def _run(self, _config, temp):
fasta_files = []
for (name, filename) in sorted(self._infiles.items()):
fasta_files.append((name, pysam.FastaFile(filename)))
for sequence_name in sorted(self._sequences):
filename = os.path.join(temp, sequence_name + ".fasta")
with open(filename, "w") as out_handle:
for (sample, fasta_file) in fasta_files:
sequence = fasta_file.fetch(sequence_name)
fasta = FASTA(sample, sequence_name, sequence)
fasta.write(out_handle)
def setup_mito_mapping(config):
genomes_root = os.path.join(config.destination, "genomes")
if not os.path.exists(genomes_root):
fileutils.make_dirs(genomes_root)
mkfile_fpath = os.path.join(config.destination, "makefile.yaml")
filenames = [mkfile_fpath]
for name, record in sorted(config.database.mitochondria.items()):
filenames.append(
os.path.join(genomes_root, "%s.fasta" % (record.name, )))
existing_filenames = [
filename for filename in filenames if os.path.exists(filename)
]
# A bit strict, but avoid accidential overwrites
if existing_filenames:
log = logging.getLogger(__name__)
log.error("Output file(s) already exists, cannot proceed:")
for filename in sorted(existing_filenames):
log.error(" - %r", filename)
return 1
with open(mkfile_fpath, "w") as mkfile:
mkfile.write(
bam_mkfile.build_makefile(add_prefix_tmpl=False,
add_sample_tmpl=False))
mkfile.write("\n\nPrefixes:\n")
for name, record in sorted(config.database.mitochondria.items()):
if "EXCLUDE" in record.meta.upper():
continue
mkfile.write(" %s:\n" % (record.name, ))
mkfile.write(" Path: genomes/%s.fasta\n" % (record.name, ))
info = config.database.samples.get(record.name)
if info is not None:
mkfile.write(" # Species: %s\n" %
(info.get("Species", "NA"), ))
mkfile.write(" # Sex: %s\n" % (info.get("Sex", "NA"), ))
mkfile.write(" # Publication: %s\n" %
(info.get("Publication", "NA"), ))
mkfile.write(" # Sample ID: %s\n" %
(info.get("SampleID", "NA"), ))
mkfile.write("\n")
fasta_fpath = os.path.join(genomes_root,
"%s.fasta" % (record.name, ))
with open(fasta_fpath, "w") as fasta_handle:
record = FASTA(
name=record.name,
meta=None,
sequence=record.sequence.replace("-", ""),
)
record.write(fasta_handle)
mkfile.write("\n")
return 0