From b4cc85c3c4456f59023f16ae4e8feb187febfb9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <mate.balajti@unibas.ch>
Date: Mon, 31 Jul 2023 15:37:27 +0200
Subject: [PATCH] feat: add cli support
---
.gitignore | 7 ++-
.../input_files}/expression.csv | 0
{input_files => tests/input_files}/test.gtf | 0
transcript_sampler/__init__.py | 2 +-
transcript_sampler/{new_exe.py => cli.py} | 59 +++++++++++-------
.../images}/.gitkeep | 0
.../screenshot_git_tutorial_1_hGillet.png | Bin
.../screenshot_git_tutorial_2_hGillet.png | Bin
.../screenshot_markdown_tutorial_hGillet.png | Bin
.../obsolete_scripts}/exon_length_filter.py | 0
.../org_test_representative.py | 0
.../obsolete_scripts}/representative.py | 0
.../obsolete_scripts}/transcript_extractor.py | 0
13 files changed, 44 insertions(+), 24 deletions(-)
rename {input_files => tests/input_files}/expression.csv (100%)
rename {input_files => tests/input_files}/test.gtf (100%)
rename transcript_sampler/{new_exe.py => cli.py} (59%)
rename {images => transcript_sampler/images}/.gitkeep (100%)
rename {images => transcript_sampler/images}/screenshot_git_tutorial_1_hGillet.png (100%)
rename {images => transcript_sampler/images}/screenshot_git_tutorial_2_hGillet.png (100%)
rename {images => transcript_sampler/images}/screenshot_markdown_tutorial_hGillet.png (100%)
rename {scripts => transcript_sampler/obsolete_scripts}/exon_length_filter.py (100%)
rename {scripts => transcript_sampler/obsolete_scripts}/org_test_representative.py (100%)
rename {scripts => transcript_sampler/obsolete_scripts}/representative.py (100%)
rename {scripts => transcript_sampler/obsolete_scripts}/transcript_extractor.py (100%)
diff --git a/.gitignore b/.gitignore
index 7a8baad..2a680d3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,4 +4,9 @@
# ignore ALL files in ANY directory named temp
temp/
__pycache__
-output_files
\ No newline at end of file
+output_files
+*_cache
+*egg-info/
+.coverage
+build/
+*/play.py
\ No newline at end of file
diff --git a/input_files/expression.csv b/tests/input_files/expression.csv
similarity index 100%
rename from input_files/expression.csv
rename to tests/input_files/expression.csv
diff --git a/input_files/test.gtf b/tests/input_files/test.gtf
similarity index 100%
rename from input_files/test.gtf
rename to tests/input_files/test.gtf
diff --git a/transcript_sampler/__init__.py b/transcript_sampler/__init__.py
index 4572092..bb7d5f3 100644
--- a/transcript_sampler/__init__.py
+++ b/transcript_sampler/__init__.py
@@ -1 +1 @@
-"""Init.py."""
+"""Initialise package."""
diff --git a/transcript_sampler/new_exe.py b/transcript_sampler/cli.py
similarity index 59%
rename from transcript_sampler/new_exe.py
rename to transcript_sampler/cli.py
index d96f613..f2d67d0 100644
--- a/transcript_sampler/new_exe.py
+++ b/transcript_sampler/cli.py
@@ -1,46 +1,56 @@
-"""This module executes the transcript_sampler"""
+"""This module executes the transcript_sampler."""
import argparse
import time
import logging
-logging.basicConfig(
- format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
- level=logging.INFO,
- )
-from find_reptrans import FindRepTrans # pylint: disable=E0401,C0413
-from match_reptrans_explvl import MatchReptransExplvl # pylint: disable=E0401,C0413
-from poisson_sampling import SampleTranscript # pylint: disable=E0401,C0413
+from find_reptrans import FindRepTrans
+from match_reptrans_explvl import MatchReptransExplvl
+from poisson_sampling import SampleTranscript
find_rep_trans = FindRepTrans()
match_reptrs_explvl = MatchReptransExplvl()
poisson_sample = SampleTranscript()
-LOG = logging.getLogger(__name__)
+logging.basicConfig(
+ format='[%(asctime)s: %(levelname)s] %(message)s \
+ (module "%(module)s")',
+ level=logging.INFO,
+)
+LOG = logging.getLogger("main")
-def exe(input_gtf, input_csv, output_gtf, output_csv, transcript_nr):
+def main(args: argparse.Namespace):
"""Execute transcript sampler."""
start = time.time()
LOG.info("Started transcript sampler...")
- dict_repr_trans = find_rep_trans.get_rep_trans(input_gtf)
+ dict_repr_trans = find_rep_trans.get_rep_trans(args.input_gtf)
df_repr = match_reptrs_explvl.match_repr_transcript_expression_level(
- dict_reprTrans=dict_repr_trans, exprTrans=input_csv, gtf_file=input_gtf
+ dict_reprTrans=dict_repr_trans,
+ exprTrans=args.input_csv,
+ gtf_file=args.input_gtf
)
LOG.info(
"Finding match between representative transcripts \
and expression level file"
)
LOG.info("Poisson sampling of transcripts")
- poisson_sample.transcript_sampling(transcript_nr, df_repr, output_csv)
+ poisson_sample.transcript_sampling(
+ args.transcript_nr, df_repr, args.output_csv)
LOG.info("Output CSV file ready")
LOG.info("Writing output GTF file")
- find_rep_trans.gtf_file_writer(input_gtf, dict_repr_trans, output_gtf)
+ find_rep_trans.gtf_file_writer(
+ args.input_gtf, dict_repr_trans, args.output_gtf)
end = time.time()
LOG.info("Script executed in %s sec", (end - start))
-if __name__ == "__main__":
+def parse_arguments() -> argparse.Namespace:
+ """Request parameters from user on CLI.
+
+ Returns:
+ argparse.Namespace: object of arguments from CLI.
+ """
parser = argparse.ArgumentParser(
description="Transcript sampler",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -67,12 +77,17 @@ if __name__ == "__main__":
help="Total number of transcripts to sample"
)
args = parser.parse_args()
- print(args)
- exe(
- args.input_gtf,
- args.input_csv,
- args.output_gtf,
- args.output_csv,
- args.n_to_sample,
+ return args
+
+
+if __name__ == '__main__':
+ logging.basicConfig(
+ format='[%(asctime)s: %(levelname)s] %(message)s \
+ (module "%(module)s")',
+ level=logging.INFO,
)
+ logger = logging.getLogger(__name__)
+
+ arguments = parse_arguments()
+ main(arguments)
diff --git a/images/.gitkeep b/transcript_sampler/images/.gitkeep
similarity index 100%
rename from images/.gitkeep
rename to transcript_sampler/images/.gitkeep
diff --git a/images/screenshot_git_tutorial_1_hGillet.png b/transcript_sampler/images/screenshot_git_tutorial_1_hGillet.png
similarity index 100%
rename from images/screenshot_git_tutorial_1_hGillet.png
rename to transcript_sampler/images/screenshot_git_tutorial_1_hGillet.png
diff --git a/images/screenshot_git_tutorial_2_hGillet.png b/transcript_sampler/images/screenshot_git_tutorial_2_hGillet.png
similarity index 100%
rename from images/screenshot_git_tutorial_2_hGillet.png
rename to transcript_sampler/images/screenshot_git_tutorial_2_hGillet.png
diff --git a/images/screenshot_markdown_tutorial_hGillet.png b/transcript_sampler/images/screenshot_markdown_tutorial_hGillet.png
similarity index 100%
rename from images/screenshot_markdown_tutorial_hGillet.png
rename to transcript_sampler/images/screenshot_markdown_tutorial_hGillet.png
diff --git a/scripts/exon_length_filter.py b/transcript_sampler/obsolete_scripts/exon_length_filter.py
similarity index 100%
rename from scripts/exon_length_filter.py
rename to transcript_sampler/obsolete_scripts/exon_length_filter.py
diff --git a/scripts/org_test_representative.py b/transcript_sampler/obsolete_scripts/org_test_representative.py
similarity index 100%
rename from scripts/org_test_representative.py
rename to transcript_sampler/obsolete_scripts/org_test_representative.py
diff --git a/scripts/representative.py b/transcript_sampler/obsolete_scripts/representative.py
similarity index 100%
rename from scripts/representative.py
rename to transcript_sampler/obsolete_scripts/representative.py
diff --git a/scripts/transcript_extractor.py b/transcript_sampler/obsolete_scripts/transcript_extractor.py
similarity index 100%
rename from scripts/transcript_extractor.py
rename to transcript_sampler/obsolete_scripts/transcript_extractor.py
--
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