bam']
command += '%s ' % os.path.join(args['outdir'], 'snps/temp/genomes.bam')
command += '/dev/stdout '
command += '%s ' % args['mapid']
command += '%s ' % args['readq']
command += '%s ' % args['mapq']
# Pipe to mpileup
command += '| %s mpileup ' % args['samtools']
command += '-d 10000 ' # set max depth
if not args['baq']: command += '-B ' # BAQ
if args['adjust_mq']: command += '-C 50 ' # adjust MQ
if not args['discard']: command += '-A ' # keep discordant read pairs
command += '-Q %s ' % (args['baseq']) # base quality filtering
command += '-f %s ' % ('%s/snps/temp/genomes.fa' % args['outdir']
) # reference fna file
command += '- ' # input bam file
command += '| gzip > %s ' % (
'%s/snps/temp/genomes.mpileup.gz' % args['outdir']) # output file
# Run command
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
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 pileup(args):
""" Filter alignments by % id, use samtools to create pileup, filter low quality bases, and write results to VCF file """
# Build command
# percent id filtering
bam_path = os.path.join(args['outdir'], 'snps/temp/genomes.bam')
command = 'python %s %s %s %s %s | ' % (args['stream_bam'], bam_path, '/dev/stdout', args['mapid'], args['readq'])
# mpileup
command += '%s mpileup -uv -A -d 10000 --skip-indels ' % args['samtools']
# quality filtering
if not args['baq']: command += '-B '
# quality filtering
if args['redo_baq']: command += '-E '
# adjust MQ
if args['adjust_mq']: command += '-C 50 '
# quality filtering
command += '-q %s -Q %s ' % (args['mapq'], args['baseq'])
# reference fna file
command += '-f %s ' % ('%s/snps/temp/genomes.fa' % args['outdir'])
# input bam file
command += '- '
# output vcf file
command += '> %s ' % ('%s/snps/temp/genomes.vcf' % args['outdir'])
# Run command
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def build_genome_db(args, species):
""" Build FASTA and BT2 database of representative genomes """
import Bio.SeqIO
# fasta database
outfile = open('/'.join([args['outdir'], 'snps/temp/genomes.fa']), 'w')
db_stats = {'total_length': 0, 'total_seqs': 0, 'species': 0}
for sp in species.values():
db_stats['species'] += 1
infile = utility.iopen(sp.paths['fna'])
for r in Bio.SeqIO.parse(infile, 'fasta'):
outfile.write('>%s\n%s\n' % (r.id, str(r.seq).upper()))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
infile.close()
outfile.close()
# print out database stats
print(" total genomes: %s" % db_stats['species'])
print(" total contigs: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([args['outdir'], 'snps/temp/genomes.fa'])
outpath = '/'.join([args['outdir'], 'snps/temp/genomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def build_genome_db(args, genome_clusters):
""" Build FASTA and BT2 database from genome cluster centroids """
# fasta database
genomes_fasta = open('/'.join([args['outdir'], 'snps/temp/genomes.fa']), 'w')
genomes_map = open('/'.join([args['outdir'], 'snps/temp/genomes.map']), 'w')
db_stats = {'total_length':0, 'total_seqs':0, 'genome_clusters':0}
for species_id in genome_clusters:
if args['tax_mask'] and fetch_centroid(args, species_id) in args['tax_mask']:
continue
db_stats['genome_clusters'] += 1
inpath = '/'.join([args['db'], 'genome_clusters', species_id, 'genome.fna.gz'])
infile = gzip.open(inpath)
for line in infile:
genomes_fasta.write(line)
db_stats['total_length'] += len(line.rstrip())
if line[0] == '>':
sid = line.rstrip().lstrip('>').split()[0]
genomes_map.write(sid+'\t'+species_id+'\n')
db_stats['total_seqs'] += 1
# print out database stats
print(" total genomes: %s" % db_stats['genome_clusters'])
print(" total contigs: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([args['outdir'], 'snps/temp/genomes.fa'])
outpath = '/'.join([args['outdir'], 'snps/temp/genomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
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 build_hsblastn_db(self, hsblastn):
command = "%s index " % hsblastn
command += " %s/phyeco.fa " % self.dir
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def hsblastn_index(self, fasta):
command = "hs-blastn index %s " % fasta
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
env={'PATH': sys.path})
utility.check_exit_code(process, command)
def hmmsearch(self, inpath, outpath, threads):
command = "hmmsearch --noali --cpu %s " % threads
command += "--domtblout %s " % outpath
command += "%s/%s " % (os.path.dirname(__file__), 'phyeco.hmm')
command += "%s > /dev/null" % inpath
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def build_hsblastn_db(self, hsblastn, resume):
header = '%s/phyeco.fa.header' % self.dir
if os.path.exists(header) and os.stat(header).st_size > 0 and resume:
return
command = "%s index " % hsblastn
command += " %s/phyeco.fa " % self.dir
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def uclust(self, genes, pid, centroids, clusters, threads):
""" Run UCLUST from shell with specified arguments """
command = "vsearch "
command += "-cluster_fast %s " % genes
command += "-id %s " % pid
command += "-centroids %s " % centroids
command += "-uc %s " % clusters
command += "-threads %s " % threads
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def index_bam(args):
start = time()
print("\nIndexing bamfile")
args['log'].write("\nIndexing bamfile\n")
command = '%s index -@ %d %s/snps/temp/genomes.bam' % (
args['samtools'], int(args['threads']), args['outdir'])
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
print(" %s minutes" % round((time() - start) / 60, 2))
print(" %s Gb maximum memory" % utility.max_mem_usage())
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)
def map_reads_hsblast(args):
""" Use hs-blastn to map reads in fasta file to marker database """
# stream sequences
command = 'python %s' % args['stream_seqs']
command += ' -1 %s' % args['m1'] # fasta/fastq
if args['m2']: command += ' -2 %s' % args['m2'] # mate
if args['max_reads']: command += ' -n %s' % args['max_reads'] # number of reads
if args['read_length']: command += ' -l %s' % args['read_length'] # read length
command += ' 2> %s/species/temp/read_count.txt' % args['outdir'] # tmpfile to store # of reads, bp sampled
# hs-blastn
command += ' | %s align' % args['hs-blastn']
command += ' -word_size %s' % args['word_size']
command += ' -query /dev/stdin'
command += ' -db %s/%s/%s' % (args['db'], 'marker_genes', args['db_type'])
command += ' -outfmt 6'
command += ' -num_threads %s' % args['threads']
command += ' -out %s/species/temp/alignments.m8' % args['outdir']
command += ' -evalue 1e-3'
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def build_genome_db(args, genome_clusters):
""" Build FASTA and BT2 database from genome cluster centroids """
# fasta database
genomes_fasta = open('/'.join([args['outdir'], 'snps/temp/genomes.fa']),
'w')
genomes_map = open('/'.join([args['outdir'], 'snps/temp/genomes.map']),
'w')
db_stats = {'total_length': 0, 'total_seqs': 0, 'genome_clusters': 0}
for species_id in genome_clusters:
if args['tax_mask'] and fetch_centroid(args,
species_id) in args['tax_mask']:
continue
db_stats['genome_clusters'] += 1
inpath = '/'.join(
[args['db'], 'genome_clusters', species_id, 'genome.fna.gz'])
infile = utility.iopen(inpath)
for line in infile:
genomes_fasta.write(line)
db_stats['total_length'] += len(line.rstrip())
if line[0] == '>':
sid = line.rstrip().lstrip('>').split()[0]
genomes_map.write(sid + '\t' + species_id + '\n')
db_stats['total_seqs'] += 1
# print out database stats
print(" total genomes: %s" % db_stats['genome_clusters'])
print(" total contigs: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([args['outdir'], 'snps/temp/genomes.fa'])
outpath = '/'.join([args['outdir'], 'snps/temp/genomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
