def process_file(self, filename):
"""Processes the given input file"""
self.log.info("Processing %s..." % filename)
parser = fasta.Parser(open_anything(filename))
parser = fasta.regexp_remapper(parser, self.options.sequence_id_regexp)
for seq in parser:
print(seq.id)
def process_file(self, filename):
"""Processes the given input file"""
self.log.info("Processing %s..." % filename)
parser = fasta.Parser(open_anything(filename))
parser = fasta.regexp_remapper(parser, self.options.sequence_id_regexp)
for seq in parser:
print seq.id
def process_sequences_file(self, fname):
self.log.info("Loading sequences from %s..." % fname)
self.seq_ids_to_length = {}
parser = fasta.Parser(open_anything(fname))
parser = fasta.regexp_remapper(parser,
self.sequence_id_regexp
)
for seq in parser:
self.seq_ids_to_length[seq.id] = len(seq.seq)
def load_sequences(self, seq_file):
"""Loads the sequences from the given sequence file in FASTA format"""
self.log.info("Loading sequences from %s..." % seq_file)
parser = fasta.Parser(open_anything(seq_file))
parser = fasta.regexp_remapper(parser,
self.options.sequence_id_regexp)
self.seqs = dict(((seq.id, seq) for seq in parser))
def process_sequences_file_old(self, fname):
""" This is the old version, all the entries are
loaded into memory
"""
self.log.info("Loading sequences from %s..." % fname)
parser = fasta.Parser(open_anything(fname))
parser = fasta.regexp_remapper(parser,
self.sequence_id_regexp)
seqs, lens = [], []
for i, seq in enumerate(parser):
seqs.append(seq.id)
lens.append(len(seq.seq))
if i % 1000000 == 0:
self.log.info("Read {} seqs".format(i))
self.log.info("...loaded")
self.seq_ids_to_length = dict(zip(seqs, lens))
def run_real(self):
"""Runs the application"""
# Load valid sequence IDs (if necessary)
if self.options.sequences_file:
self.log.info("Loading sequences from %s..." %
self.options.sequences_file)
self.total_sequence_length = 0
self.valid_sequence_ids = set()
parser = fasta.Parser(open_anything(self.options.sequences_file))
parser = fasta.regexp_remapper(parser,
self.options.sequence_id_regexp)
for seq in parser:
self.valid_sequence_ids.add(seq.id)
self.total_sequence_length += len(seq.seq)
else:
self.valid_sequence_ids = complementerset()
self.total_sequence_length = None
# Find which sources will be allowed
if not self.options.include_sources:
self.sources = complementerset()
else:
self.sources = set(self.options.include_sources)
self.sources.difference_update(self.options.exclude_sources)
if isinstance(self.sources, complementerset):
self.log.info("Ignored sources: %s" %
", ".join(self.sources.iterexcluded()))
else:
self.log.info("Accepted sources: %s" % ", ".join(self.sources))
if not self.args:
self.args = ["-"]
for arg in self.args:
# Set up the output formatter
if self.options.print_totals:
self.output_formatter = GenomeLevelOutputFormatter(self)
else:
self.output_formatter = SequenceLevelOutputFormatter(self)
# Process the file
self.process_infile(arg)
# Print the results
self.output_formatter.finish()
def run_real(self):
"""Runs the application"""
# Load valid sequence IDs (if necessary)
if self.options.sequences_file:
self.log.info("Loading sequences from %s..." % self.options.sequences_file)
self.total_sequence_length = 0
self.valid_sequence_ids = set()
parser = fasta.Parser(open_anything(self.options.sequences_file))
parser = fasta.regexp_remapper(parser, self.options.sequence_id_regexp)
for seq in parser:
self.valid_sequence_ids.add(seq.id)
self.total_sequence_length += len(seq.seq)
else:
self.valid_sequence_ids = complementerset()
self.total_sequence_length = None
# Find which sources will be allowed
if not self.options.include_sources:
self.sources = complementerset()
else:
self.sources = set(self.options.include_sources)
self.sources.difference_update(self.options.exclude_sources)
if isinstance(self.sources, complementerset):
self.log.info("Ignored sources: %s" % ", ".join(self.sources.iterexcluded()))
else:
self.log.info("Accepted sources: %s" % ", ".join(self.sources))
if not self.args:
self.args = ["-"]
for arg in self.args:
# Set up the output formatter
if self.options.print_totals:
self.output_formatter = GenomeLevelOutputFormatter(self)
else:
self.output_formatter = SequenceLevelOutputFormatter(self)
# Process the file
self.process_infile(arg)
# Print the results
self.output_formatter.finish()
def process_sequences_file(self, fname):
""" In this version we use `shelve` to save
memory (the pairs (protein accession, length) are
stored in a temporary database. See `process_sequences_file_old`
for the old version.
"""
self.log.info("Loading sequences from {}...".format(fname))
parser = fasta.Parser(open_anything(fname))
parser = fasta.regexp_remapper(parser,
self.sequence_id_regexp)
self.filename_shelve = os.path.join(tempfile.gettempdir(),
"shelve_file")
self.seq_ids_to_length = shelve.open(self.filename_shelve)
for i, seq in enumerate(parser):
self.seq_ids_to_length[seq.id] = len(seq.seq)
if i % 1000000 == 0:
self.log.info("Read {} seqs".format(i))
self.seq_ids_to_length.sync()
self.log.info("...loaded")
def process_sequences_file(self, seq_file):
"""Processes the sequences one by one, extracting all the pieces into
an output fasta file"""
self.log.info("Processing fasta file %s..." %seq_file)
parser = fasta.Parser(open_anything(seq_file))
parser = fasta.regexp_remapper(parser,
self.options.sequence_id_regexp)
ids_to_process = set(self.parts.keys())
writer = fasta.FastWriter(sys.stdout)
if self.output_file is not None:
output_fd = open(self.output_file,"w")
writer_file = fasta.FastWriter(output_fd)
for seq in parser:
seq_id = seq.id
if seq_id not in self.parts:
if self.options.try_alternative_splicing:
seq_id = seq_id.strip().rstrip(".1")
if seq_id not in self.parts:
continue
else:
continue
sequence = seq.seq
length_seq = len(sequence)
ids_to_process.remove(seq_id)
for left, right in self.parts[seq_id]:
if left < 0:
left = length_seq + left + 1
if right < 0:
right = length_seq + right + 1
right = min(right, length_seq)
#just in case...
if left > right:
#again, just in case
self.log.warning("Problem with fragment of %s, "
"the right part is smaller than the left" % seq_id)
continue
new_record = None
if left == 1 and right == length_seq:
new_record = seq.fragment(not self.options.keep_ids)
else:
if not self.options.keep_ids:
new_id = "%s:%d-%d" % (seq_id, left, right)
else:
new_id = seq_id
new_record = SeqRecord(sequence[(left-1):right],
id=new_id, name=seq.name, description="")
writer.write(new_record)
if self.output_file is not None:
writer_file.write(new_record)
if self.output_file is not None:
output_fd.close()
if len(ids_to_process) > 0:
self.log.fatal("The following identifiers of sequences (%s) were"
"found in the fragments file, but not in the fasta file"
% ",".join(ids_to_process))
return 1
def process_sequences_file(self, seq_file):
"""Processes the sequences one by one, extracting all the pieces into
an output fasta file"""
self.log.info("Processing fasta file %s...", seq_file)
parser = fasta.Parser(open_anything(seq_file))
parser = fasta.regexp_remapper(parser, self.options.sequence_id_regexp)
ids_to_process = set(self.parts.keys())
writer = fasta.FastWriter(sys.stdout)
if self.output_file is not None:
output_fd = open(self.output_file, "w")
writer_file = fasta.FastWriter(output_fd)
for seq in parser:
seq_id = seq.id
if seq_id not in self.parts:
if self.options.try_alternative_splicing:
seq_id = seq_id.strip().rstrip(".1")
if seq_id not in self.parts:
continue
else:
continue
sequence = seq.seq
length_seq = len(sequence)
ids_to_process.remove(seq_id)
for left, right in self.parts[seq_id]:
if left < 0:
left = length_seq + left + 1
if right < 0:
right = length_seq + right + 1
right = min(right, length_seq)
# just in case...
if left > right:
# again, just in case
self.log.warning(
"Problem with fragment of %s, "
"the right part is smaller than "
"the left", seq_id)
continue
new_record = None
if left == 1 and right == length_seq:
new_record = seq.fragment(not self.options.keep_ids)
else:
if not self.options.keep_ids:
new_id = "%s:%d-%d" % (seq_id, left, right)
else:
new_id = seq_id
new_record = SeqRecord(sequence[(left - 1):right],
id=new_id,
name=seq.name,
description="")
writer.write(new_record)
if self.output_file is not None:
writer_file.write(new_record)
if self.output_file is not None:
output_fd.close()
if ids_to_process:
self.log.fatal(
"The following identifiers of sequences (%s) were"
"found in the fragments file, but not in the "
"fasta file ", ",".join(ids_to_process))
return 1
return 0