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Renamed project to "SplitMSA" and added pipeline file
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Harrison Deng
2023-04-11 12:33:52 -05:00
parent 419adcd098
commit 0548a80cd2
7 changed files with 117 additions and 111 deletions
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26
Jenkinsfile vendored Normal file
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@@ -0,0 +1,26 @@
pipeline {
agent any
stages {
stage("install") {
steps {
sh 'conda env update --file environment.yml'
sh 'echo "conda activate splitmsa" >> ~/.bashrc'
}
}
stage("build") {
steps {
sh "python -m build"
}
}
stage("publish") {
when {
branch '**/master'
}
steps {
withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
sh "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
}
}
}
}
}

2
README.md
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@@ -1,4 +1,4 @@
# MSA Splitter
# SplitMSA
Simple FASTA file splitter. Capable of batch trimming a large amount of sequences in the form of a MSA in a FASTA file.

45
environment.yaml
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@@ -1,46 +1,5 @@
name: /home/ydeng/msa-splitter/envs
name: splitmsa
channels:
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- biopython=1.81=py311h2582759_0
- black=23.3.0=py311h38be061_0
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2022.12.7=ha878542_0
- click=8.1.3=unix_pyhd8ed1ab_2
- ld_impl_linux-64=2.40=h41732ed_0
- libblas=3.9.0=16_linux64_openblas
- libcblas=3.9.0=16_linux64_openblas
- libexpat=2.5.0=hcb278e6_1
- libffi=3.4.2=h7f98852_5
- libgcc-ng=12.2.0=h65d4601_19
- libgfortran-ng=12.2.0=h69a702a_19
- libgfortran5=12.2.0=h337968e_19
- libgomp=12.2.0=h65d4601_19
- liblapack=3.9.0=16_linux64_openblas
- libnsl=2.0.0=h7f98852_0
- libopenblas=0.3.21=pthreads_h78a6416_3
- libsqlite=3.40.0=h753d276_0
- libstdcxx-ng=12.2.0=h46fd767_19
- libuuid=2.38.1=h0b41bf4_0
- libzlib=1.2.13=h166bdaf_4
- mypy_extensions=1.0.0=pyha770c72_0
- ncurses=6.3=h27087fc_1
- numpy=1.24.2=py311h8e6699e_0
- openssl=3.1.0=h0b41bf4_0
- packaging=23.0=pyhd8ed1ab_0
- pathspec=0.11.1=pyhd8ed1ab_0
- pip=23.0.1=pyhd8ed1ab_0
- platformdirs=3.2.0=pyhd8ed1ab_0
- python=3.11.1=h2755cc3_0_cpython
- python_abi=3.11=3_cp311
- readline=8.2=h8228510_1
- setuptools=67.6.1=pyhd8ed1ab_0
- tk=8.6.12=h27826a3_0
- typing-extensions=4.5.0=hd8ed1ab_0
- typing_extensions=4.5.0=pyha770c72_0
- tzdata=2023c=h71feb2d_0
- wheel=0.40.0=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
prefix: /home/ydeng/msa-splitter/envs
- biopython=1.81

3
pyproject.toml Normal file
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@@ -0,0 +1,3 @@
[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools", "wheel"]

12
setup.cfg Normal file
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@@ -0,0 +1,12 @@
[metadata]
name = splitmsa
version = 0.0.1
[options]
packages = splitmsa
install_requires =
Bio
[options.entry_points]
console_scripts =
splitmsa = splitmsa.splitmsa:main

3
setup.py Normal file
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@@ -0,0 +1,3 @@
from setuptools import setup
setup()

137
msa_splitter.py → splitmsa/splitmsa.py
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@@ -203,7 +203,7 @@ def trim(
)
if perform_translation and not skip_translation:
if '-' in nt_sequence:
if "-" in nt_sequence:
sequence_with_ambiguity = []
for codon_in_sequence in range(0, len(nt_sequence), 3):
codon = nt_sequence[codon_in_sequence : codon_in_sequence + 3]
@@ -247,72 +247,9 @@ def output_as_csv(gene: str, problems: list[list[str]], output_path: str):
writer.writerows(problems)
def main(args):
logging.basicConfig(level=args.log_level.upper())
msa_records = list(read_msa_file(args.input))
info(f"MSA records read complete. Found {len(msa_records)} records.")
genes = []
if args.gene_list:
genes = read_genes_from_csv(args.gene_list)
info(f"Gene list read from {args.gene_list} resulted in {len(genes)} " "genes.")
else:
if args.gene_name and args.start and args.end:
genes.append([args.gene_name, args.start, args.end])
info(
f"Extracting {args.gene_name} starting at {args.start} to "
f"{args.end}."
)
else:
raise Exception(
"Need either a gene list by --gene-list or a start and end "
"via --start, and --end respectively."
)
for gene_name, start, end in genes:
info(f"Started on gene {gene_name} ({start} - {end})")
(
nt_sequence_records,
nt_no_stop_sequence_records,
aa_sequence_records,
aa_no_stop_sequence_records,
problems,
) = trim(
start,
end,
args.gen_cut_stop_codon,
args.do_translate,
msa_records,
correction_range=args.correction_range,
)
if len(problems) > 0:
warning(
f"There were {len(problems)} problems " f"during trimming {gene_name}!"
)
if args.catalogue_problems:
output_as_csv(
gene_name,
problems,
os.path.join(args.output_dir, f"{gene_name} - problems.csv"),
)
write_to_file(
args.output_dir,
gene_name,
start,
end,
args.full_suffix,
args.ns_suffix,
args.aa_suffix,
nt_sequence_records,
nt_no_stop_sequence_records,
aa_sequence_records,
aa_no_stop_sequence_records,
)
info(f"Completed gene {gene_name} ({start} - {end})")
if __name__ == "__main__":
def main():
parser = argparse.ArgumentParser(
prog="msa_splitter",
prog="splitmsa",
description="""
The MSA splitter is a simple program that takes in two positions
and a MSA file and produces two separate FASTA files
@@ -453,4 +390,70 @@ if __name__ == "__main__":
action="store_true",
)
main(parser.parse_args())
args = parser.parse_args()
logging.basicConfig(level=args.log_level.upper())
msa_records = list(read_msa_file(args.input))
info(f"MSA records read complete. Found {len(msa_records)} records.")
genes = []
if args.gene_list:
genes = read_genes_from_csv(args.gene_list)
info(f"Gene list read from {args.gene_list} resulted in {len(genes)} " "genes.")
else:
if args.gene_name and args.start and args.end:
genes.append([args.gene_name, args.start, args.end])
info(
f"Extracting {args.gene_name} starting at {args.start} to "
f"{args.end}."
)
else:
raise Exception(
"Need either a gene list by --gene-list or a start and end "
"via --start, and --end respectively."
)
for gene_name, start, end in genes:
info(f"Started on gene {gene_name} ({start} - {end})")
(
nt_sequence_records,
nt_no_stop_sequence_records,
aa_sequence_records,
aa_no_stop_sequence_records,
problems,
) = trim(
start,
end,
args.gen_cut_stop_codon,
args.do_translate,
msa_records,
correction_range=args.correction_range,
)
if len(problems) > 0:
warning(
f"There were {len(problems)} problems " f"during trimming {gene_name}!"
)
if args.catalogue_problems:
output_as_csv(
gene_name,
problems,
os.path.join(args.output_dir, f"{gene_name} - problems.csv"),
)
write_to_file(
args.output_dir,
gene_name,
start,
end,
args.full_suffix,
args.ns_suffix,
args.aa_suffix,
nt_sequence_records,
nt_no_stop_sequence_records,
aa_sequence_records,
aa_no_stop_sequence_records,
)
info(f"Completed gene {gene_name} ({start} - {end})")
if __name__ == "__main__":
main()