def main():
(options, args) = setup_options()
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
# Split backbone fasta file into chunks.
backbone_to_id = split_backbone(options)
# Find the reads that correspond to a given backbone.
reads_to_backbone = build_reads_to_backbone_dict(options)
# Split the reads based on their corresponding backbone file.
file_pointers_dict = {}
pf = ParseFasta(options.reads_filename)
tuple = pf.getRecord()
id = None
while tuple is not None:
if len(reads_to_backbone[tuple[0]]) > 0:
for backbone in reads_to_backbone[tuple[0]]:
id = backbone_to_id[backbone]
new_fp = open(
options.output_dir + '/' + str(id) + '.reads.fasta', 'a')
new_fp.write('>' + tuple[0] + '\n' + tuple[1] + '\n')
new_fp.close()
tuple = pf.getRecord()
def split_backbone(options):
"""
Split backbone fasta file into chunks.
Returns dictionary of backbone -> id.
"""
backbone_to_id = {}
id_counter = 0
# Write all backbone files to their own fasta file.
pf = ParseFasta(options.backbone_filename)
tuple = pf.getRecord()
while tuple is not None:
print tuple[0]
split_backbone = open(
options.output_dir + '/' + options.prefix + '-' + str(id_counter) +
'.fasta', 'w')
split_backbone.write('>' + tuple[0] + '\n' + tuple[1])
split_backbone.close()
backbone_to_id[tuple[0]] = options.prefix + '-' + str(id_counter)
id_counter += 1
tuple = pf.getRecord()
return backbone_to_id
def main():
(options, args) = setup_options()
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
# Split backbone fasta file into chunks.
backbone_to_id = split_backbone(options)
# Find the reads that correspond to a given backbone.
reads_to_backbone = build_reads_to_backbone_dict(options)
# Split the reads based on their corresponding backbone file.
file_pointers_dict = {}
pf = ParseFasta(options.reads_filename)
tuple = pf.getRecord()
id = None
while tuple is not None:
if len(reads_to_backbone[tuple[0]]) > 0:
for backbone in reads_to_backbone[tuple[0]]:
id = backbone_to_id[backbone]
new_fp = open(options.output_dir + '/' + str(id) + '.reads.fasta', 'a')
new_fp.write('>' + tuple[0] + '\n' + tuple[1] + '\n')
new_fp.close()
tuple = pf.getRecord()
def split_backbone(options):
"""
Split backbone fasta file into chunks.
Returns dictionary of backbone -> id.
"""
backbone_to_id = {}
id_counter = 0
# Write all backbone files to their own fasta file.
pf = ParseFasta(options.backbone_filename)
tuple = pf.getRecord()
while tuple is not None:
print tuple[0]
split_backbone = open(options.output_dir + '/' + options.prefix + '-' + str(id_counter) + '.fasta', 'w')
split_backbone.write('>' + tuple[0] + '\n' + tuple[1])
split_backbone.close()
backbone_to_id[tuple[0]] = options.prefix + '-' + str(id_counter)
id_counter += 1
tuple = pf.getRecord()
return backbone_to_id
def build_readseqs_dict(options):
readseqs = {}
pf = ParseFasta(options.reads_filename) ## typically 'ctg_pb.fasta' in pipeline
tuple = pf.getRecord()
while tuple is not None:
readseqs[tuple[0]] = tuple[1]
tuple = pf.getRecord()
return readseqs
def main():
(options, args) = setup_options()
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
# Split backbone fasta file into chunks.
backbone_to_id = split_backbone(options)
# use: backbone_to_id[seqname] = fileprefix-number
# Find the reads that correspond to a given backbone.
reads_to_backbone = build_reads_to_backbone_dict(options)
## use: reads_to_backbone[read_or_contig_name].append(backbone_name)
## New approach:
## open and close files as you need them
## A little slower than original
pf = ParseFasta(options.reads_filename)
tuple = pf.getRecord()
id = None
while tuple is not None:
if len(reads_to_backbone[tuple[0]]) > 0:
for backbone in reads_to_backbone[tuple[0]]:
id = backbone_to_id[backbone]
fname = options.output_dir + '/' + str(id) + '.reads.fasta'
if os.path.isfile(fname):
with open(fname, 'a') as f:
f.write('>' + tuple[0] + '\n' + tuple[1] + '\n')
else:
with open(fname, 'w') as f:
f.write('>' + tuple[0] + '\n' + tuple[1] + '\n')
tuple = pf.getRecord()
def main():
(options, args) = setup_options()
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
# Split backbone fasta file into chunks.
backbone_to_id = split_backbone(options)
# Find the reads that correspond to a given backbone.
reads_to_backbone = build_reads_to_backbone_dict(options)
# Split the reads based on their corresponding backbone file.
file_pointers_dict = {}
pf = ParseFasta(options.reads_filename)
tuple = pf.getRecord()
id = None
while tuple is not None:
if len(reads_to_backbone[tuple[0]]) > 0:
for backbone in reads_to_backbone[tuple[0]]:
id = backbone_to_id[backbone]
# print tuple[0] + '\t-->\t' + options.output_dir + '/' + str(id) + '.reads.fasta'
if id in file_pointers_dict:
file_pointers_dict[id].write(">" + tuple[0] + "\n" + tuple[1] + "\n")
else:
new_fp = open(options.output_dir + "/" + str(id) + ".reads.fasta", "w")
file_pointers_dict[id] = new_fp
file_pointers_dict[id].write(">" + tuple[0] + "\n" + tuple[1] + "\n")
# else:
# print 'MISSING\t' + tuple[0]
tuple = pf.getRecord()
