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Fixes to v0.9.92 (11)
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Final fixes and improvements before releasing new version in `bioconda`


Former-commit-id: 5daf47a
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@edgardomortiz
edgardomortiz committed May 26, 2023
1 parent bd79535 commit 80b217c
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Showing 2 changed files with 40 additions and 37 deletions.
70 changes: 37 additions & 33 deletions captus/bait.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@ def bait(full_command, args):
log.log(f"'{long_exons_path}'")
else:
baits_full_exons_path, baits_full_no_exons_path, long_exons_path = create_baits(
raw_baits_dir_path, Path(args.captus_clusters_dir), args.bait_length,
raw_baits_dir_path, args.captus_clusters_dir, args.bait_length,
fastas_auto, fastas_manual, args.overwrite, args.show_more
)
baits_exons_gz_path, baits_no_exons_gz_path = dereplicate_compress_baits(
Expand Down Expand Up @@ -209,7 +209,7 @@ def bait(full_command, args):
"Now Captus will cluster the filtered baits at '--clust_threshold' percent identity"
" and tiled at '--tiling_percentage_overlap' to create the final set of baits ready to be"
" sent for synthesis. Increase the clustering threshold to increase the final number of"
" or reduce it to achieve the opposite result."
" baits or reduce it to achieve the opposite result."
)
mincols = math.ceil(args.tiling_percentage_overlap / 100 * args.bait_length)
log.log(f'{"Bait length":>{mar}}: {bold(args.bait_length)}')
Expand Down Expand Up @@ -249,19 +249,21 @@ def find_fastas(fastas_dir: Path):
return []


def find_fastas_in_dir(cluster_dir_path: Path, extension: str):
def find_fastas_in_dir(cluster_dir_path: str, extension: str):
cluster_dir_path = Path(cluster_dir_path)
if cluster_dir_path.exists() and not dir_is_empty(cluster_dir_path):
fastas_to_process = list(Path(cluster_dir_path).rglob(f"*{extension}"))
fastas_to_process = list(cluster_dir_path.rglob(f"*{extension}"))
return fastas_to_process
else:
quit_with_error(
f"The directory {cluster_dir_path} does not exist or it is empty, no files to process"
f"The directory '{cluster_dir_path}' does not exist or it is empty, no files to process"
)


def find_and_merge_exon_data(cluster_dir_path: Path):
if cluster_dir_path is None: return {}
tsvs = []
if cluster_dir_path.exists():
if Path(cluster_dir_path).exists():
sample_dirs = list(Path(cluster_dir_path).rglob("*__captus-clr"))
for sample_dir in sample_dirs:
tsvs += list(Path(sample_dir).rglob(f'*{settings.DES_SUFFIXES["DATA"]}'))
Expand Down Expand Up @@ -296,7 +298,7 @@ def find_and_merge_exon_data(cluster_dir_path: Path):


def create_baits(
raw_baits_dir_path: Path, cluster_dir_path: Path, bait_length: int,
raw_baits_dir_path: Path, cluster_dir_path: str, bait_length: int,
fastas_auto: list, fastas_manual: list, overwrite: bool, show_more: bool
):
baits_full_exons_path = Path(raw_baits_dir_path, settings.DES_FILES["BFEX"])
Expand Down Expand Up @@ -335,7 +337,7 @@ def create_baits(
if seq_id in exons_data: cds_ids.append(seq_id)
seq = fasta_in[seq_name]["sequence"].replace("-","").upper()
for p in range(0, len(seq) - (bait_length - 1)):
bait_name = f"{locus}{settings.SEQ_NAME_SEP}b{bait_count:05}"
bait_name = f"{locus}{settings.SEQ_NAME_SEP}b{bait_count:06}"
baits[bait_name] = {
"sequence": seq[p:p+bait_length],
"description": des,
Expand All @@ -357,30 +359,32 @@ def create_baits(
log.log("")

if long_exons_path.exists(): long_exons_path.unlink()
long_exons_fastas = find_fastas_in_dir(cluster_dir_path, settings.DES_SUFFIXES["LONG"])
if all_cds_ids and long_exons_fastas:
start = time.time()
log.log(bold(f"Saving FASTA file with the long exons found in selected loci:"))
tqdm_cols = min(shutil.get_terminal_size().columns, 120)
with tqdm(total=len(long_exons_fastas), ncols=tqdm_cols, unit="file") as pbar:
inner_start = time.time()
for fasta_path in long_exons_fastas:
long_exons = fasta_to_dict(fasta_path)
lef = {}
for seq_name in long_exons:
cds_id = seq_name.split("_exon")[0]
if cds_id in all_cds_ids:
lef[seq_name] = long_exons[seq_name]
dict_to_fasta(lef, long_exons_path, append=True)
msg = f"'{fasta_path.name}': processed in {elapsed_time(time.time() - inner_start)}"
if show_more: tqdm.write(msg)
log.log(msg, print_to_screen=False)
pbar.update()
log.log(bold(
f" \u2514\u2500\u2192 FASTA file '{long_exons_path.name}' succesfully created"
f" [{elapsed_time(time.time() - start)}]"
))
log.log("")
if cluster_dir_path:
long_exons_fastas = find_fastas_in_dir(cluster_dir_path, settings.DES_SUFFIXES["LONG"])
if all_cds_ids and long_exons_fastas:
start = time.time()
log.log(bold(f"Saving FASTA file with the long exons found in selected loci:"))
tqdm_cols = min(shutil.get_terminal_size().columns, 120)
with tqdm(total=len(long_exons_fastas), ncols=tqdm_cols, unit="file") as pbar:
inner_start = time.time()
for fasta_path in long_exons_fastas:
long_exons = fasta_to_dict(fasta_path)
lef = {}
for seq_name in long_exons:
cds_id = seq_name.split("_exon")[0]
if cds_id in all_cds_ids:
lef[seq_name] = long_exons[seq_name]
dict_to_fasta(lef, long_exons_path, append=True)
msg = (f"'{fasta_path.name}': processed in"
f" {elapsed_time(time.time() - inner_start)}")
if show_more: tqdm.write(msg)
log.log(msg, print_to_screen=False)
pbar.update()
log.log(bold(
f" \u2514\u2500\u2192 FASTA file '{long_exons_path.name}' succesfully created"
f" [{elapsed_time(time.time() - start)}]"
))
log.log("")

else:
log.log(bold("The following output files were already found:"))
Expand Down Expand Up @@ -616,7 +620,7 @@ def concat_refex_mask_baits(

inner_start = time.time()
if not exclude_reference or not Path(exclude_reference).exists():
msg = (f"'{baits_tomap_path}': SKIPPED mapping against excluding"
msg = (f"'{baits_tomap_path.name}': SKIPPED mapping against excluding"
f" reference [{elapsed_time(time.time() - inner_start)}]")
baits_tomap_path.replace(baits_unmap_path)
else:
Expand Down
7 changes: 3 additions & 4 deletions captus/captus_design.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -641,14 +641,13 @@ def bait(self):
input_group.add_argument(
"-c", "--captus_clusters_dir",
action="store",
default="./01_clustered_markers",
type=str,
dest="captus_clusters_dir",
help="Path to the output directory that contains the curated aligned clusters found"
" during the previous 'cluster' step of Captus-design. This directory is called"
" '01_clustered_markers' if you did not specify a different name during the"
" 'cluster' step. Captus uses the exon data table to create baits that do not span"
" exonic boundaries"
" 'cluster' step. When provided, Captus uses the exon data table to create baits"
" that do not span exonic boundaries"
)

output_group = parser.add_argument_group("Output")
Expand Down Expand Up @@ -775,7 +774,7 @@ def bait(self):
clustering_group.add_argument(
"--ct", "--clust_threshold",
action="store",
type=int,
type=float,
dest="clust_threshold",
default=86,
help="The entire set of potential baits are finally clustered at this identity, keeping"
Expand Down

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