From f8aefb8283986d1d02be9ad6cf3e10a9c2b3dc8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <mate.balajti@unibas.ch> Date: Mon, 4 Sep 2023 16:50:44 +0200 Subject: [PATCH] refactor: update main.py with TSL support --- setup.py | 2 +- tsg/main.py | 13 ++++++------- 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/setup.py b/setup.py index 7ebb48d..638df50 100644 --- a/setup.py +++ b/setup.py @@ -12,7 +12,7 @@ URL = ('https://git.scicore.unibas.ch/zavolan_group/' setup( name='transcript-structure-generator', - version='0.1.0', + version='0.2.0', url=URL, license='MIT', author='Larissa Glass, Michael Zimmermann, Andri Fraenkl', diff --git a/tsg/main.py b/tsg/main.py index c86c741..8307b79 100644 --- a/tsg/main.py +++ b/tsg/main.py @@ -55,7 +55,7 @@ def filter_df(gtf_df: pd.DataFrame, transcripts: list) -> pd.DataFrame: transcripts = [] df_filter = gtf_df[ (gtf_df["feature"] == "exon") - & (gtf_df["free_text"].str.contains('transcript_support_level "1"')) + & (gtf_df["free_text"].str.contains('transcript_support_level "1')) ] if len(transcripts) > 0: df_filter = df_filter[df_filter["free_text"].str.contains( @@ -316,16 +316,15 @@ class TranscriptGenerator: strands = transcript_df["strand"].unique() if len(transcript_df) == 0: LOG.warning( - "Transcript %s can't be sampled. \ - Annotation is missing", transcript_id + "Transcript %s can't be sampled. " + "Annotation is missing or TSL is not 1.", transcript_id ) instance = None elif len(strands) > 1: LOG.warning( - "Transcript %s can't be sampled. Transcript generator \ - is not implemented for transcripts with \ - exons annotated on different strands", - transcript_id, + "Transcript %s can't be sampled. Transcript generator is " + "not implemented for transcripts with exons annotated on " + "different strands", transcript_id, ) instance = None else: -- GitLab