def build_fastas_call(sample):
os.chdir(join(mglobals.original_path, sample))
log.info("Beginning to build alternate fasta for: " + sample)
fixed_vcf = sample + "_fix.vcf"
log.info("Removing duplicated annotations (per transcript annotations)")
helpers.remove_dups(input_f=(sample + in_file_extension), output_f=(sample + ".temp"))
log.info("Removing duplicate alleles and adding header")
# The fact that the original vcf was named sample.vcf is hardcoded
# here. Be careful.
helpers.vcf_fix(template_f=(sample + ".vcf"), input_f=(sample + ".temp"), output_f=fixed_vcf)
# Delete temporary file
os.remove(sample + ".temp")
log.info("Creating alternate fasta")
new_fasta = sample + "_unfixed.fa"
helpers.sub_call(
[
"nice",
"-n",
"5",
"java",
"-Xmx2g",
"-jar",
mglobals.gatk_path,
"-R",
"genome.fa",
"-T",
"FastaAlternateReferenceMaker",
"-o",
new_fasta,
"--variant",
fixed_vcf,
]
)
# Fix the fasta
log.info("Fixing gatk fasta")
# If you change this name, you need to change the alternate fastas list as well.
final_fasta = sample + ".fa"
helpers.fasta_fix(input_f=new_fasta, output_f=final_fasta)
# Delete the unfixed version
os.remove(new_fasta)
log.info("Moving new fasta to: " + join(mglobals.alternate_path, sample))
shutil.move(final_fasta, join(mglobals.alternate_path, sample))
log.info("Indexing new fasta")
os.chdir(join(mglobals.alternate_path, sample))
helpers.sub_call(["bowtie2-build", "-f", final_fasta, sample])
def build_fastas_call(sample):
os.chdir(join(mglobals.original_path, sample))
log.info('Beginning to build alternate fasta for: ' + sample)
fixed_vcf = sample + '_fix.vcf'
log.info('Removing duplicated annotations (per transcript annotations)')
helpers.remove_dups(input_f=(sample + in_file_extension),
output_f=(sample + '.temp'))
log.info('Removing duplicate alleles and adding header')
# The fact that the original vcf was named sample.vcf is hardcoded
# here. Be careful.
helpers.vcf_fix(template_f=(sample + '.vcf'),
input_f=(sample + '.temp'),
output_f=fixed_vcf)
# Delete temporary file
os.remove(sample + '.temp')
log.info('Creating alternate fasta')
new_fasta = sample + '_unfixed.fa'
helpers.sub_call(['nice', '-n', '5',
'java', '-Xmx2g', '-jar',
mglobals.gatk_path,
'-R', 'genome.fa',
'-T', 'FastaAlternateReferenceMaker',
'-o', new_fasta,
'--variant', fixed_vcf])
# Fix the fasta
log.info('Fixing gatk fasta')
# If you change this name, you need to change the alternate fastas list as well.
final_fasta = sample + '.fa'
helpers.fasta_fix(input_f=new_fasta, output_f=final_fasta)
# Delete the unfixed version
os.remove(new_fasta)
log.info('Moving new fasta to: ' + join(mglobals.alternate_path, sample))
shutil.move(final_fasta, join(mglobals.alternate_path, sample))
log.info('Indexing new fasta')
os.chdir(join(mglobals.alternate_path, sample))
helpers.sub_call(['bowtie2-build',
'-f', final_fasta,
sample])
def build_fastas_call(sample):
os.chdir(join(mglobals.original_path, sample))
log.info('Beginning to build alternate fasta for: ' + sample)
fixed_vcf = sample + '_fix.vcf'
log.info('Removing duplicated annotations (per transcript annotations)')
helpers.remove_dups(input_f=(sample + in_file_extension),
output_f=(sample + '.temp'))
log.info('Removing duplicate alleles and adding header')
# The fact that the original vcf was named sample.vcf is hardcoded
# here. Be careful.
helpers.vcf_fix(template_f=(sample + '.vcf'),
input_f=(sample + '.temp'),
output_f=fixed_vcf)
# Delete temporary file
os.remove(sample + '.temp')
log.info('Creating alternate fasta')
new_fasta = sample + '_unfixed.fa'
helpers.sub_call(['nice', '-n', '5',
'java', '-Xmx2g', '-jar',
mglobals.gatk_path,
'-R', 'genome.fa',
'-T', 'FastaAlternateReferenceMaker',
'-o', new_fasta,
'--variant', fixed_vcf])
# Fix the fasta
log.info('Fixing gatk fasta')
# If you change this name, you need to change the alternate fastas list as well.
final_fasta = sample + '.fa'
helpers.fasta_fix(input_f=new_fasta, output_f=final_fasta)
# Delete the unfixed version
os.remove(new_fasta)
log.info('Moving new fasta to: ' + join(mglobals.alternate_path, sample))
shutil.move(final_fasta, join(mglobals.alternate_path, sample))
log.info('Indexing new fasta')
os.chdir(join(mglobals.alternate_path, sample))
helpers.sub_call(['bowtie2-build',
'-f', final_fasta,
sample])
