def Builder(self, fasta_file, aligner, aligner_path, ref_path):
"""
Function to submit the FASTA file for the reference sequence and build
the required index file used by the aligner.
This only needs to be done once, so there needs to be a check to ensure
that if the index file have already been generated then they do no need
to be analysed again
"""
builder_exec = os.path.join(
aligner_path,
{
BOWTIE: 'bowtie-build',
BOWTIE2: 'bowtie2-build',
SOAP: '2bwt-builder',
RMAP: '' # do nothing
}[aligner])
build_command = builder_exec + {
BOWTIE: ' -f %(fname)s.fa %(fname)s',
BOWTIE2: ' -f %(fname)s.fa %(fname)s',
SOAP: ' %(fname)s.fa'
}[aligner]
wg_build(fasta_file, build_command, ref_path, aligner)
BOWTIE2: 'bowtie2-build',
SOAP: '2bwt-builder'
}[options.aligner])
build_command = builder_exec + {
BOWTIE: ' -f %(fname)s.fa %(fname)s',
BOWTIE2: ' -f %(fname)s.fa %(fname)s',
SOAP: ' %(fname)s.fa'
}[options.aligner]
print "Reference genome file: %s" % fasta_file
print "Reduced Representation Bisulfite Sequencing: %s" % rrbs
print "Builder path: %s" % builder_exec
#---------------------------------------------------------------
ref_path = options.dbpath
if os.path.exists(ref_path):
if not os.path.isdir(ref_path):
error(
"%s must be a directory. Please, delete it or change the -d option."
% ref_path)
else:
os.mkdir(ref_path)
if rrbs: # RRBS preprocessing
rrbs_build(fasta_file, build_command, ref_path, options.low_bound,
options.up_bound, options.aligner)
else: # Whole genome preprocessing
wg_build(fasta_file, build_command, ref_path, options.aligner)
error('-a option should be: %s' % ' ,'.join(supported_aligners)+'.')
builder_exec = os.path.join(options.aligner_path or aligner_path[options.aligner],
{BOWTIE : 'bowtie-build',
BOWTIE2 : 'bowtie2-build',
SOAP : '2bwt-builder'}[options.aligner])
build_command = builder_exec + { BOWTIE : ' -f %(fname)s.fa %(fname)s',
BOWTIE2 : ' -f %(fname)s.fa %(fname)s',
SOAP : ' %(fname)s.fa'
}[options.aligner]
print "Reference genome file: %s" % fasta_file
print "Reduced Representation Bisulfite Sequencing: %s" % rrbs
print "Builder path: %s" % builder_exec
#---------------------------------------------------------------
ref_path = options.dbpath
if os.path.exists(ref_path):
if not os.path.isdir(ref_path):
error("%s must be a directory. Please, delete it or change the -d option." % ref_path)
else:
os.mkdir(ref_path)
if rrbs: # RRBS preprocessing
rrbs_build(fasta_file, build_command, ref_path, options.low_bound, options.up_bound, options.aligner)
else: # Whole genome preprocessing
wg_build(fasta_file, build_command, ref_path, options.aligner)