| Previous changeset 5:b3ba0c84667c (2018-04-16) Next changeset 7:9ef7661e8e9c (2018-04-25) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960 |
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modified:
gstf_preparation.py gstf_preparation.xml schema/gstf.mwb schema/gstf.png schema/gstf.svg test-data/test1.sqlite |
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added:
test-data/test1.ns.fasta test-data/test4.fasta test-data/test4.ns.fasta test-data/test4.sqlite test-data/test5.ns.fasta test-data/test5.sqlite test-data/test5_filtered.fasta |
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removed:
test-data/test2.sqlite |
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| diff -r b3ba0c84667c -r 56bbdbfe3eaa gstf_preparation.py --- a/gstf_preparation.py Mon Apr 16 14:05:09 2018 -0400 +++ b/gstf_preparation.py Wed Apr 25 11:00:33 2018 -0400 |
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| @@ -6,7 +6,7 @@ import sqlite3 import sys -version = "0.3.0" +version = "0.4.0" gene_count = 0 Sequence = collections.namedtuple('Sequence', ['header', 'sequence']) @@ -41,6 +41,10 @@ cur.execute('''CREATE TABLE gene ( gene_id VARCHAR PRIMARY KEY NOT NULL, gene_symbol VARCHAR, + seq_region_name VARCHAR NOT NULL, + seq_region_start INTEGER NOT NULL, + seq_region_end INTEGER NOT NULL, + seq_region_strand INTEGER NOT NULL, species VARCHAR NOT NULL, gene_json VARCHAR NOT NULL)''') cur.execute('CREATE INDEX gene_symbol_index ON gene (gene_symbol)') @@ -52,7 +56,7 @@ gene_id VARCHAR NOT NULL REFERENCES gene(gene_id))''') cur.execute('''CREATE VIEW transcript_species AS - SELECT transcript_id, species + SELECT transcript_id, species, seq_region_name FROM transcript JOIN gene ON transcript.gene_id = gene.gene_id''') @@ -225,8 +229,8 @@ # This can happen when loading a JSON file from Ensembl continue gene_id = gene['id'] - cur.execute('INSERT INTO gene (gene_id, gene_symbol, species, gene_json) VALUES (?, ?, ?, ?)', - (gene_id, gene.get('display_name', None), gene['species'], json.dumps(gene))) + cur.execute('INSERT INTO gene (gene_id, gene_symbol, seq_region_name, seq_region_start, seq_region_end, seq_region_strand, species, gene_json) VALUES (?, ?, ?, ?, ?, ?, ?, ?)', + (gene_id, gene.get('display_name', None), gene['seq_region_name'], gene['start'], gene['end'], gene['strand'], gene['species'], json.dumps(gene))) if "Transcript" in gene: for transcript in gene["Transcript"]: @@ -241,15 +245,15 @@ conn.commit() -def fetch_species_for_transcript(conn, transcript_id): +def fetch_species_and_seq_region_for_transcript(conn, transcript_id): cur = conn.cursor() - cur.execute('SELECT species FROM transcript_species WHERE transcript_id=?', + 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[0] + return results def fetch_gene_id_for_transcript(conn, transcript_id): @@ -280,8 +284,11 @@ parser.add_option('--fasta', action='append', default=[], help='Path of the input FASTA files') parser.add_option('-l', action='store_true', default=False, dest='longestCDS', help='Keep only the longest CDS per gene') parser.add_option('--headers', action='store_true', default=False, help='Change the header line of the FASTA sequences to the >TranscriptId_species format') + parser.add_option('--regions', default="", help='Comma-separated list of region IDs for which FASTA sequences should be filtered') parser.add_option('-o', '--output', help='Path of the output SQLite file') parser.add_option('--of', help='Path of the output FASTA file') + parser.add_option('--ff', help='Path of the filtered sequences output FASTA file') + options, args = parser.parse_args() if args: raise Exception('Use options to provide inputs') @@ -368,14 +375,15 @@ # 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()] - with open(options.of, 'w') as output_fasta_file: + 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: for entry in FASTAReader_gen(fasta_arg): transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0]) if options.longestCDS and transcript_id not in selected_transcript_ids: continue - species_for_transcript = fetch_species_for_transcript(conn, transcript_id) + 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) continue @@ -387,7 +395,10 @@ else: header = entry.header - output_fasta_file.write("%s\n%s\n" % (header, entry.sequence)) + if seq_region_for_transcript.lower() in regions: + filtered_fasta_file.write("%s\n%s\n" % (header, entry.sequence)) + else: + output_fasta_file.write("%s\n%s\n" % (header, entry.sequence)) conn.close() |
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| diff -r b3ba0c84667c -r 56bbdbfe3eaa gstf_preparation.xml --- a/gstf_preparation.xml Mon Apr 16 14:05:09 2018 -0400 +++ b/gstf_preparation.xml Wed Apr 25 11:00:33 2018 -0400 |
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| @@ -20,8 +20,12 @@ #if $longestCDS -l #end if +#if $regions + --regions '$regions' +#end if -o '$output_db' --of '$output_fasta' +--ff '$filtered_fasta' ]]> </command> @@ -36,11 +40,13 @@ <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" /> <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" /> <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the >TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" /> + <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" /> </inputs> <outputs> <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" /> <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" /> + <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences" /> </outputs> <tests> @@ -53,6 +59,7 @@ <output name="output_db" file="test1.sqlite" compare="sim_size" /> <output name="output_fasta" file="test1.fasta" /> + <output name="filtered_fasta" file="test1.ns.fasta" /> </test> <test> <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> @@ -63,6 +70,7 @@ <output name="output_db" file="test1.sqlite" compare="sim_size" /> <output name="output_fasta" file="test1_longest.fasta" /> + <output name="filtered_fasta" file="test1.ns.fasta" /> </test> <test> <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> @@ -73,6 +81,7 @@ <output name="output_db" file="test1.sqlite" compare="sim_size" /> <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> + <output name="filtered_fasta" file="test1.ns.fasta" /> </test> <test> <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" /> @@ -80,8 +89,20 @@ <param name="longestCDS" value="false" /> <param name="headers" value="true" /> - <output name="output_db" file="test2.sqlite" compare="sim_size" /> - <output name="output_fasta" file="test2.fasta" /> + <output name="output_db" file="test4.sqlite" compare="sim_size" /> + <output name="output_fasta" file="test4.fasta" /> + <output name="filtered_fasta" file="test4.ns.fasta" /> + </test> + <test> + <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" /> + <param name="json" ftype="json" value="gene.json" /> + <param name="longestCDS" value="false" /> + <param name="headers" value="true" /> + <param name="regions" value="X" /> + + <output name="output_db" file="test5.sqlite" compare="sim_size" /> + <output name="output_fasta" file="test5_filtered.fasta" /> + <output name="filtered_fasta" file="test5.ns.fasta" /> </test> </tests> <help> |
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| diff -r b3ba0c84667c -r 56bbdbfe3eaa schema/gstf.png |
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| diff -r b3ba0c84667c -r 56bbdbfe3eaa schema/gstf.svg --- a/schema/gstf.svg Mon Apr 16 14:05:09 2018 -0400 +++ b/schema/gstf.svg Wed Apr 25 11:00:33 2018 -0400 |
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| diff -r b3ba0c84667c -r 56bbdbfe3eaa test-data/test4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4.fasta Wed Apr 25 11:00:33 2018 -0400 |
| b |
| b'@@ -0,0 +1,1265 @@\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' |
| b |
| diff -r b3ba0c84667c -r 56bbdbfe3eaa test-data/test4.sqlite |
| b |
| Binary file test-data/test4.sqlite has changed |
| b |
| diff -r b3ba0c84667c -r 56bbdbfe3eaa test-data/test5.ns.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5.ns.fasta Wed Apr 25 11:00:33 2018 -0400 |
| b |
| b'@@ -0,0 +1,423 @@\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+TGTGGCTGCATGATCATTGAAGATGAAGA'..b'TGAGAAACCAGCTCATCACTCGTGTACCTCTGGGCTCTGTCATCAAG\n+TGTATAGTTTATTACAAAGAGCCCTTCTGGAGGCATAAGGATTACTGTGGAAGCATGATT\n+ATTGAAGGAGAGGAAGCTCCAATCGCCTACACGTTGGATGATTCCAAGCCTGATGGCAGC\n+TGTGCCGCCATCATAGGATTTATCCTTGCCCACAAAGCCAGAAAACTGGCCCGTCTTACC\n+AAAGAAGAAAGGCTGAAGAAACTTTGCGACCTCTATGCAAAAGTTCTGGGTTCAAAAGAA\n+GCTTTGAACCCCGTGCACTATGAAGAGAAGAACTGGTGCGAGGAGCAGTACTCGGCGGGC\n+TGCTACACGACCTACTTCCCCCCTGGGATCATGACTCAGTATGGAAGGGTTCTACGCCAG\n+CCAGTCGGCAGGATTTATTTCGCCGGCACGGAGACTGCCACGCACTGGAGTGGCTACATG\n+GAGGGGGCCGTGGAGGCCGGAGAGAGAGCGGCCCGAGAGATCCTGCATGCTATGGGAAAG\n+ATCCCAGAAGATGAAATCTGGCAGTCTGAACCAGAGTCCGTGGATGTGCCTGCGAAGCCC\n+ATTACCACGACCTTCTTGGAGAGACACTTGCCCTCGGTGCCCGGCCTGCTGAGGCTGATT\n+GGATTGACCGCCATCTTTTCAGCCACTGCTCTCGGCTACCTGGCCCACAAAAGGGGGCTA\n+CTCGTGCGGGTCTGA\n+>ENSSSCT00000023183_susscrofa\n+ATGGCAGCGGCCAAACTTCTGCATGACTCTGGCCTGAGTGTGATTGTTCTGGAAGCCCGG\n+GACCGCGTGGGAGGCAGGACTTACACCGTCAGGAACCAACAAGTTAAATATGTGGACCTT\n+GGAGGATCTTATGTTGGGCCAACTCAGAATCGCATCTTAAGATTGTCCAAGGAGCTAGGA\n+TTGGAGACCTACAAAGTGAATGAAGTGGAGCGTCTGATTCACTATATCAAAGGCAAATCC\n+TACCCCTTCAGGGGCCCATTACCACCTGTGAGGAATCCGATTACCTTCCTAGATCTTAAC\n+AACCTTTGGAGGACGGTGGATGACATGGGACGAGAGATTCCCAGTGATGCCCCATGGAAG\n+GCGCCCCTTGCAGAACAGTGGGACCAGATGACAATGAAGGAGCTGTTGGACAAGCTCTGC\n+TGGACTGAATCTTCGAAGCAGCTGGCCACCCTTTTTGTGAACCTGTGTGTCACCGCGGAG\n+ACCCATGAGGTCTCTGCTCTCTGGTTCCTGTGGTATGTGAAGCAGTGTGGAGGCACCACC\n+AGGATCATCTCAACAACTAACGGAGGGCAGGAGAGGAAATTTGTGGGCGGATCTGGTCAA\n+GTGACCGAGCGGATAAAGGACCTCCTTGGAGACCGAGTGAAGCTGGAGAGGCCTGTGGTC\n+CACATTGACCAGACAGGAGAAAATGTCCTCGTGGAGACCCTAAACCACGAGGTGTACGAG\n+GCTAAGTATGTGATTAGCGCCATTCCTCCTGTCCTGGGCATGAAGATTCATTTCAGTCCC\n+CCTCTGCCAATGATGAGAAACCAGCTCATCACTCGTGTACCTCTGGGCTCTGTCATCAAG\n+TGTATAGTTTATTACAAAGAGCCCTTCTGGAGGCATAAGGATTACTGTGGAAGCATGATT\n+ATTGAAGGAGAGGAAGCTCCAATCGCCTACACGTTGGATGATTCCAAGCCTGATGGCAGC\n+TGTGCCGCCATCATAGGATTTATCCTTGCCCACAAAGCCAGAAAACTGGCCCGTCTTACC\n+AAAGAAGAAAGGCTGAAGAAACTTTGCGACCTCTATGCAAAAGTTCTGGGTTCAAAAGAA\n+GCTTTGAACCCCGTGCACTATGAAGAGAAGAACTGGTGCGAGGAGCAGTACTCGGCGGGC\n+TGCTACACGACCTACTTCCCCCCTGGGATCATGACTCAGTATGGAAGGGTTCTACGCCAG\n+CCAGTCGGCAGGATTTATTTCGCCGGCACGGAGACTGCCACGCACTGGAGTGGCTACATG\n+GAGGGGGCCGTGGAGGCCGGAGAGAGAGCGGCCCGAGAGATCCTGCATGCTATGGGAAAG\n+ATCCCAGAAGATGAAATCTGGCAGTCTGAACCAGAGTCCGTGGATGTGCCTGCGAAGCCC\n+ATTACCACGACCTTCTTGGAGAGACACTTGCCCTCGGTGCCCGGCCTGCTGAGGCTGATT\n+GGATTGACCGCCATCTTTTCAGCCACTGCTCTCGGCTACCTGGCCCACAAAAGGGGGCTA\n+CTCGTGCGGGTCTGA\n+>ENSCAFT00000022963_canisfamiliaris\n+ATGAGCGGCAAGTGCGACGTGGTCATGGTGGGGGGCGGCATCTCAGGCATGGCAGCAGCC\n+AAACTTCTGCATGATTTTGGCCTGAACGTGGTTGTTCTGGAGGCCCGGGACCGAGTGGGA\n+GGCAGGACTTACACCATCAGGAACCAAAAGGTTAAATATTTGGACCTTGGAGGATCTTAT\n+GTTGGGCCAACTCAGAATTGTATCTTAAGGTTAGCCAAGGAGCTAGGATTGGAGACCTAC\n+AAAGTGAATGAAGTAGAGCGTCTCATCCATCATGTAAAGGGCAAATCGTACCCCTTCAGG\n+GGCCCCTTCCCACCTGTATGGAACCCAATTGCATACCTAGATCATAACAACCTCTGGAGG\n+ACGATGGACGACATGGGGCGAGAGATTCCCAGTGATGCCCCATGGAAGGCACCTCTTGCG\n+GAGGAGTGGGACCACATGACAATGAAGGAGCTTCTGGACAAGATCTGCTGGACAGAATCT\n+GCCAAGCAACTTGCTACTCTCTTTGTGAATCTGTGTGTCACTGCAGAGACCCATGAGGTC\n+TCTGCTCTCTGGTTCCTGTGGTATGTGAAGCAGTGTGGAGGCACGACCAGGATCATCTCA\n+ACAACCAATGGAGGGCAGGAGAGAAAATTTGTGGGCGGATCTGGTCAAGTGAGTGAACGG\n+ATAATGGACCTCCTTGGAGACCAAGTGAAGCTGGAGAGGCCTGTGACCCACATTGACCAG\n+ACAGGAGAAAATGTCCTTGTGGAGACCCTAAACCATGAGGTGTATGAGGCTAAGTATGTG\n+ATTAGTGCCATTCCTCCTACTCTGGGCATGAAGATTCATTTCAACCCCCCTCTGCCAATG\n+ATGAGAAACCAGCTGATCACTCGTGTGCCTTTGGGCTCAGTCATCAAGTGCATAGTTTAT\n+TATAAAGAGCCCTTCTGGAGGAAAAAGGATTACTGTGGAACCATGATTATCGAAGGAGAG\n+GAAGCTCCAATTGCTTACACGTTGGATGATACCAAACCTGATGGCAACTATGCCGCCATA\n+ATGGGATTTATCCTTGCCCACAAAGCCAGAAAACTGGCACGTCTTACCAAAGATGAAAGG\n+ATGAAGAAACTTTGTGAGCTCTATGCAAAAGTCCTGGGTTCCCAAGAAGCTTTGCAGCCC\n+GTACACTACGAAGAGAAGAACTGGTGCGAGGAGCAGTACTCCGGGGGCTGCTACACCACC\n+TACTTTCCCCCTGGGATCATGACTCAATATGGAAGGGTTCTACGACAGCCTGTGGGCAGG\n+ATTTATTTTGCAGGCACGGAGACTGCCACCCACTGGAGTGGCTACATGGAGGGCGCTGTG\n+GAGGCTGGAGAGAGAGCGGCCCGAGAGATCCTGCATGCCATGGGGAAGATCCCAGAGGAT\n+GAAATCTGGCAGTCAGAACCAGAATCAGTGGATGTCCCTGCGCAGCCCATCACCACGACC\n+TTCTTGGAGAGACATTTGCCCTCTGTGCCAGGCCTGCTGAGGCTGATCGGATTGACCGCC\n+ATCTTTTCTGCAACTGCTCTTGGCGTCCTGGCACACAAAAGGGGTCTGCTTGTGCGGGTC\n+TAA\n' |
| b |
| diff -r b3ba0c84667c -r 56bbdbfe3eaa test-data/test5.sqlite |
| b |
| Binary file test-data/test5.sqlite has changed |
| b |
| diff -r b3ba0c84667c -r 56bbdbfe3eaa test-data/test5_filtered.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5_filtered.fasta Wed Apr 25 11:00:33 2018 -0400 |
| b |
| b'@@ -0,0 +1,842 @@\n+>ENSPTRT00000034846_pantroglodytes\n+ATGGACCCGGAATGCGCCCAGCTGCTCCCGGCTCTCTGTGCTGTTCTGGTAGATCCCAGG\n+CAGCCGGTGGCAGATGACACCTGTTTGGAGAAGCTCCTGGACTGGTTTAAAACGGTCACT\n+GAAGGAGAGTCCAGTGTCGTGCTGCTGCAGGAGCACCCCTGCCTGGTGGAGCTGCTGTCC\n+CATGTGCTGAAAGTCCAGGACCTGAGTTCTGGGGTCCTCTCCTTCTCACTCCGCCTGGCA\n+GGAACCTTCGCAGCCCAGGAAAACTGCTTCCAGTATCTTCAGCAGGGGGAGTTACTACCA\n+GGGCTCTTTGGGGAGGCAGGACCCCTCGGCCGAGCAGCCTGGGCCGTCCCCACCGTGCGC\n+AGCGGCTGGATCCAGGGCCTGCGCTCCCTGGCACAGCACCCCAGCGCCCTGCGCTTCCTG\n+GCCGACCACGGTGCGGTCGACACCATCTTCTCCCTTCAGGGAGACTCCAGCCTGTTTGTG\n+GCCTCGGCGGCCAGTCAGCTCCTGGTACACGTCCTGGCTTTGTCCATGCAAGGTGGAGCC\n+GAGGGACAGCCCTGCCTGCCGGGGGGTGACTGGCCCGCGTGTGCCCAGAGGATCATGGAT\n+CACGTTGAAGAGTCCTTGTGCTCCGCGGCCACCCCCAAGGTCACTCAGGCCCTGAACGTC\n+CTGACCACAACCTTCGGGCGCTGCCAGAGCCCCTGGACGGAAGCCCTGTGGGTGCGGCTG\n+AGTCCCCGCGTGGCGTGTCTGCTGGAGAGAGACCCCATCCCCGCCGCACACTCGTTCGTG\n+GACCTGCTTCTCTGTGTGGCTCGTTCTCCCGTGTTCAGTTCTTCCGACGGCAGCCTGTGG\n+GAGACAGTGGCGCGGGCTCTGAGCTGCCTGGGTCCCACCCACATGGGACCCCTGGCTTTG\n+GGGATCCTGAAGCTCGAGCACTGTCCACAGGCACTGAGGACCCAGGCCTTCCAGGTCCTT\n+CTCCAGCCCCTGGCCTGTGTCCTGAAGGCCACGGTTCAGGCCCCCGGACCCCCAGGCTTG\n+CTGGACGGGACGGCAGACGATGCCACGACGGTGGACACACTCCTGGCCTCCAAGTCGTCC\n+TGCGCGGGCCTCCTGTGCCGCACCCTGGCTCACCTGGAGGAGCTGCAGCCGCTGCCCCAG\n+CGCCCTTCACCGTGGCCCCAGGCGTCTCTACTGGGGGCTACAGTGACTGTCCTGCGGCTC\n+TGTGACGGCTCAGCTGCCCCTGCCTCCAGTGTGGGGGGCCACCTCTGTGGGACCCTGGCG\n+GGCTGCGTCCGGGTCCAGCGAGCAGCCCTCGACTTCCTGGGGACACTGTCACAGGGGACA\n+GGCCCCCAGGAGCTGGTGACGCAGGCGCTTGCTGTCCTCCTGGAGTGCCTCGAGAGCCCC\n+GGCTCCAGCCCCACGGTTCTGAAGAAGGCCTTCCAGGCCACGCTCAGGTGGCTCCTGAGC\n+TCACCCAAGACCCCCGGCTGCTCTGATCTCGGCCCCCTCATCCCGCAGTTCCTCAGAGAG\n+CTGTTCCCTGTGCTGCAGAAACGCCTGTGCCACCCCTGCTGGGAGGTGAGGGACTCCGCC\n+CTCGAGTTCCTGACCCAGCTGAGCAGGCACTGGGGAGGACAGGCCGACTTCAGATGCGCA\n+CTCTTGGCTTCAGAGGTGCCTGAGCTGGCCCTGCAGCTCCTCCAGGACCCTGAGAGTTAT\n+GTCCGAGCGAGCGCGGTGACCGCCATGGGGCAGCTGTCCAGCCAGGGCCTGCACGCCCCC\n+ACCAGCCCTGAGCATGCAGAGGCCCGGCAGAGCCTGTTCCCGGAGCTCCTGCACATCCTC\n+TCCGTAGACTCGGAGGGCTTCCCACGGCGGGCGGTCATGCAAGTCTTCACTGAGTGGCTG\n+CGGGACGGCCACGCCGACGCGGCCCGGGACACGGAGCAGTTCGTGGCCACTGTGCTGCAG\n+GTGGCGAGCCGGGACCTGGACTGGGAGGTCCGCGCCCAGGGCCTGGAGCTGGCCCTCGTG\n+TTCCTGGGCCAGACTTTGGGGCCGCCGCGTACCCACTGCCCCTATGCCGTGGCCCTACCC\n+GAGGTGGCCCCAGCCCAGCCACTCACCGAGGCACTGAGGGCTCTCTGCCACGTGGGGCTC\n+TTTGACTTCGCCTTTTGTGCCTTGTTTGACTGCGACCGCCCTGTGGCGCAGAAGTCTTGT\n+GACCTCCTTCTCTTCCTGAGGGACAAGATTGCTTCCTACAGCAGCCTGCGGGAGGCCAGG\n+GGCGGCCCCAACACTGCCTCCGCAGAGGCCACCCTGCCGAGGTGGCGGGCGGGTGAGCAG\n+GCCCAGCCCCCAGGGGACCAGGAGCCTGAGGCTGTGCTGGCCATGCTCAGGTCCCTAGAC\n+CTGGAGGGCCTGCGGAGCACACTGGCCGAGAGCAGCGACCACGTGGAGAAGAGTCCCCAG\n+TCCCTCCTGCAGGACATGCTGGCCACGGGAGGCTTCCTGCAGGGGGATGAGGCCGACTGC\n+TACTGA\n+>ENST00000340611_homosapiens\n+ATGGACCCAGAATGCGCCCAGCTGCTCCCGGCTCTCTGTGCTGTTCTGGTAGATCCCAGG\n+CAGCCGGTGGCAGATGACACCTGTTTGGAGAAGCTCCTGGACTGGTTTAAAACGGTCACT\n+GAAGGAGAGTCCAGTGTCGTGCTGCTGCAGGAGCACCCCTGCCTGGTGGAGCTGCTGTCC\n+CATGTGCTGAAAGTCCAGGACCTGAGTTCTGGGGTCCTCTCCTTCTCACTGCGCCTGGCA\n+GGAACCTTCGCAGCCCAGGAAAACTGCTTCCAGTATCTTCAGCAGGGGGAGTTACTACCA\n+GGGCTCTTTGGGGAGCCAGGACCCCTCGGCCGAGCAACCTGGGCCGTCCCCACCGTGCGC\n+AGCGGCTGGATCCAGGGCCTGCGCTCCCTGGCACAGCACCCCAGCGCCCTGCGCTTCCTG\n+GCCGACCATGGTGCGGTCGACACCATCTTCTCCCTGCAGGGAGACTCCAGCCTGTTTGTG\n+GCCTCGGCGGCCAGTCAGCTCCTGGTGCACGTCCTGGCTTTGTCCATGCGAGGTGGAGCC\n+GAGGGGCAGCCCTGCCTGCCGGGGGGTGACTGGCCCGCGTGTGCCCAGAAGATCATGGAT\n+CACGTTGAAGAGTCCTTGTGCTCCGCGGCCACCCCCAAGGTCACTCAGGCCCTGAACGTC\n+CTGACCACGACCTTCGGGCGCTGCCAGAGCCCCTGGACGGAAGCCCTGTGGGTGCGGCTG\n+AGTCCCCGCGTGGCCTGTCTGCTGGAGAGAGACCCCATCCCCGCCGCACACTCGTTCGTG\n+GACCTGCTTCTCTGTGTGGCTCGTTCTCCCGTGTTCAGTTCTTCCGACGGCAGCCTGTGG\n+GAGACAGTGGCGCGGGCTCTGAGCTGCCTGGGTCCCACCCACATGGGACCCCTGGCTTTG\n+GGGATCCTGAAGCTCGAGCACTGTCCACAGGCACTGAGGACCCAGGCCTTCCAGGTCCTT\n+CTCCAGCCCCTGGCCTGTGTCCTGAAGGCCACGGTTCAGGCCCCCGGACCCCCAGGCTTG\n+CTGGACGGGACGGCAGACGATGCCACGACGGTGGACACACTCCTGGCCTCCAAGTCGTCC\n+TGCGCCGGCCTCCTGTGCCGCACCCTGGCTCACCTGGAGGAGCTGCAGCCGCTGCCCCAG\n+CGCCCTTCACCGTGGCCCCAGGCGTCTCTACTGGGGGCTACAGTGACTGTCCTGCGGCTC\n+TGTGACGGCTCGGCTGCCCCTGCCTCCAGTGTGGGGGGCCACCTCTGTGGGACCCTGGCG\n+GGCTGCGTCCGGGTCCAGCGAGCAGCCCTCGACTTCCTGGGGACGCTGTCACAGGGGACA\n+'..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' |
