refactor: update main.py with TSL support

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',

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: