Étienne Mollier pushed to branch upstream at Debian Med / parsnp
Commits:
bfc0d9b7 by Étienne Mollier at 2022-07-11T21:57:14+02:00
New upstream version 1.7.4+dfsg
- - - - -
2 changed files:
- extend.py
- parsnp
Changes:
=====================================
extend.py
=====================================
@@ -15,7 +15,6 @@ import numpy as np
from Bio.AlignIO.MafIO import MafWriter, MafIterator
from Bio.AlignIO.MauveIO import MauveWriter, MauveIterator
from logger import logger
-import pyabpoa as pa
import time
#%%
@@ -306,7 +305,7 @@ def write_extended_xmfa(
cluster_idx = int(msa_record._annotations["pass"])
(record_matches, record_maxmatches), _ =
get_ani_cutoff([record.seq for record in msa_record])
old_matches, old_max_matches = record_matches + old_matches,
record_maxmatches + old_max_matches
- old_nucs_aligned += sum(len(record.seq) for record in msa_record)
+ old_nucs_aligned += sum(len(str(record.seq).replace("-", "")) for
record in msa_record)
for direction in ("right", "left"):
expand_by = clusterdir_expand[(cluster_idx, direction)]
flanks = []
@@ -355,23 +354,20 @@ def write_extended_xmfa(
empty_seqs = [i for i in range(len(seqlist)) if seqlist[i] ==
""]
nonempty_seqs = [s for s in seqlist if s != ""]
msa_result_temp = []
- if minlen < 50:
- aligner = pa.msa_aligner()
- # time.sleep(.25)
- res = aligner.msa(nonempty_seqs, out_cons=False,
out_msa=True)
- msa_result_temp = res.msa_seq
- else:
+ if len(nonempty_seqs) > 1:
nonempty_seq_file =
f"{cluster_directory}/cluster{cluster_idx}_{direction}_nonempty.fa"
SeqIO.write(
(SeqIO.SeqRecord(Seq(sequence), id=str(seq_idx)) for
seq_idx, sequence in enumerate(nonempty_seqs)),
nonempty_seq_file,
"fasta")
subprocess.check_call(
- f"muscle -super5 {nonempty_seq_file} -output
{nonempty_seq_file}_aligned.fa -threads {cpu_count}",
+ f"mafft --thread {cpu_count} {nonempty_seq_file} >
{nonempty_seq_file}_aligned.fa",
stdout=subprocess.DEVNULL,
stderr=subprocess.STDOUT,
shell=True)
msa_result_temp = [str(record.seq) for record in
SeqIO.parse(f"{nonempty_seq_file}_aligned.fa", "fasta")]
+ else:
+ msa_result_temp = nonempty_seqs
msa_result = []
idx = 0
for aligned_seq in msa_result_temp:
@@ -423,7 +419,7 @@ def write_extended_xmfa(
msa_record.annotations["cluster"] = cluster_idx
(record_matches, record_maxmatches), _ =
get_ani_cutoff([record.seq for record in msa_record])
new_matches, new_max_matches = record_matches + new_matches,
record_maxmatches + new_max_matches
- new_nucs_aligned += sum(len(record.seq) for record in msa_record)
+ new_nucs_aligned += sum(len(str(record.seq).replace("-", "")) for
record in msa_record)
write_xmfa_cluster(extended_maf_file, [msa_record],
fname_header_to_gcontigidx)
# maf_writer.write_alignment(msa_record)
total_length = sum(l for l in fname_contigid_to_length.values())
=====================================
parsnp
=====================================
@@ -19,7 +19,7 @@ from glob import glob
import extend as ext
-__version__ = "1.7.3"
+__version__ = "1.7.4"
reroot_tree = True #use --midpoint-reroot
try:
View it on GitLab:
https://salsa.debian.org/med-team/parsnp/-/commit/bfc0d9b76c2db93f416f8278cbbb68125a66be79
--
View it on GitLab:
https://salsa.debian.org/med-team/parsnp/-/commit/bfc0d9b76c2db93f416f8278cbbb68125a66be79
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