From cbae9956b20dd0cea1c026b4ad574955346783fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <mate.balajti@unibas.ch>
Date: Wed, 9 Aug 2023 17:33:52 +0200
Subject: [PATCH] refactor: update main.py for CI
---
tsg/main.py | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/tsg/main.py b/tsg/main.py
index e53a5ab..f85a8c6 100644
--- a/tsg/main.py
+++ b/tsg/main.py
@@ -58,9 +58,9 @@ def filter_df(gtf_df: pd.DataFrame, transcripts: list) -> pd.DataFrame:
& (gtf_df["free_text"].str.contains('transcript_support_level "1"'))
]
if len(transcripts) > 0:
- df_filter = df_filter["free_text"].str.contains(
+ df_filter = df_filter[df_filter["free_text"].str.contains(
"|".join(transcripts), regex=True
- )
+ )]
return df_filter
@@ -159,7 +159,6 @@ def write_gtf(gtf_df: pd.DataFrame, filename: str) -> None:
sep="\t",
header=False,
index=False,
- quoting=None,
quotechar="'",
mode="a",
)
@@ -226,7 +225,7 @@ class Gtf:
annotations_file,
sep="\t",
comment="#",
- names=self.dtypes.keys(),
+ names=list(self.dtypes.keys()),
dtype=self.dtypes,
chunksize=100000,
iterator=True,
@@ -515,15 +514,15 @@ def sample_transcripts(
transcript_count = row["count"]
transcript_df = annotations.pick_transcript(transcript_id)
- transcripts = TranscriptGenerator(
+ transcript_generator = TranscriptGenerator(
transcript_id,
transcript_count,
transcript_df,
prob_inclusion=prob_inclusion,
)
try:
- transcripts.write_annotations(output_annotations_file)
- transcripts.write_sequences(output_transcripts_file)
+ transcript_generator.write_annotations(output_annotations_file)
+ transcript_generator.write_sequences(output_transcripts_file)
except AttributeError:
pass
LOG.info("Done.")
--
GitLab