Renamed project to "SplitMSA" and added pipeline file
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26
Jenkinsfile
vendored
Normal file
26
Jenkinsfile
vendored
Normal file
@ -0,0 +1,26 @@
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pipeline {
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agent any
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stages {
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stage("install") {
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steps {
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sh 'conda env update --file environment.yml'
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sh 'echo "conda activate splitmsa" >> ~/.bashrc'
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}
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}
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stage("build") {
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steps {
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sh "python -m build"
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}
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}
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stage("publish") {
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when {
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branch '**/master'
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}
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steps {
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withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
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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/*"
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}
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}
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}
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}
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}
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@ -1,4 +1,4 @@
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# MSA Splitter
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# SplitMSA
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Simple FASTA file splitter. Capable of batch trimming a large amount of sequences in the form of a MSA in a FASTA file.
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@ -1,46 +1,5 @@
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name: /home/ydeng/msa-splitter/envs
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name: splitmsa
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channels:
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- conda-forge
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dependencies:
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- _libgcc_mutex=0.1=conda_forge
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- _openmp_mutex=4.5=2_gnu
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- biopython=1.81=py311h2582759_0
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- black=23.3.0=py311h38be061_0
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- bzip2=1.0.8=h7f98852_4
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- ca-certificates=2022.12.7=ha878542_0
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- click=8.1.3=unix_pyhd8ed1ab_2
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- ld_impl_linux-64=2.40=h41732ed_0
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- libblas=3.9.0=16_linux64_openblas
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- libcblas=3.9.0=16_linux64_openblas
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- libexpat=2.5.0=hcb278e6_1
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- libffi=3.4.2=h7f98852_5
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- libgcc-ng=12.2.0=h65d4601_19
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- libgfortran-ng=12.2.0=h69a702a_19
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- libgfortran5=12.2.0=h337968e_19
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- libgomp=12.2.0=h65d4601_19
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- liblapack=3.9.0=16_linux64_openblas
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- libnsl=2.0.0=h7f98852_0
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- libopenblas=0.3.21=pthreads_h78a6416_3
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- libsqlite=3.40.0=h753d276_0
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- libstdcxx-ng=12.2.0=h46fd767_19
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- libuuid=2.38.1=h0b41bf4_0
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- libzlib=1.2.13=h166bdaf_4
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- mypy_extensions=1.0.0=pyha770c72_0
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- ncurses=6.3=h27087fc_1
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- numpy=1.24.2=py311h8e6699e_0
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- openssl=3.1.0=h0b41bf4_0
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- packaging=23.0=pyhd8ed1ab_0
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- pathspec=0.11.1=pyhd8ed1ab_0
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- pip=23.0.1=pyhd8ed1ab_0
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- platformdirs=3.2.0=pyhd8ed1ab_0
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- python=3.11.1=h2755cc3_0_cpython
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- python_abi=3.11=3_cp311
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- readline=8.2=h8228510_1
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- setuptools=67.6.1=pyhd8ed1ab_0
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- tk=8.6.12=h27826a3_0
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- typing-extensions=4.5.0=hd8ed1ab_0
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- typing_extensions=4.5.0=pyha770c72_0
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- tzdata=2023c=h71feb2d_0
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- wheel=0.40.0=pyhd8ed1ab_0
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- xz=5.2.6=h166bdaf_0
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prefix: /home/ydeng/msa-splitter/envs
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- biopython=1.81
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3
pyproject.toml
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3
pyproject.toml
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[build-system]
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build-backend = "setuptools.build_meta"
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requires = ["setuptools", "wheel"]
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12
setup.cfg
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12
setup.cfg
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[metadata]
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name = splitmsa
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version = 0.0.1
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[options]
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packages = splitmsa
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install_requires =
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Bio
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[options.entry_points]
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console_scripts =
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splitmsa = splitmsa.splitmsa:main
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@ -203,7 +203,7 @@ def trim(
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)
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if perform_translation and not skip_translation:
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if '-' in nt_sequence:
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if "-" in nt_sequence:
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sequence_with_ambiguity = []
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for codon_in_sequence in range(0, len(nt_sequence), 3):
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codon = nt_sequence[codon_in_sequence : codon_in_sequence + 3]
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@ -247,72 +247,9 @@ def output_as_csv(gene: str, problems: list[list[str]], output_path: str):
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writer.writerows(problems)
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def main(args):
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logging.basicConfig(level=args.log_level.upper())
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msa_records = list(read_msa_file(args.input))
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info(f"MSA records read complete. Found {len(msa_records)} records.")
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genes = []
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if args.gene_list:
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genes = read_genes_from_csv(args.gene_list)
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info(f"Gene list read from {args.gene_list} resulted in {len(genes)} " "genes.")
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else:
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if args.gene_name and args.start and args.end:
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genes.append([args.gene_name, args.start, args.end])
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info(
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f"Extracting {args.gene_name} starting at {args.start} to "
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f"{args.end}."
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)
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else:
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raise Exception(
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"Need either a gene list by --gene-list or a start and end "
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"via --start, and --end respectively."
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)
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for gene_name, start, end in genes:
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info(f"Started on gene {gene_name} ({start} - {end})")
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(
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nt_sequence_records,
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nt_no_stop_sequence_records,
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aa_sequence_records,
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aa_no_stop_sequence_records,
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problems,
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) = trim(
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start,
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end,
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args.gen_cut_stop_codon,
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args.do_translate,
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msa_records,
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correction_range=args.correction_range,
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)
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if len(problems) > 0:
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warning(
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f"There were {len(problems)} problems " f"during trimming {gene_name}!"
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)
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if args.catalogue_problems:
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output_as_csv(
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gene_name,
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problems,
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os.path.join(args.output_dir, f"{gene_name} - problems.csv"),
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)
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write_to_file(
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args.output_dir,
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gene_name,
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start,
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end,
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args.full_suffix,
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args.ns_suffix,
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args.aa_suffix,
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nt_sequence_records,
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nt_no_stop_sequence_records,
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aa_sequence_records,
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aa_no_stop_sequence_records,
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)
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info(f"Completed gene {gene_name} ({start} - {end})")
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if __name__ == "__main__":
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def main():
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parser = argparse.ArgumentParser(
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prog="msa_splitter",
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prog="splitmsa",
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description="""
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The MSA splitter is a simple program that takes in two positions
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and a MSA file and produces two separate FASTA files
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@ -453,4 +390,70 @@ if __name__ == "__main__":
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action="store_true",
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)
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main(parser.parse_args())
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args = parser.parse_args()
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logging.basicConfig(level=args.log_level.upper())
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msa_records = list(read_msa_file(args.input))
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info(f"MSA records read complete. Found {len(msa_records)} records.")
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genes = []
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if args.gene_list:
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genes = read_genes_from_csv(args.gene_list)
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info(f"Gene list read from {args.gene_list} resulted in {len(genes)} " "genes.")
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else:
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if args.gene_name and args.start and args.end:
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genes.append([args.gene_name, args.start, args.end])
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info(
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f"Extracting {args.gene_name} starting at {args.start} to "
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f"{args.end}."
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)
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else:
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raise Exception(
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"Need either a gene list by --gene-list or a start and end "
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"via --start, and --end respectively."
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)
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for gene_name, start, end in genes:
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info(f"Started on gene {gene_name} ({start} - {end})")
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(
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nt_sequence_records,
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nt_no_stop_sequence_records,
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aa_sequence_records,
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aa_no_stop_sequence_records,
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problems,
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) = trim(
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start,
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end,
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args.gen_cut_stop_codon,
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args.do_translate,
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msa_records,
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correction_range=args.correction_range,
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)
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if len(problems) > 0:
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warning(
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f"There were {len(problems)} problems " f"during trimming {gene_name}!"
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)
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if args.catalogue_problems:
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output_as_csv(
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gene_name,
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problems,
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os.path.join(args.output_dir, f"{gene_name} - problems.csv"),
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)
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write_to_file(
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args.output_dir,
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gene_name,
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start,
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end,
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args.full_suffix,
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args.ns_suffix,
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args.aa_suffix,
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nt_sequence_records,
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nt_no_stop_sequence_records,
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aa_sequence_records,
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aa_no_stop_sequence_records,
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)
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info(f"Completed gene {gene_name} ({start} - {end})")
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if __name__ == "__main__":
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main()
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