ydeng/bmlsa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

CLI will now recursively make output directory if needed

Browse Source
This commit is contained in:
Harrison Deng 2023-04-28 11:31:41 -05:00
parent 6017eadb2c
commit c34b219306
1 changed files with 3 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
src/bmlsa/cli.py
View File

@ -28,7 +28,7 @@ def run(args):
'"--alignment-mode", or, at least "--behave-as". See help (-h) for ' '"--alignment-mode", or, at least "--behave-as". See help (-h) for '
"more information." "more information."
) )
exit(1) exit(3)
queries = read_annotations_from_csv( queries = read_annotations_from_csv(
args.annotations, args.annotations,
args.id_header, args.id_header,
@ -41,7 +41,7 @@ def run(args):
if args.behave_as and args.behave_as not in DEFAULT_ALIGNMENT_PARAMETERS: if args.behave_as and args.behave_as not in DEFAULT_ALIGNMENT_PARAMETERS:
logger.error('"--behave-as" received bad option.') logger.error('"--behave-as" received bad option.')
exit(1) exit(3)
scoring_parameter = ( scoring_parameter = (
{ {
@ -56,6 +56,7 @@ def run(args):
else DEFAULT_ALIGNMENT_PARAMETERS[args.behave_as] else DEFAULT_ALIGNMENT_PARAMETERS[args.behave_as]
) )
os.makedirs(args.output, exist_ok=True)
with open(args.sequence, "r") as sequence_fd: with open(args.sequence, "r") as sequence_fd:
for sequence in SeqIO.parse(sequence_fd, "fasta"): for sequence in SeqIO.parse(sequence_fd, "fasta"):
aligned_annotations = align_many_to_one_ssw( aligned_annotations = align_many_to_one_ssw(