| Previous changeset 8:92f3966d5bc3 (2018-05-16) Next changeset 10:e8e75a79de59 (2019-10-31) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 2f56285b1ef694d732c8b2637e3e924f8a626e55 |
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modified:
gstf_preparation.py |
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removed:
test-data/test2.fasta |
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| diff -r 92f3966d5bc3 -r f4acbfe8d6fe gstf_preparation.py --- a/gstf_preparation.py Wed May 16 20:03:57 2018 -0400 +++ b/gstf_preparation.py Wed Oct 17 07:31:29 2018 -0400 |
| [ |
| @@ -264,10 +264,10 @@ cur.execute('SELECT species, seq_region_name FROM transcript_species WHERE transcript_id=?', (transcript_id, )) - results = cur.fetchone() - if not results: - return None - return results + row = cur.fetchone() + if not row: + return (None, None) + return row def fetch_gene_id_for_transcript(conn, transcript_id): @@ -275,17 +275,18 @@ cur.execute('SELECT gene_id FROM transcript WHERE transcript_id=?', (transcript_id, )) - results = cur.fetchone() - if not results: + row = cur.fetchone() + if not row: return None - return results[0] + return row[0] -def remove_id_version(s): +def remove_id_version(s, force=False): """ - Remove the optional '.VERSION' from an Ensembl id. + Remove the optional '.VERSION' from an id if it's an Ensembl id or if + `force` is True. """ - if s.startswith('ENS'): + if force or s.startswith('ENS'): return s.split('.')[0] else: return s @@ -358,7 +359,7 @@ print("Line %i in file '%s': %s" % (i, filename, e), file=sys.stderr) for unimplemented_feature, nlines in unimplemented_feature_nlines_dict.items(): - print("Skipped %d lines in file '%s': '%s' is not an implemented feature type" % (nlines, filename, unimplemented_feature), file=sys.stderr) + print("Skipped %d lines in GFF3 file '%s': '%s' is not an implemented feature type" % (nlines, filename, unimplemented_feature), 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) @@ -367,47 +368,68 @@ with open(json_arg) as f: write_gene_dict_to_db(conn, json.load(f)) - if options.longestCDS: - gene_transcripts_dict = dict() - for fasta_arg in options.fasta: - for entry in FASTAReader_gen(fasta_arg): - # Extract the transcript id by removing everything after the first space and then removing the version if it is an Ensembl id - transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0]) + # Read the FASTA files a first time to: + # - determine for each file if we need to force the removal of the version + # from the transcript id + # - fill gene_transcripts_dict when keeping only the longest CDS per gene + force_remove_id_version_file_list = [] + gene_transcripts_dict = dict() + for fasta_arg in options.fasta: + force_remove_id_version = False + found_gene_transcript = False + for entry in FASTAReader_gen(fasta_arg): + # Extract the transcript id by removing everything after the first space and then removing the version if needed + transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0], force_remove_id_version) - if len(entry.sequence) % 3 != 0: - print("Transcript '%s' in file '%s' has a coding sequence length which is not multiple of 3" % (transcript_id, fasta_arg), file=sys.stderr) - continue + if len(entry.sequence) % 3 != 0: + continue + gene_id = fetch_gene_id_for_transcript(conn, transcript_id) + if not gene_id and not found_gene_transcript: + # We have not found a proper gene transcript in this file yet, + # try to force the removal of the version from the transcript id + transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0], True) gene_id = fetch_gene_id_for_transcript(conn, transcript_id) - if not gene_id: - print("Transcript '%s' in file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr) - continue + # Remember that we need to force the removal for this file + if gene_id: + 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) + if not gene_id: + print("Transcript '%s' in FASTA file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr) + continue + if options.longestCDS: + found_gene_transcript = True + else: + break - if gene_id in gene_transcripts_dict: - gene_transcripts_dict[gene_id].append((transcript_id, len(entry.sequence))) - else: - gene_transcripts_dict[gene_id] = [(transcript_id, len(entry.sequence))] + if gene_id in gene_transcripts_dict: + gene_transcripts_dict[gene_id].append((transcript_id, len(entry.sequence))) + else: + gene_transcripts_dict[gene_id] = [(transcript_id, len(entry.sequence))] - # For each gene, select the transcript with the longest sequence - # If more than one transcripts have the same longest sequence for a gene, the - # first one to appear in the FASTA file is selected + if options.longestCDS: + # For each gene, select the transcript with the longest sequence. + # If more than one transcripts have the same longest sequence for a + # gene, the first one to appear in the FASTA file is selected selected_transcript_ids = [max(transcript_id_lengths, key=lambda _: _[1])[0] for transcript_id_lengths in gene_transcripts_dict.values()] regions = [_.strip().lower() for _ in options.regions.split(",")] with open(options.of, 'w') as output_fasta_file, open(options.ff, 'w') as filtered_fasta_file: for fasta_arg in options.fasta: + force_remove_id_version = fasta_arg in force_remove_id_version_file_list for entry in FASTAReader_gen(fasta_arg): - transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0]) + transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0], force_remove_id_version) if options.longestCDS and transcript_id not in selected_transcript_ids: continue if len(entry.sequence) % 3 != 0: - print("Transcript '%s' in file '%s' has a coding sequence length which is not multiple of 3" % (transcript_id, fasta_arg), file=sys.stderr) + print("Transcript '%s' in FASTA file '%s' has a coding sequence length which is not multiple of 3" % (transcript_id, fasta_arg), file=sys.stderr) continue species_for_transcript, seq_region_for_transcript = fetch_species_and_seq_region_for_transcript(conn, transcript_id) if not species_for_transcript: - print("Transcript '%s' in file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr) + print("Transcript '%s' in FASTA file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr) continue if options.headers: |
| b |
| diff -r 92f3966d5bc3 -r f4acbfe8d6fe test-data/test2.fasta --- a/test-data/test2.fasta Wed May 16 20:03:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1265 +0,0 @@\n->ENST00000338702_homosapiens\n-ATGGAGAATCAAGAGAAGGCGAGTATCGCGGGCCACATGTTCGACGTAGTCGTGATCGGA\n-GGTGGCATTTCAGGACTATCTGCTGCCAAACTCTTGACTGAATATGGCGTTAGTGTTTTG\n-GTTTTAGAAGCTCGGGACAGGGTTGGAGGAAGAACATATACTATAAGGAATGAGCATGTT\n-GATTACGTAGATGTTGGTGGAGCTTATGTGGGACCAACCCAAAACAGAATCTTACGCTTG\n-TCTAAGGAGCTGGGCATAGAGACTTACAAAGTGAATGTCAGTGAGCGTCTCGTTCAATAT\n-GTCAAGGGGAAAACATATCCATTTCGGGGCGCCTTTCCACCAGTATGGAATCCCATTGCA\n-TATTTGGATTACAATAATCTGTGGAGGACAATAGATAACATGGGGAAGGAGATTCCAACT\n-GATGCACCCTGGGAGGCTCAACATGCTGACAAATGGGACAAAATGACCATGAAAGAGCTC\n-ATTGACAAAATCTGCTGGACAAAGACTGCTAGGCGGTTTGCTTATCTTTTTGTGAATATC\n-AATGTGACCTCTGAGCCTCACGAAGTGTCTGCCCTGTGGTTCTTGTGGTATGTGAAGCAG\n-TGCGGGGGCACCACTCGGATATTCTCTGTCACCAATGGTGGCCAGGAACGGAAGTTTGTA\n-GGTGGATCTGGTCAAGTGAGCGAACGGATAATGGACCTCCTCGGAGACCAAGTGAAGCTG\n-AACCATCCTGTCACTCACGTTGACCAGTCAAGTGACAACATCATCATAGAGACGCTGAAC\n-CATGAACATTATGAGTGCAAATACGTAATTAATGCGATCCCTCCGACCTTGACTGCCAAG\n-ATTCACTTCAGACCAGAGCTTCCAGCAGAGAGAAACCAGTTAATTCAGCGGCTTCCAATG\n-GGAGCTGTCATTAAGTGCATGATGTATTACAAGGAGGCCTTCTGGAAGAAGAAGGATTAC\n-TGTGGCTGCATGATCATTGAAGATGAAGATGCTCCAATTTCAATAACCTTGGATGACACC\n-AAGCCAGATGGGTCACTGCCTGCCATCATGGGCTTCATTCTTGCCCGGAAAGCTGATCGA\n-CTTGCTAAGCTACATAAGGAAATAAGGAAGAAGAAAATCTGTGAGCTCTATGCCAAAGTG\n-CTGGGATCCCAAGAAGCTTTACATCCAGTGCATTATGAAGAGAAGAACTGGTGTGAGGAG\n-CAGTACTCTGGGGGCTGCTACACGGCCTACTTCCCTCCTGGGATCATGACTCAATATGGA\n-AGGGTGATTCGTCAACCCGTGGGCAGGATTTTCTTTGCGGGCACAGAGACTGCCACAAAG\n-TGGAGCGGCTACATGGAAGGGGCAGTTGAGGCTGGAGAACGAGCAGCTAGGGAGGTCTTA\n-AATGGTCTCGGGAAGGTGACCGAGAAAGATATCTGGGTACAAGAACCTGAATCAAAGGAC\n-GTTCCAGCGGTAGAAATCACCCACACCTTCTGGGAAAGGAACCTGCCCTCTGTTTCTGGC\n-CTGCTGAAGATCATTGGATTTTCCACATCAGTAACTGCCCTGGGGTTTGTGCTGTACAAA\n-TACAAGCTCCTGCCACGGTCTTGA\n->ENST00000542639_homosapiens\n-ATGGGGAAGGAGATTCCAACTGATGCACCCTGGGAGGCTCAACATGCTGACAAATGGGAC\n-AAAATGACCATGAAAGAGCTCATTGACAAAATCTGCTGGACAAAGACTGCTAGGCGGTTT\n-GCTTATCTTTTTGTGAATATCAATGTGACCTCTGAGCCTCACGAAGTGTCTGCCCTGTGG\n-TTCTTGTGGTATGTGAAGCAGTGCGGGGGCACCACTCGGATATTCTCTGTCACCAATGGT\n-GGCCAGGAACGGAAGTTTGTAGGTGGATCTGGTCAAGTGAGCGAACGGATAATGGACCTC\n-CTCGGAGACCAAGTGAAGCTGAACCATCCTGTCACTCACGTTGACCAGTCAAGTGACAAC\n-ATCATCATAGAGACGCTGAACCATGAACATTATGAGTGCAAATACGTAATTAATGCGATC\n-CCTCCGACCTTGACTGCCAAGATTCACTTCAGACCAGAGCTTCCAGCAGAGAGAAACCAG\n-TTAATTCAGCGGCTTCCAATGGGAGCTGTCATTAAGTGCATGATGTATTACAAGGAGGCC\n-TTCTGGAAGAAGAAGGATTACTGTGGCTGCATGATCATTGAAGATGAAGATGCTCCAATT\n-TCAATAACCTTGGATGACACCAAGCCAGATGGGTCACTGCCTGCCATCATGGGCTTCATT\n-CTTGCCCGGAAAGCTGATCGACTTGCTAAGCTACATAAGGAAATAAGGAAGAAGAAAATC\n-TGTGAGCTCTATGCCAAAGTGCTGGGATCCCAAGAAGCTTTACATCCAGTGCATTATGAA\n-GAGAAGAACTGGTGTGAGGAGCAGTACTCTGGGGGCTGCTACACGGCCTACTTCCCTCCT\n-GGGATCATGACTCAATATGGAAGGGTGATTCGTCAACCCGTGGGCAGGATTTTCTTTGCG\n-GGCACAGAGACTGCCACAAAGTGGAGCGGCTACATGGAAGGGGCAGTTGAGGCTGGAGAA\n-CGAGCAGCTAGGGAGGTCTTAAATGGTCTCGGGAAGGTGACCGAGAAAGATATCTGGGTA\n-CAAGAACCTGAATCAAAGGACGTTCCAGCGGTAGAAATCACCCACACCTTCTGGGAAAGG\n-AACCTGCCCTCTGTTTCTGGCCTGCTGAAGATCATTGGATTTTCCACATCAGTAACTGCC\n-CTGGGGTTTGTGCTGTACAAATACAAGCTCCTGCCACGGTCTTGA\n->ENSPTRT00000040520_pantroglodytes\n-ATGGAGAATCAAGAGAAGGCGAGTATCGCGGGCCACATGTTCGACGTAGTCGTGATCGGA\n-GGTGGCATTTCAGGACTATCTGCTGCCAAACTCTTGACTGAATATGGCGTTAGTGTTTTA\n-GTTTTAGAAGCTCGGGACAGGGTTGGAGGAAGAACATATACTATAAGGAATGAGCATGTT\n-GATTACGTAGATGTTGGTGGAGCTTATGTGGGACCAACCCAAAACAGAATCTTACGCTTG\n-TCTAAGGAGCTGGGCATAGAGACTTACAAAGTGAATGTCAGTGAGCGTCTCGTTCAATAT\n-GTCAAGGGGAAAACATATCCATTTCGGGGCGCCTTTCCACCAGTATGGAATCCCATTGCA\n-TATTTGGATTACAATAATCTGTGGCGGACAATAGATAACATGGGGAAGGAGATTCCAAAT\n-GATGCACCCTGGGAGGCTCAACATGCTGACGAATGGGACAAAATGACCATGAAAGAGCTC\n-ATTGACAAAATCTGCTGGACAAAGACTGCTAGGCGGTTTGCTTATCTTTTTGTGAATATC\n-AATGTGACCTCTGAGCCTCACGAAGTGTCTGCCCTGTGGTTCTTGTGGTATGTGAAGCAG\n-TGCGGGGGCACCACTCGGATATTCTCTGTCACCAATGGCGGCCAGGAACGGAAGTTTGTA\n-GGTGGATCTGGTCAAGTGAGCGAACGGATAATGGACCTCCTTGGAGACCAAGTGAAGCTG\n-AACCATCCTGTCACTCATGTTGACCAGTCAAGTGACAACATCATCATAGAGACACTGAAC\n-CATGAACATTATGAGTGCAAATACGTAATTAATGCGATCCCTCCGACCTTGACTGCCAAG\n-ATTCACTTCAGACCAGAGCTTCCAGCAGAGAGAAACCAGTTAATTCAGCGTCTTCCAATG\n-GGAGCTATCATTAAGTGCATGATGTATTACAAGGAGGCCTTCTGGAAGAAGAAGGATTAC\n-TGTGGCTGCATGATCATTGAAGATGAAG'..b'GCACAATCAG\n-AGTGAGTATGACGACTCGGCCAGCGAGTGCTGCTCATGTCCTAAGACTGACTCTCAGATC\n-CTGAAGGAGCTGGAGGAGTCTTCATTCAGGAAGACCTTCGAGGATTACCTGCACAACGTG\n-GTTTTTGTTCCCAGAAAAACCTCTTCAGGCAATGGTGCTGAGGACACTAGGCCATCCCGA\n-AAGCGAAGATCCCTTGAAGAGGTGGGCAATGTGACAGCCACTACACCCACACTTCCAGAT\n-TTTCCCAACATCTCCTCCACCATCGCGCCCACAAGCCACGAAGAGCACAGACCATTTGAG\n-AAAGTAGTAAACAAGGAGTCACTTGTCATCTCTGGCCTGAGACACTTCACTGGGTACCGC\n-ATTGAGCTGCAGGCATGCAATCAGGACTCCCCAGAAGAGAGGTGCAGCGTGGCTGCCTAC\n-GTCAGTGCCCGGACCATGCCTGAAGCTAAGGCAGATGACATCGTTGGCCCTGTGACCCAT\n-GAAATCTTTGAGAACAATGTTGTACACTTAATGTGGCAAGAGCCAAAGGAACCTAATGGT\n-CTGATTGTGCTATATGAAGTGAGCTATCGGCGATATGGTGATGAGGAGCTGCACCTCTGT\n-GTCTCCCGGAAGCATTTTGCCCTGGAGCGGGGCTGCAGGCTTCGAGGGCTCTCTCCAGGA\n-AACTACAGTGTTCGAGTCCGGGCTACCTCTCTGGCAGGAAATGGCTCCTGGACAGAACCC\n-ACCTATTTTTATGTGACTGATTATTTAGATGTCCCATCAAATATTGCCAAAATTATCATC\n-GGGCCCCTCATCTTCGTCTTCCTCTTCAGTGTCGTGATCGGAAGTATTTATCTATTCTTG\n-AGGAAGAGGCAGCCAGATGGGCCAATGGGACCACTGTACGCTTCTTCAAACCCAGAGTAC\n-CTCAGTGCCAGTGATGTCTTTCCATCTTCCGTATACGTTCCGGATGAGTGGGAGGTACCT\n-CGAGAGAAGATCACCCTCCTCCGAGAGCTGGGGCAGGGATCCTTCGGTATGGTGTACGAA\n-GGCAATGCCAAGGATATCATCAAGGGTGAGGTAGAGACCCGTGTTGCGGTGAAGACGGTC\n-AATGAGTCAGCCAGTCTTCGAGAACGGATCGAGTTCCTCAATGAGGCATCAGTCATGAAG\n-GGCTTCACCTGTCATCACGTGGTCCGCCTTCTTGGGGTGGTGTCCAAAGGCCAGCCCACA\n-TTGGTAGTGATGGAACTGATGGCTCATGGAGACCTGAAAAGTCACCTCCGTTCTCTGCGG\n-CCCGATGCTGAGAACAACCCAGGCCGTCCTCCCCCTACCTTGCAAGAAATGATTCAGATG\n-ACAGCAGAAATTGCCGATGGCATGGCATACTTGAACGCCAAGAAGTTTGTGCACCGGGAC\n-CTGGCAGCTCGGAACTGCATGGTTGCCCATGATTTTACTGTCAAAATCGGAGACTTTGGA\n-ATGACGAGAGACATCTACGAGACAGATTACTATCGGAAAGGGGGCAAGGGGTTGCTGCCC\n-GTGAGGTGGATGTCACCCGAGTCCCTGAAGGACGGAGTCTTCACTGCTTCTTCCGACATG\n-TGGTCCTTTGGGGTGGTCCTTTGGGAAATCACCAGCCTGGCTGAGCAACCTTACCAAGGC\n-CTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGCTATCTGGATCCCCCTGAT\n-AACTGTCCAGAGAGACTCACTGACCTGATGCGCATGTGCTGGCAGTTCAACCCCAAGATG\n-AGGCCGACCTTCCTGGAAATCGTCAACCTGCTCAAGGACGACCTCCACCCCAGCTTTCCG\n-GAAGTTTCCTTCTTCTACAGCGAGGAGAACAAGGCTCCCGAGAGTGAAGAGCTGGAGATG\n-GAGTTCGAGGACATGGAGAATGTCCCCTTGGATCGTTCCTCTCACTGTCAGAGAGAAGAG\n-GCTGGATGCCGGGAGGGAGGGTCCTCTCTGAGCATCAAACGGACCTATGATGAACACATC\n-CCCTACACCCACATGAACGGGGGCAAGAAGAATGGGCGGGTCCTCACCCTGCCGAGGTCG\n-AACCCTTCCTAA\n->ENSSSCT00000014817_susscrofa\n-GTGTGCCCAGGGATGGATATCCGGAATAACCTTACACGGCTGCACGAGTTGGCCAACTGC\n-TCGGTCATCGAAGGACATTTGCAGATCCTGTTGATGTTCAAAACGCGGCCCGAGGATTTC\n-CGAGACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTC\n-TACGGGCTGGAGAGCCTGAAGGACCTGTTCCCCAACCTCACCGTCATCCGGGGCTCACGC\n-CTCTTCTTTAACTATGCGCTGGTCATCTTTGAGATGGTTCACTTGAAGGAGCTTGGCCTC\n-TACAATTTGATGAACATCACCAGGGGTGCTGTCCGCATCGAGAAGAACAATGAGCTCTGC\n-TACCTGGCGACCATTGACTGGTCGCGCATCCTGGACTCTGTGGAGGATAATTACATTGTG\n-CTGAACAAAGACGACAACGAGGAGTGTGGGGACATTTGCCCAGGCACTGCGAAGGGCAAG\n-ACCAATTGCCCTGCCACCGTCATCAATGGGCAATTTGTCGAGCGGTGTTGGACGCACAGT\n-CACTGCCAGAAAGTGTGCCCGACCATCTGTAAGTCGCACGGCTGCACTGCTGAGGGCCTC\n-TGCTGTCACAGCGAGTGTTTGGGCAACTGCTCTGAGCCAGACGACCCCACCAAGTGCGTG\n-GCCTGCCGCAACTTCTACCTGGACGGCAGATGCGTGGAGACCTGCCCGCCCCCCTACTAC\n-CACTTCCAAGACTGGCGCTGCGTGAACTTCAGCTTCTGCCAGGACCTGCACAACAAATGC\n-AAGAACTCAAGGAGGCAGGGCTGCCACCAGTACGTCATTCACAACAACAAGTGTATCCCT\n-GAGTGCCCCTCAGGGTACACGATGAATTCCAGCAACTTGATGTGCACTCCGTGCCTAGGC\n-CCCTGTCCCAAAGTGTGTCACCTCCTGGAAGGCGAGAAGACCATCGACTCAGTGACATCC\n-GCCCAGGAGCTCCGAGGCTGCACCATTATCAACGGGAGCCTAATCATCAACATTCGAGGA\n-GGCAACAACCTGGCAGCCGAACTAGAGGCCAACCTTGGACTCATTGAGGAGATTTCAGGG\n-TACCTGAAAATCCGCCGATCCTATGCCCTCGTGTCACTTTCCTTCTTCCGGAAGTTGCGT\n-CTGATCCGAGGGGAGACGTTGGAAATTGGGAACTATTCTTTCTATGCCTTGGACAACCAG\n-AACCTAAGGCAACTGTGGGACTGGAGCAAACACAACCTCACCATCACTCAGGGGAAACTC\n-TTCTTCCATTATAATCCCAAACTCTGCTTGTCGGAAATTCACAAGATGGAGGAAGTTTCT\n-GGAACCAAGGGGCGCCAGGAGAGAAATGATATTGCCCTGAAGACCAATGGGGACCAGGCG\n-TCCTGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTATGACAAGATCTTG\n-CTGAAGTGGGAGCCGTATTGGCCCCCCGACTTCCGAGACCTCCTGGGGTTCATGCTCTTC\n-TACAAAGAGGCCCCTTATCAGAACGTGACGGAGTTTGACGGGCAGGATGCGTGTGGCTCC\n-AACAGCTGGACGGTGGTGGACATTGACCCGCCTACGAGGTCCAATGACCCCAAGTCCCAG\n-AACCATCCTGGGTGGCTGATGCGTGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTC\n-AAGACTTTGGTCACCTTTTCTGATGAACGACGCACCTATGGAGCCAAGAGTGACATCATC\n-TACGTCCAGACAGATGCCACAAGTAAGCATGTC\n-\n' 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