| Previous changeset 14:598e9172b8e7 (2020-12-18) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit a4e49466bf746633ddc26d052b65ca41576d18fb" |
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modified:
gstf_preparation.py |
| b |
| diff -r 598e9172b8e7 -r 9c62ad7dd113 gstf_preparation.py --- a/gstf_preparation.py Fri Dec 18 08:57:43 2020 +0000 +++ b/gstf_preparation.py Thu Apr 29 19:46:38 2021 +0000 |
| [ |
| @@ -136,7 +136,7 @@ elif cols[6] == '-': d['strand'] = -1 else: - raise Exception("Unrecognized strand '%s'" % cols[6]) + raise Exception(f"Unrecognized strand: {cols[6]}") if parent_dict is not None and 'Parent' in d: # a 3' UTR can be split among multiple exons # a 5' UTR can be split among multiple exons @@ -150,7 +150,7 @@ global gene_count gene = feature_to_dict(cols) if not gene['id']: - raise Exception("Id not found among column 9 attribute tags: %s" % cols[8]) + raise Exception(f"Id not found among column 9 attribute tags: {cols[8]}") gene.update({ 'member_id': gene_count, 'object_type': 'Gene', @@ -217,11 +217,11 @@ cds_list = cds_parent_dict[transcript_id] unique_cds_ids = {cds['id'] for cds in cds_list} if len(unique_cds_ids) > 1: - msg = """Found multiple CDS IDs (%s) for transcript '%s'. + msg = f"""Found multiple CDS IDs ({unique_cds_ids}) for transcript '{transcript_id}'. This is not supported by the Ensembl JSON format. If a CDS is split across multiple discontinuous genomic locations, the GFF3 standard requires that all corresponding lines use the same ID attribute.""" - raise Exception(msg % (unique_cds_ids, transcript_id)) + raise Exception(msg) cds_id = unique_cds_ids.pop() translation['id'] = cds_id cds_list.sort(key=lambda _: _['start']) @@ -292,7 +292,7 @@ cur.execute('INSERT INTO transcript (transcript_id, transcript_symbol, protein_id, biotype, is_canonical, gene_id) VALUES (?, ?, ?, ?, ?, ?)', to_insert) except Exception as e: - raise Exception("Error while inserting {} into transcript table: {}".format(str(to_insert), e)) + raise Exception(f"Error while inserting {to_insert} into transcript table: {e}") conn.commit() @@ -335,7 +335,7 @@ try: (species, filename) = gff3_arg.split(':') except ValueError: - raise Exception("Argument for --gff3 '%s' is not in the SPECIES:FILENAME format" % gff3_arg) + raise Exception(f"Argument for --gff3 '{gff3_arg}' is not in the SPECIES:FILENAME format") gene_dict = dict() transcript_dict = dict() exon_parent_dict = dict() @@ -355,7 +355,7 @@ continue cols = line.split('\t') if len(cols) != 9: - raise Exception("Line %i in file '%s': '%s' does not have 9 columns" % (i, filename, line)) + raise Exception(f"Line {i} in file '{filename}': '{line}' does not have 9 columns") feature_type = cols[2] try: if feature_type == 'gene': @@ -375,10 +375,10 @@ else: unimplemented_feature_nlines_dict[feature_type] = 0 except Exception as e: - print("Line %i in file '%s': %s" % (i, filename, e), file=sys.stderr) + print(f"Line {i} in file '{filename}': {e}", file=sys.stderr) for unimplemented_feature, nlines in unimplemented_feature_nlines_dict.items(): - print("Skipped %d lines in GFF3 file '%s': '%s' is not an implemented feature type" % (nlines, filename, unimplemented_feature), file=sys.stderr) + print(f"Skipped {nlines} lines in GFF3 file '{filename}': '{unimplemented_feature}' is not an implemented feature type", file=sys.stderr) join_dicts(gene_dict, transcript_dict, exon_parent_dict, cds_parent_dict, five_prime_utr_parent_dict, three_prime_utr_parent_dict) write_gene_dict_to_db(conn, gene_dict) @@ -410,7 +410,7 @@ if transcript: force_remove_id_version = True force_remove_id_version_file_list.append(fasta_arg) - print("Forcing removal of id version in FASTA file '%s'" % fasta_arg, file=sys.stderr) + print(f"Forcing removal of id version in FASTA file '{fasta_arg}'", file=sys.stderr) if not transcript: print(f"Transcript '{transcript_id}' in FASTA file '{fasta_arg}' not found in the gene feature information", file=sys.stderr) continue @@ -435,7 +435,7 @@ # first one to appear in the FASTA file is selected. selected_transcript_id = max(transcript_tuples, key=lambda transcript_tuple: transcript_tuple[2])[0] elif len(canonical_transcript_ids) > 1: - raise Exception("Gene %s has more than 1 canonical transcripts" % (gene_id)) + raise Exception(f"Gene {gene_id} has more than 1 canonical transcripts") else: selected_transcript_id = canonical_transcript_ids[0] selected_transcript_ids.append(selected_transcript_id) |