def filter_by_occupancy(filename_in, filename_out, min_occupancy=0.5):
"""
Filter an alignment in fasta format according to the occupancy of the
columns. Store the results in fasta format.
"""
fasta_raw = fasta_to_dict(filename_in)
n_sequences = len(fasta_raw.keys())
alignment_length = len(fasta_raw[tuple(fasta_raw.keys())[0]])
columns = tuple("".join(fasta_raw[seqname][column_index]
for seqname in fasta_raw.keys())
for column_index in range(alignment_length))
columns_to_keep = []
for column_number, column in enumerate(columns):
n_gaps = column.count("-")
if 1 - float(n_gaps) / float(n_sequences) >= min_occupancy:
columns_to_keep.append(column_number)
fasta_trimmed = {}
for seqname, sequence in fasta_raw.items():
fasta_trimmed[seqname] = "".join(fasta_raw[seqname][column_to_keep]
for column_to_keep in columns_to_keep)
if not os.path.exists(os.path.dirname(filename_out)):
os.makedirs(os.path.dirname(filename_out))
with open(filename_out, "w") as f_out:
for seqname, sequence in fasta_trimmed.items():
f_out.write(">{seqname}\n{sequence}\n".format(seqname=seqname,
sequence=sequence))
def subset_file(pep_fn, cds_fn, cds_dict):
"""Write to cds_fn the cds sequences that are in pep_fn"""
with open(cds_fn, "w") as cds_out:
for seqid in fasta_to_dict(pep_fn).keys():
cds_out.write(
">{seqid}\n{sequence}\n".format(seqid=seqid, sequence=cds_dict[seqid])
)
def remove_gaps(fasta_in, fasta_out):
"""Remove all gaps in the alignment"""
with open(fasta_out, "w") as f_out:
for name, sequence in fasta_to_dict(fasta_in).items():
f_out.write(f">{name}\n{sequence.replace('-', '')}\n")
def translate_fasta(fasta_in, fasta_out):
"""Translate an entire fasta aligment"""
with open(fasta_out, "w") as f_out:
for name, sequence in fasta_to_dict(fasta_in).items():
f_out.write(f">{name}\n{translate(sequence)}\n")
"""Write to cds_fn the cds sequences that are in pep_fn"""
with open(cds_fn, "w") as cds_out:
for seqid in fasta_to_dict(pep_fn).keys():
cds_out.write(
">{seqid}\n{sequence}\n".format(seqid=seqid, sequence=cds_dict[seqid])
)
if __name__ == "__main__":
if len(sys.argv) != 6:
sys.stderr.write(
"Error. Usage: python split_cds.py folder_in ext_in folder_out "
"ext_out all_cds.fa"
)
sys.exit(1)
IN_DIR = fix_dir_path(sys.argv[1])
IN_EXT = sys.argv[2]
OUT_DIR = fix_dir_path(sys.argv[3])
OUT_EXT = sys.argv[4]
CDS_FN = sys.argv[5]
CDS_DICT = fasta_to_dict(CDS_FN)
def process(pep_fn, cds_fn):
"""Fix parameter"""
return subset_file(pep_fn, cds_fn, CDS_DICT)
process_folders(IN_DIR, IN_EXT, OUT_DIR, OUT_EXT, process)