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Commit d686c170 authored by Mate Balajti's avatar Mate Balajti
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Merge branch 'dev' into 'main' 

refactor: update tests, CI, main script

See merge request !40
parents 586ebf6e 7b1148fc
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1 merge request!40refactor: update tests, CI, main script
Pipeline #17404 passed
Stage: build
Stage: test
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.gitlab-ci.yml
+ 3
− 10
View file @ d686c170
......@@ -6,7 +6,6 @@ default: # Set default
stages: # List of stages for jobs, and their order of execution
- build
- test
- deploy
build-job: # This job runs in the build stage, which runs first.
stage: build
......@@ -30,12 +29,6 @@ lint-test-job: # This job also runs in the test stage.
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
- pip install -e .
- flake8 --docstring-convention google --max-line-length 120 readsequencer/ --ignore=D212,D103,D104,D107,D100,D017,D415
#- pylint readsequencer/ tests/
deploy-job: # This job runs in the deploy stage.
stage: deploy # It only runs when *both* jobs in the test stage complete successfully.
environment: production
script:
- echo "Deploying application..."
- echo "Application successfully deployed."
- flake8 --docstring-convention google readsequencer/ tests/
- pylint readsequencer/ tests/
- mypy readsequencer/ tests/
\ No newline at end of file
Dockerfile deleted 100644 → 0
+ 0
− 42
View file @ 586ebf6e
FROM python:3.11.1-slim-bullseye
# MAINTAINER add_maintainer
MAINTAINER "Christoph Harmel"
# set names for user, group and user home
ARG USER="bioc"
ARG GROUP="bioc"
ARG WORKDIR="/home/${USER}"
# create user, group, user home & makes the user and group
# the owner of the user home
RUN mkdir -p $WORKDIR \
&& groupadd -r $GROUP \
&& useradd --no-log-init -r -g $GROUP $USER \
&& chown -R ${USER}:${GROUP} $WORKDIR \
&& chmod 700 $WORKDIR
# set the user, make sure the location where pip
# installs binaries/executables is part of the $PATH
# and set the working directory to the user's home
USER $USER
ENV PATH="${WORKDIR}/.local/bin:${PATH}"
WORKDIR $WORKDIR
# copy entire content of the current directory to the
# working directory; ensure that this does not contain any
# files that you don't want to have end up in the Docker
# image, especially not any secrets!
# use `.dockerignore` to set files that you do NOT want
# Docker to copy
COPY --chown=${USER}:${GROUP} . $WORKDIR
# install app and development dependencies
# assumes that dependencies in `requirements.txt` are
# automatically installed when installing the app; if
# that is not the case, they need to be installed
# _before_ installing the app
RUN pip install . \
&& pip install --no-cache-dir -r requirements-dev.txt
# set default command; optional
CMD ["readsequencer"]
readsequencer/__init__.py
+ 1
− 0
View file @ d686c170
"""Initialise read-sequencer."""
readsequencer/cli.py
+ 29
− 13
View file @ d686c170
"""Receive command line arguments."""
import argparse
import logging
from readsequencer.read_sequencer import ReadSequencer
logging.basicConfig(
format='[%(asctime)s: %(levelname)s] %(message)s \
(module "%(module)s")',
level=logging.INFO,
)
logger = logging.getLogger(__name__)
LOG = logging.getLogger(__name__)
def main():
"""Use CLI arguments to simulate sequencing."""
parser = argparse.ArgumentParser(
prog="readsequencer",
description="Simulates sequencing of DNA sequences specified by an FASTA file.",
description="Simulates sequencing of DNA sequences specified \
by an FASTA file.",
)
parser.add_argument(
"output",
help="path to FASTA file"
)
parser.add_argument(
"-i",
"--input",
default=None,
help="path to FASTA file"
)
parser.add_argument("output", help="path to FASTA file")
parser.add_argument("-i", "--input", default=None, help="path to FASTA file")
parser.add_argument(
"-r", "--read-length", default=100, help="read length for sequencing", type=int
"-r",
"--read-length",
type=int,
default=100,
help="read length for sequencing",
)
parser.add_argument(
"-n",
"--n_random",
default=100,
type=int,
help="n random sequences. Just used if input fasta file is not specified.",
help="n random sequences. Just used if input"
"fasta file is not specified.",
)
parser.add_argument(
"-s",
......@@ -30,7 +52,6 @@ def main():
type=int,
help="chunk_size for batch processing",
)
args = parser.parse_args()
LOG.info("Read sequencer started.")
if args.input is not None:
......@@ -55,10 +76,5 @@ def main():
LOG.info("Read sequencer finished.")
if __name__ == "__main__":
logging.basicConfig(
format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
level=logging.INFO,
)
LOG = logging.getLogger(__name__)
if __name__ == '__main__':
main()
readsequencer/read_sequencer.py
+ 42
− 35
View file @ d686c170
"""Main module for read sequencer."""
from random import choices
from collections.abc import Generator, Iterator
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO # type: ignore
from Bio.Seq import Seq # type: ignore
from Bio.SeqRecord import SeqRecord # type: ignore
class ReadSequencer:
"""ReadSequencer class
"""ReadSequencer class.
Args:
fasta: path fasta file
......@@ -22,23 +23,22 @@ class ReadSequencer:
def __init__(
self,
fasta: str = None,
output: str = None,
fasta=None,
output=None,
read_length: int = 150,
chunk_size: int = 10000,
) -> None:
"""Initialise class."""
self.fasta = fasta
self.output = output
self.read_length = read_length
self.chunk_size = chunk_size
self.random = False
self.bases = ("A", "T", "C", "G")
self.n_sequences = None
self.n_sequences: int
def get_n_sequences(self) -> None:
"""
Helper function to detect number of sequences present in set fasta file.
"""Detect number of sequences present in set fasta file.
Returns:
None
......@@ -46,8 +46,7 @@ class ReadSequencer:
self.n_sequences = len(list(SeqIO.parse(self.fasta, "fasta")))
def define_random_sequences(self, n_seq: int) -> None:
"""
Defines random sequences.
"""Define random sequences.
Args:
n_seq: number of random sequences to be generated
......@@ -59,8 +58,7 @@ class ReadSequencer:
self.n_sequences = n_seq
def generate_random_sequence(self, length: int) -> Seq:
"""
Generates random sequence.
"""Generate random sequence.
Args:
length: length of sequence
......@@ -73,7 +71,7 @@ class ReadSequencer:
return seq
def resize_sequence(self, record: SeqRecord) -> SeqRecord:
"""Resizes sequence
"""Resize sequence.
Resizes sequence according to set read length. If sequence is
shorter than read length, fills up with random nucleotides.
......@@ -93,7 +91,7 @@ class ReadSequencer:
return record.seq
def batch_iterator(self, iterator: Iterator, batch_size: int) -> Generator:
"""Generates batch iterator.
"""Generate batch iterator.
This is a generator function, and it returns lists of the
entries from the supplied iterator. Each list will have
......@@ -114,7 +112,7 @@ class ReadSequencer:
batch = []
def run_sequencing(self) -> None:
"""Runs sequencing.
"""Run sequencing.
Runs read sequencing of specified sequences from input fasta file or
generates random sequences for a given read length. If number of
......@@ -125,7 +123,7 @@ class ReadSequencer:
"""
if self.random:
if self.n_sequences <= self.chunk_size:
with open(self.output, "w") as output_handle:
with open(self.output, "w", encoding="utf-8") as output_handle:
for i in range(self.n_sequences):
record = SeqRecord(
self.generate_random_sequence(self.read_length),
......@@ -134,35 +132,44 @@ class ReadSequencer:
SeqIO.write(record, output_handle, "fasta")
else:
batch_generator = self.batch_iterator(
range(self.n_sequences), self.chunk_size
iter(range(self.n_sequences)), self.chunk_size
)
for i, batch in enumerate(batch_generator):
filename = self.output.replace(".fasta", "") + "_chunk_%i.fasta" % (
i + 1
filename = (
self.output.replace(".fasta", "") +
f"_chunk_{i + 1}.fasta"
)
with open(filename, "w") as output_handle:
for j, k in enumerate(batch):
with open(
filename, "w", encoding="utf-8"
) as output_handle:
for j, _ in enumerate(batch):
record = SeqRecord(
self.generate_random_sequence(self.read_length),
self.generate_random_sequence(
self.read_length
),
id="random_seq: " + str(j + 1),
)
SeqIO.write(record, output_handle, "fasta")
else:
if self.n_sequences <= self.chunk_size:
with open(self.fasta) as input_handle, open(
self.output, "w"
with open(self.fasta, encoding="utf-8") as input_handle, open(
self.output, "w", encoding="utf-8"
) as output_handle:
for record in SeqIO.parse(input_handle, "fasta"):
record.seq = self.resize_sequence(record)
SeqIO.write(record, output_handle, "fasta")
else:
record_iter = SeqIO.parse(open(self.fasta), "fasta")
for i, batch in enumerate(
self.batch_iterator(record_iter, self.chunk_size)
):
filename = self.output.replace(".fasta", "") + "_chunk_%i.fasta" % (i + 1)
for j, record in enumerate(batch):
batch[j].seq = self.resize_sequence(record)
with open(filename, "w") as handle:
SeqIO.write(batch, handle, "fasta")
with open(self.fasta, encoding="utf-8") as file:
record_iter = SeqIO.parse(file, "fasta")
for i, batch in enumerate(
self.batch_iterator(record_iter, self.chunk_size)
):
filename = (
self.output.replace(".fasta", "") +
f"_chunk_{i + 1}.fasta"
)
for j, record in enumerate(batch):
record.seq = self.resize_sequence(record)
with open(filename, "w", encoding="utf-8") as handle:
SeqIO.write(batch, handle, "fasta")
setup.py
+ 17
− 5
View file @ d686c170
from setuptools import setup, find_packages
"""Setup tool."""
from pathlib import Path
from setuptools import setup, find_packages # type: ignore
project_root_dir = Path(__file__).parent.resolve()
with open(project_root_dir / "requirements.txt", "r", encoding="utf-8") as _file:
with open(
project_root_dir / "requirements.txt", "r", encoding="utf-8"
) as _file:
INSTALL_REQUIRES = _file.read().splitlines()
URL = ('https://git.scicore.unibas.ch/zavolan_group/'
'tools/read-sequencer')
setup(
name='readsequencer',
version='0.1.1',
url='https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer',
url=URL,
license='MIT',
author='Clara Serger, Michael Sandholzer and Christoph Harmel',
author_email='christoph.harmel@unibas.ch',
description='Simulates sequencing with a specified read length from sequences specified by a FASTA file.',
description='Simulates sequencing with a specified read length from'
'sequences specified by a FASTA file.',
packages=find_packages(),
install_requires=INSTALL_REQUIRES,
entry_points={'console_scripts': ['readsequencer=readsequencer.cli:main']}
entry_points={
'console_scripts': [
'readsequencer=readsequencer.cli:main'
]
}
)
tests/__init__.py 0 → 100644
+ 1
− 0
View file @ d686c170
"""Initialise testing."""
tests/test_cli.py
+ 8
− 10
View file @ d686c170
import readsequencer.cli
"""Test cli.py."""
import pytest
from cli_test_helpers import ArgvContext, shell
import os
import glob
from cli_test_helpers import ArgvContext, shell # type: ignore
import readsequencer.cli
def test_entrypoint():
"""
Is entrypoint script installed? (setup.py)
"""
"""Test if entrypoint script is installed (setup.py)."""
result = shell('readsequencer --help')
assert result.exit_code == 0
def test_usage_no_args():
"""
Does CLI abort w/o arguments, displaying usage instructions?
"""
"""Test if CLI aborts w/o arguments, displaying usage instructions."""
with ArgvContext('readsequencer'), pytest.raises(SystemExit):
readsequencer.cli.main()
......
tests/test_read_sequencer.py
+ 9
− 4
View file @ d686c170
import pytest
"""Test read_sequencer.py."""
import os
import glob
from readsequencer.read_sequencer import ReadSequencer
def test_init_default():
"""Test default initation."""
sequencer = ReadSequencer()
assert sequencer.fasta is None
assert sequencer.read_length == 150
......@@ -13,6 +15,7 @@ def test_init_default():
def test_run_random():
"""Test random run."""
sequencer = ReadSequencer(
output="./tests/fasta_testfile/results.fasta")
sequencer.define_random_sequences(n_seq=100)
......@@ -23,7 +26,9 @@ def test_run_random():
sequencer.run_sequencing()
os.remove("./tests/fasta_testfile/results.fasta")
def test_run_random_chunks():
"""Test random run chunks."""
# setup class
sequencer = ReadSequencer(
output="./tests/fasta_testfile/results.fasta",
......@@ -44,6 +49,7 @@ def test_run_random_chunks():
def test_run_sequencing():
"""Test sequencing run."""
sequencer = ReadSequencer(
fasta="./tests/fasta_testfile/50_seqs_50_1000_bp.fasta",
output="./tests/fasta_testfile/results.fasta",
......@@ -59,7 +65,9 @@ def test_run_sequencing():
for file in result_file:
os.remove(file)
def test_run_sequencing_chunks():
"""Test run sequencing chunks."""
# setup class
sequencer = ReadSequencer(
fasta="./tests/fasta_testfile/50_seqs_50_1000_bp.fasta",
......@@ -78,6 +86,3 @@ def test_run_sequencing_chunks():
assert len(result_files) == 5
for file in result_files:
os.remove(file)
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