def store_short_reads_for_splits(self):
short_reds_for_splits_dict = self.get_short_reads_for_splits_dict()
self.progress.new('Storing reads')
self.progress.update('...')
utils.store_dict_as_FASTA_file(short_reds_for_splits_dict, self.output_file_path)
self.progress.end()
self.run.info('Num reads stored', pp(len(short_reds_for_splits_dict)))
self.run.info('FASTA output', self.output_file_path)
def store_short_reads_for_splits(self):
short_reds_for_splits_dict = self.get_short_reads_for_splits_dict()
self.progress.new('Storing reads')
self.progress.update('...')
utils.store_dict_as_FASTA_file(short_reds_for_splits_dict, self.output_file_path)
self.progress.end()
self.run.info('Num reads stored', pp(len(short_reds_for_splits_dict)))
self.run.info('FASTA output', self.output_file_path)
def store_short_reads_for_splits(self):
self.sanity_check()
if not self.sanity_checked:
raise ConfigError(
"store_short_reads_for_splits :: Cannot be called before running sanity_check"
)
short_reds_for_splits_dict = self.get_short_reads_for_splits_dict()
self.progress.new("Storing reads")
self.progress.update("...")
if self.split_R1_and_R2:
for read_type in sorted(list(short_reds_for_splits_dict.keys())):
output_file_path = '%s_%s.fa' % (self.output_file_prefix,
read_type)
utils.store_dict_as_FASTA_file(
short_reds_for_splits_dict[read_type], output_file_path)
if self.gzip:
utils.gzip_compress_file(output_file_path)
output_file_path = output_file_path + ".gz"
self.run.info('Output file for %s' % read_type,
output_file_path,
progress=self.progress)
self.progress.end()
self.run.info('Num paired-end reads stored',
pp(len(short_reds_for_splits_dict['R1'])),
mc='green',
nl_before=1)
self.run.info('Num unpaired reads stored',
pp(len(short_reds_for_splits_dict['UNPAIRED'])),
mc='green')
else:
output_file_path = self.output_file_path or 'short_reads.fa'
utils.store_dict_as_FASTA_file(short_reds_for_splits_dict['all'],
output_file_path)
if self.gzip:
utils.gzip_compress_file(output_file_path)
output_file_path = output_file_path + ".gz"
self.progress.end()
self.run.info('Output file for all short reads', output_file_path)
self.run.info('Num reads stored',
pp(len(short_reds_for_splits_dict['all'])),
mc='green')
def store_short_reads_for_splits(self):
self.sanity_check()
if not self.sanity_checked:
raise ConfigError("store_short_reads_for_splits :: Cannot be called before running sanity_check")
short_reds_for_splits_dict = self.get_short_reads_for_splits_dict()
self.progress.new("Storing reads")
self.progress.update("...")
if self.split_R1_and_R2:
for read_type in sorted(list(short_reds_for_splits_dict.keys())):
output_file_path = '%s_%s.fa' % (self.output_file_prefix, read_type)
utils.store_dict_as_FASTA_file(short_reds_for_splits_dict[read_type], output_file_path)
if self.gzip:
utils.gzip_compress_file(output_file_path)
output_file_path = output_file_path + ".gz"
self.run.info('Output file for %s' % read_type, output_file_path, progress=self.progress)
self.progress.end()
self.run.info('Num paired-end reads stored',pp(len(short_reds_for_splits_dict['R1'])), mc='green', nl_before=1)
self.run.info('Num unpaired reads stored',pp(len(short_reds_for_splits_dict['UNPAIRED'])), mc='green')
else:
output_file_path = self.output_file_path or 'short_reads.fa'
utils.store_dict_as_FASTA_file(short_reds_for_splits_dict['all'], output_file_path)
if self.gzip:
utils.gzip_compress_file(output_file_path)
output_file_path = output_file_path + ".gz"
self.progress.end()
self.run.info('Output file for all short reads',output_file_path)
self.run.info('Num reads stored', pp(len(short_reds_for_splits_dict['all'])), mc='green')
def process(self):
self.sanity_check()
output_fasta = {}
output_gene_calls = {}
output_functions = {}
num_genbank_records_processed = 0
num_genes_found = 0
num_genes_reported = 0
num_genes_with_functions = 0
try:
if self.input_genbank_path.endswith('.gz'):
genbank_file_object = SeqIO.parse(
io.TextIOWrapper(gzip.open(self.input_genbank_path, 'r')),
"genbank")
else:
genbank_file_object = SeqIO.parse(
open(self.input_genbank_path, "r"), "genbank")
except Exception as e:
raise ConfigError(
"Someone didn't like your unput 'genbank' file :/ Here's what they said "
"about it: '%s'." % e)
for genbank_record in genbank_file_object:
num_genbank_records_processed += 1
output_fasta[genbank_record.name] = str(genbank_record.seq)
genes = [
gene for gene in genbank_record.features if gene.type == "CDS"
] # focusing on features annotated as "CDS" by NCBI's PGAP
for gene in genes:
num_genes_found += 1
location = str(gene.location)
# dumping gene if "location" section contains any of these terms set above: "join" means the gene call spans multiple contigs; "<" or ">" means the gene call runs off a contig
if any(exclusion_term in location
for exclusion_term in self.location_terms_to_exclude):
continue
if "note" in gene.qualifiers:
note = str(gene.qualifiers["note"][0])
# dumping gene if noted as any of these in the "note" section set above
if any(exclusion_term in note
for exclusion_term in self.note_terms_to_exclude):
continue
# dumping if overlapping translation frame
if "transl_except" in gene.qualifiers:
continue
# dumping if gene declared a pseudogene
if "pseudo" in gene.qualifiers or "pseudogene" in gene.qualifiers:
continue
# cleaning up gene coordinates to more easily parse:
location = location.replace("[", "")
location = re.sub('](.*)', '', location)
location = location.split(":")
start = location[0] # start coordinate
end = location[1] # end coordinate
# setting direction to "f" or "r":
if gene.strand == 1:
direction = "f"
else:
direction = "r"
# for accession, storing protein id if it has one, else the the locus tag, else "None"
if "protein_id" in gene.qualifiers:
accession = gene.qualifiers["protein_id"][0]
elif "locus_tag" in gene.qualifiers:
accession = gene.qualifiers["locus_tag"][0]
else:
accession = "None"
# storing gene product annotation if present
if "product" in gene.qualifiers:
function = gene.qualifiers["product"][0]
# trying to capture all different ways proteins are listed as hypothetical and setting to same thing so can prevent from adding to output functions table below
if function in [
"hypothetical", "hypothetical protein",
"conserved hypothetical",
"conserved hypotheticals",
"Conserved hypothetical protein"
]:
function = "hypothetical protein"
else:
function = "hypothetical protein"
# if present, adding gene name to product annotation (so long as not a hypothetical, sometimes these names are useful, sometimes they are not):
if "gene" in gene.qualifiers:
if function not in "hypothetical protein":
gene_name = str(gene.qualifiers["gene"][0])
function = function + " (" + gene_name + ")"
output_gene_calls[self.gene_callers_id] = {
'contig': genbank_record.name,
'start': start,
'stop': end,
'direction': direction,
'partial': 0,
'call_type': 1,
'source': self.source,
'version': self.version
}
num_genes_reported += 1
# not writing gene out to functions table if no annotation
if "hypothetical protein" not in function:
output_functions[self.gene_callers_id] = {
'source': self.source,
'accession': accession,
'function': function,
'e_value': 0
}
num_genes_with_functions += 1
# increment the gene callers id fo rthe next
self.gene_callers_id += 1
if num_genbank_records_processed == 0:
raise ConfigError(
"It seems there was no records in your input genbank file :/ Are you sure you "
"gave the right file path that actually resolves to a genbank formatted "
"text file?")
self.run.info('Num GenBank entries processed',
num_genbank_records_processed)
self.run.info('Num gene records found', num_genes_found)
self.run.info('Num genes reported', num_genes_reported, mc='green')
self.run.info('Num genes with functions',
num_genes_with_functions,
mc='green',
nl_after=1)
# time to write these down:
utils.store_dict_as_FASTA_file(output_fasta,
self.output_fasta_path,
wrap_from=None)
self.run.info('FASTA file path', self.output_fasta_path)
if len(output_gene_calls):
utils.store_dict_as_TAB_delimited_file(output_gene_calls,
self.output_gene_calls_path,
headers=[
"gene_callers_id",
"contig", "start",
"stop", "direction",
"partial", "call_type",
"source", "version"
])
self.run.info('External gene calls file',
self.output_gene_calls_path)
utils.store_dict_as_TAB_delimited_file(output_functions,
self.output_functions_path,
headers=[
'gene_callers_id',
'source', 'accession',
'function', 'e_value'
])
self.run.info('TAB-delimited functions',
self.output_functions_path)
else:
self.output_gene_calls_path = None
self.output_functions_path = None
self.run.warning(
"Anvi'o couldn't find any gene calles in the GenBank file, hence you will get "
"no output files for external gene calls or functions :/ We hope you can "
"survive this terrible terrible news :(")
self.run.info_single('Mmmmm ☘ ', nl_before=1, nl_after=1)
return {
'external_gene_calls': self.output_gene_calls_path,
'gene_functional_annotation': self.output_functions_path,
'path': self.output_fasta_path
}
