Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix phipack #154

Merged
merged 3 commits into from
Jun 28, 2024
Merged

Fix phipack #154

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
5ff4df6
Remove log-to-file for phipack
bkille Jun 28, 2024
d8e8f85
Use regex strings to avoid warnings
bkille Jun 28, 2024
33464ca
Update version
bkille Jun 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 5 additions & 5 deletions parsnp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ from pathlib import Path
import extend as ext
from tqdm import tqdm

__version__ = "2.0.5"
__version__ = "2.0.6"
reroot_tree = True #use --midpoint-reroot
random_seeded = random.Random(42)

Expand Down Expand Up @@ -144,13 +144,13 @@ signal.signal(signal.SIGINT, handler)
def xmfa_to_maf(xmfa_path, maf_path, all_input_paths):
sample_delim = '#'
SeqInfo = namedtuple("SeqInfo", "cid seq_length")
hdr_block_pattern = re.compile("##SequenceIndex (\d+)\n##SequenceFile (.+)\n##SequenceHeader >\s*(\S+).*\n##SequenceLength (\d+)bp")
hdr_block_pattern = re.compile(r"##SequenceIndex (\d+)\n##SequenceFile (.+)\n##SequenceHeader >\s*(\S+).*\n##SequenceLength (\d+)bp")
idx_to_fname = {}
ref_fname = ""
with open(xmfa_path) as xmfa_in:
next(xmfa_in) # skip version
line = next(xmfa_in)
seq_count = int(re.match("#SequenceCount (\d+)\n", line).groups()[0])
seq_count = int(re.match(r"#SequenceCount (\d+)\n", line).groups()[0])
for i in range(seq_count):
info_block = ""
for _ in range(4):
Expand Down Expand Up @@ -1774,9 +1774,9 @@ SETTINGS:
# Harvest seems to fail sometimes when piping to stderr/stdout...
run_command(command)

if run_recomb_filter and not args.partition:
if run_recomb_filter:
command = "harvesttools -q -b %s/parsnp.rec,REC,\"PhiPack\" -o %s/parsnp.ggr -i %s/parsnp.ggr"%(outputDir,outputDir,outputDir)
run_logged_command(command, outputDir, label="recomb-filter")
run_command(command)

run_logged_command(
f"harvesttools -i {outputDir}/parsnp.ggr -S {outputDir}/parsnp.snps.mblocks",
Expand Down