def main(in_path, out_folder, fasta_path, deselected_scaffolds_path):
coords_df = None
deselected_scaffolds = []
if fasta_path == "":
coords_df = get_scaffold_coords_by_source_features(in_path)
else:
coords_df = get_scaffold_coords_by_fasta(in_path, fasta_path)
if deselected_scaffolds_path != "":
deselected_scaffolds = hpf.l(deselected_scaffolds_path)
records = list(SeqIO.parse(in_path, "embl"))
t = os.system("mkdir -p " + out_folder)
if t != 0:
sys.stderr.write(
"Error occurred when checking for the presence of output folder or creating the output folder ()"
+ out_folder + ")\n")
sys.exit(1)
for selected_scaff in range(0, coords_df.shape[0]):
coords_df_entry = coords_df.iloc[selected_scaff]
scaff_name = coords_df_entry["header"]
scaff_id = coords_df_entry["id"]
my_sequence_record = None
if scaff_name not in deselected_scaffolds:
query_start_coord = int(coords_df_entry.start_coord)
query_end_coord = int(coords_df_entry.end_coord)
out_path = out_folder + "/" + scaff_id + ".embl"
union_seq = str(records[0].seq)
seq = union_seq[query_start_coord - 1:query_end_coord - 1]
my_sequence = Seq(seq)
my_sequence_record = SeqRecord(my_sequence,
id=scaff_id,
name=scaff_name,
description="unknown_description",
dbxrefs=[])
my_sequence_record.seq.alphabet = generic_dna
my_sequence_record.accession = "unknown_accession"
my_sequence_record = process_record_features(
records, coords_df, query_start_coord, query_end_coord,
my_sequence_record)
SeqIO.write(my_sequence_record, out_path, "embl")
