| Next changeset 1:a36645976342 (2017-03-16) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 |
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added:
gstf_preparation.py gstf_preparation.xml schema/gstf.mwb schema/gstf.png schema/gstf.svg test-data/CDS.fasta test-data/Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 test-data/Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa test-data/gene.json test-data/test1.fasta test-data/test1.sqlite test-data/test2.fasta test-data/test2.sqlite |
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| diff -r 000000000000 -r 28879ca33b5f gstf_preparation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gstf_preparation.py Wed Mar 15 20:18:57 2017 -0400 |
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| b'@@ -0,0 +1,343 @@\n+from __future__ import print_function\n+\n+import collections\n+import json\n+import optparse\n+import sqlite3\n+import sys\n+\n+version = "0.3.0"\n+gene_count = 0\n+\n+Sequence = collections.namedtuple(\'Sequence\', [\'header\', \'sequence\'])\n+\n+\n+def FASTAReader_gen(fasta_filename):\n+ with open(fasta_filename) as fasta_file:\n+ line = fasta_file.readline()\n+ while True:\n+ if not line:\n+ return\n+ assert line.startswith(\'>\'), "FASTA headers must start with >"\n+ header = line.rstrip()\n+ sequence_parts = []\n+ line = fasta_file.readline()\n+ while line and line[0] != \'>\':\n+ sequence_parts.append(line.rstrip())\n+ line = fasta_file.readline()\n+ sequence = "\\n".join(sequence_parts)\n+ yield Sequence(header, sequence)\n+\n+\n+def create_tables(conn):\n+ cur = conn.cursor()\n+\n+ cur.execute(\'\'\'CREATE TABLE meta (\n+ version VARCHAR PRIMARY KEY NOT NULL)\'\'\')\n+\n+ cur.execute(\'INSERT INTO meta (version) VALUES (?)\',\n+ (version, ))\n+\n+ cur.execute(\'\'\'CREATE TABLE gene (\n+ gene_id VARCHAR PRIMARY KEY NOT NULL,\n+ gene_symbol VARCHAR,\n+ species VARCHAR NOT NULL,\n+ gene_json VARCHAR NOT NULL)\'\'\')\n+ cur.execute(\'CREATE INDEX gene_symbol_index ON gene (gene_symbol)\')\n+\n+ cur.execute(\'\'\'CREATE TABLE transcript (\n+ transcript_id VARCHAR PRIMARY KEY NOT NULL,\n+ protein_id VARCHAR UNIQUE,\n+ protein_sequence VARCHAR,\n+ gene_id VARCHAR NOT NULL REFERENCES gene(gene_id))\'\'\')\n+\n+ cur.execute(\'\'\'CREATE VIEW transcript_species AS\n+ SELECT transcript_id, species\n+ FROM transcript JOIN gene\n+ ON transcript.gene_id = gene.gene_id\'\'\')\n+\n+ conn.commit()\n+\n+\n+def remove_type_from_list_of_ids(l):\n+ return \',\'.join(remove_type_from_id(_) for _ in l.split(\',\'))\n+\n+\n+def remove_type_from_id(id_):\n+ colon_index = id_.find(\':\')\n+ if colon_index >= 0:\n+ return id_[colon_index + 1:]\n+ else:\n+ return id_\n+\n+\n+def feature_to_dict(cols, parent_dict=None):\n+ d = {\n+ \'end\': int(cols[4]),\n+ \'start\': int(cols[3]),\n+ }\n+ for attr in cols[8].split(\';\'):\n+ if \'=\' in attr:\n+ (tag, value) = attr.split(\'=\')\n+ if tag == \'ID\':\n+ tag = \'id\'\n+ value = remove_type_from_id(value)\n+ elif tag == \'Parent\':\n+ value = remove_type_from_list_of_ids(value)\n+ d[tag] = value\n+ if cols[6] == \'+\':\n+ d[\'strand\'] = 1\n+ elif cols[6] == \'-\':\n+ d[\'strand\'] = -1\n+ else:\n+ raise Exception("Unrecognized strand \'%s\'" % cols[6])\n+ if parent_dict is not None and \'Parent\' in d:\n+ # a 3\' UTR can be split among multiple exons\n+ # a 5\' UTR can be split among multiple exons\n+ # a CDS can be part of multiple transcripts\n+ for parent in d[\'Parent\'].split(\',\'):\n+ if parent not in parent_dict:\n+ parent_dict[parent] = [d]\n+ else:\n+ parent_dict[parent].append(d)\n+ return d\n+\n+\n+def add_gene_to_dict(cols, species, gene_dict):\n+ global gene_count\n+ gene = feature_to_dict(cols)\n+ gene.update({\n+ \'member_id\': gene_count,\n+ \'object_type\': \'Gene\',\n+ \'seq_region_name\': cols[0],\n+ \'species\': species,\n+ \'Transcript\': [],\n+ \'display_name\': gene[\'Name\']\n+ })\n+ if gene[\'id\']:\n+ gene_dict[gene[\'id\']] = gene\n+ gene_count = gene_count + 1\n+\n+\n+def add_transcript_to_dict(cols, species, transcript_dict):\n+ transcript = feature_to_dict(cols)\n+ transcript.update({\n+ \'object_type\': \'Transcript\',\n+ \'seq_region_name\': cols[0],\n+ \'species\': species,\n+ })\n+ transcript_dict[transcript[\'id\']] = transcript\n+\n+\n+def add_exon_to_dict(cols, species, exon_parent_dict):\n+ exon = feature_to_dict(cols, exon_parent_dict)\n+ exon'..b'asta\', action=\'append\', default=[], help=\'Path of the input FASTA files\')\n+ parser.add_option(\'-o\', \'--output\', help=\'Path of the output SQLite file\')\n+ parser.add_option(\'--of\', help=\'Path of the output FASTA file\')\n+ options, args = parser.parse_args()\n+ if args:\n+ raise Exception(\'Use options to provide inputs\')\n+\n+ conn = sqlite3.connect(options.output)\n+ conn.execute(\'PRAGMA foreign_keys = ON\')\n+ create_tables(conn)\n+\n+ for gff3_arg in options.gff3:\n+ try:\n+ (species, filename) = gff3_arg.split(\':\')\n+ except ValueError:\n+ raise Exception("Argument for --gff3 \'%s\' is not in the SPECIES:FILENAME format" % gff3_arg)\n+ gene_dict = dict()\n+ transcript_dict = dict()\n+ exon_parent_dict = dict()\n+ cds_parent_dict = dict()\n+ five_prime_utr_parent_dict = dict()\n+ three_prime_utr_parent_dict = dict()\n+ with open(filename) as f:\n+ for i, line in enumerate(f, start=1):\n+ line = line.strip()\n+ if not line:\n+ # skip empty lines\n+ continue\n+ if line[0] == \'#\':\n+ # skip comment lines\n+ continue\n+ cols = line.split(\'\\t\')\n+ if len(cols) != 9:\n+ raise Exception("Line %i in file \'%s\': \'%s\' does not have 9 columns" % (i, filename, line))\n+ feature_type = cols[2]\n+ try:\n+ if feature_type == \'gene\':\n+ add_gene_to_dict(cols, species, gene_dict)\n+ elif feature_type in (\'mRNA\', \'transcript\'):\n+ add_transcript_to_dict(cols, species, transcript_dict)\n+ elif feature_type == \'exon\':\n+ add_exon_to_dict(cols, species, exon_parent_dict)\n+ elif feature_type == \'five_prime_UTR\':\n+ feature_to_dict(cols, five_prime_utr_parent_dict)\n+ elif feature_type == \'three_prime_UTR\':\n+ feature_to_dict(cols, three_prime_utr_parent_dict)\n+ elif feature_type == \'CDS\':\n+ add_cds_to_dict(cols, cds_parent_dict)\n+ else:\n+ print("Line %i in file \'%s\': \'%s\' is not an implemented feature type" % (i, filename, feature_type), file=sys.stderr)\n+ except Exception as e:\n+ print("Line %i in file \'%s\': %s" % (i, filename, e), file=sys.stderr)\n+\n+ join_dicts(gene_dict, transcript_dict, exon_parent_dict, cds_parent_dict, five_prime_utr_parent_dict, three_prime_utr_parent_dict)\n+ write_gene_dict_to_db(conn, gene_dict)\n+\n+ for json_arg in options.json:\n+ with open(json_arg) as f:\n+ write_gene_dict_to_db(conn, json.load(f))\n+\n+ with open(options.of, \'w\') as output_fasta_file:\n+ for fasta_arg in options.fasta:\n+ for entry in FASTAReader_gen(fasta_arg):\n+ # Extract the transcript id by removing everything after the first space and then removing the version if it is an Ensembl id\n+ transcript_id = remove_id_version(entry.header[1:].lstrip().split(\' \')[0])\n+ species_for_transcript = fetch_species_for_transcript(conn, transcript_id)\n+ if not species_for_transcript:\n+ print("Transcript \'%s\' not found in the gene feature information" % transcript_id, file=sys.stderr)\n+ continue\n+ # Remove any underscore in the species\n+ species_for_transcript = species_for_transcript.replace(\'_\', \'\')\n+ # Write the FASTA sequence using \'>TranscriptId_species\' as the header, as required by TreeBest\n+ output_fasta_file.write(">%s_%s\\n%s\\n" % (transcript_id, species_for_transcript, entry.sequence))\n+\n+ conn.close()\n+\n+\n+if __name__ == \'__main__\':\n+ __main__()\n' |
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| diff -r 000000000000 -r 28879ca33b5f gstf_preparation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gstf_preparation.xml Wed Mar 15 20:18:57 2017 -0400 |
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| @@ -0,0 +1,82 @@ +<tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.3.0"> + <description>converts data for the workflow</description> + <command detect_errors="exit_code"> +<![CDATA[ +python '$__tool_directory__/gstf_preparation.py' +#for $q in $queries + --gff3 '${q.genome}:${q.gff3_input}' +#end for +#if str($json) != 'None' + #for $v in $json + --json '$v' + #end for +#end if +#for $fasta_input in $fasta_inputs + --fasta '${fasta_input}' +#end for +-o '$output_db' +--of '$output_fasta' +]]> + </command> + + <inputs> + <repeat name="queries" title="GFF3 dataset"> + <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" /> + <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters"> + <validator type="empty_field" /> + </param> + </repeat> + <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" /> + <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" /> + </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" /> + </outputs> + + <tests> + <test> + <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> + <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" /> + <param name="genome" value="caenorhabditis_elegans" /> + <output name="output_db" file="test1.sqlite" compare="sim_size" /> + <output name="output_fasta" file="test1.fasta" /> + </test> + <test> + <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" /> + <param name="json" ftype="json" value="gene.json" /> + + <output name="output_db" file="test2.sqlite" compare="sim_size" /> + <output name="output_fasta" file="test2.fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format and modify the header lines of a corresponding CDS FASTA to be used with the GeneSeqToFamily workflow. + +Example GFF3 file:: + + scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding + scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31 + scaffold_0 MYZPE13164_Clone_G006_v1.0 three_prime_utr 44968 46637 . - . ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 44968 47432 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 46638 47432 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 53325 53539 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 53325 53539 . - 2 ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54614 54719 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54614 54719 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54852 55106 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54852 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 55107 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1 + scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1 + +The following features are parsed: **gene**, **mRNA**, **transcript**, **exon**, **five_prime_utr**, **three_prime_utr** and **CDS**, all other are ignored. Also, **ID** and **Parent** tags are needed to create relations. +]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 28879ca33b5f schema/gstf.mwb |
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| diff -r 000000000000 -r 28879ca33b5f schema/gstf.png |
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| diff -r 000000000000 -r 28879ca33b5f schema/gstf.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/schema/gstf.svg Wed Mar 15 20:18:57 2017 -0400 |
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| b |
| diff -r 000000000000 -r 28879ca33b5f test-data/CDS.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CDS.fasta Wed Mar 15 20:18:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,1265 @@\n+>ENST00000338702\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\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\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+TGTGGCTGCATGATCATTGAAGATGAAGATGCCCCAATTTCAATAACCTTGGATGACACC\n+AAGCC'..b'ATTCTCAAAAGCACAATCAG\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\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 000000000000 -r 28879ca33b5f test-data/Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 Wed Mar 15 20:18:57 2017 -0400 |
| [ |
| b'@@ -0,0 +1,199 @@\n+##gff-version 3\n+##sequence-region I 1 15072434\n+#!genome-build WormBase WBcel235\n+#!genome-version WBcel235\n+#!genome-date 2012-12\n+#!genome-build-accession NCBI:GCA_000002985.3\n+#!genebuild-last-updated 2015-10\n+I\tWormBase\tchromosome\t1\t15072434\t.\t.\t.\tID=chromosome:I;Alias=BX284601.5,NC_003279.8\n+###\n+I\tWormBase\tsnoRNA_gene\t3747\t3909\t.\t-\t.\tID=gene:WBGene00023193;Name=Y74C9A.6;biotype=snoRNA;gene_id=WBGene00023193;logic_name=wormbase_non_coding\n+I\tWormBase\tsnoRNA\t3747\t3909\t.\t-\t.\tID=transcript:Y74C9A.6;Parent=gene:WBGene00023193;Name=Y74C9A.6;biotype=snoRNA;transcript_id=Y74C9A.6\n+I\tWormBase\texon\t3747\t3909\t.\t-\t.\tParent=transcript:Y74C9A.6;Name=Y74C9A.6.e1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Y74C9A.6.e1;rank=1\n+###\n+I\tWormBase\tgene\t4119\t10230\t.\t-\t.\tID=gene:WBGene00022277;Name=homt-1;biotype=protein_coding;description=Alpha N-terminal protein methyltransferase 1 [Source:UniProtKB/Swiss-Prot%3BAcc:Q9N4D9];gene_id=WBGene00022277;logic_name=wormbase\n+I\tWormBase\tmRNA\t4119\t10230\t.\t-\t.\tID=transcript:Y74C9A.3;Parent=gene:WBGene00022277;Name=Y74C9A.3;biotype=protein_coding;transcript_id=Y74C9A.3\n+I\tWormBase\tthree_prime_UTR\t4119\t4220\t.\t-\t.\tParent=transcript:Y74C9A.3\n+I\tWormBase\texon\t4119\t4358\t.\t-\t.\tParent=transcript:Y74C9A.3;Name=Y74C9A.3.e5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Y74C9A.3.e5;rank=5\n+I\tWormBase\tCDS\t4221\t4358\t.\t-\t0\tID=CDS:Y74C9A.3;Parent=transcript:Y74C9A.3;protein_id=Y74C9A.3\n+I\tWormBase\texon\t5195\t5296\t.\t-\t.\tParent=transcript:Y74C9A.3;Name=Y74C9A.3.e4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Y74C9A.3.e4;rank=4\n+I\tWormBase\tCDS\t5195\t5296\t.\t-\t0\tID=CDS:Y74C9A.3;Parent=transcript:Y74C9A.3;protein_id=Y74C9A.3\n+I\tWormBase\texon\t6037\t6327\t.\t-\t.\tParent=transcript:Y74C9A.3;Name=Y74C9A.3.e3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Y74C9A.3.e3;rank=3\n+I\tWormBase\tCDS\t6037\t6327\t.\t-\t0\tID=CDS:Y74C9A.3;Parent=transcript:Y74C9A.3;protein_id=Y74C9A.3\n+I\tWormBase\texon\t9727\t9846\t.\t-\t.\tParent=transcript:Y74C9A.3;Name=Y74C9A.3.e2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Y74C9A.3.e2;rank=2\n+I\tWormBase\tCDS\t9727\t9846\t.\t-\t0\tID=CDS:Y74C9A.3;Parent=transcript:Y74C9A.3;protein_id=Y74C9A.3\n+I\tWormBase\tCDS\t10095\t10148\t.\t-\t0\tID=CDS:Y74C9A.3;Parent=transcript:Y74C9A.3;protein_id=Y74C9A.3\n+I\tWormBase\texon\t10095\t10230\t.\t-\t.\tParent=transcript:Y74C9A.3;Name=Y74C9A.3.e1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Y74C9A.3.e1;rank=1\n+I\tWormBase\tfive_prime_UTR\t10149\t10230\t.\t-\t.\tParent=transcript:Y74C9A.3\n+###\n+I\tWormBase\tgene\t10413\t16842\t.\t+\t.\tID=gene:WBGene00022276;Name=nlp-40;biotype=protein_coding;description=Neuropeptide-Like Protein [Source:RefSeq peptide%3BAcc:NP_001293206];gene_id=WBGene00022276;logic_name=wormbase\n+I\tWormBase\tmRNA\t10413\t16842\t.\t+\t.\tID=transcript:Y74C9A.2a.2;Parent=gene:WBGene00022276;Name=Y74C9A.2a.2;biotype=protein_coding;transcript_id=Y74C9A.2a.2\n+I\tWormBase\texon\t10413\t10585\t.\t+\t.\tParent=transcript:Y74C9A.2a.2;Name=Y74C9A.2a.2.e1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Y74C9A.2a.2.e1;rank=1\n+I\tWormBase\tfive_prime_UTR\t10413\t10585\t.\t+\t.\tParent=transcript:Y74C9A.2a.2\n+I\tWormBase\tfive_prime_UTR\t11618\t11640\t.\t+\t.\tParent=transcript:Y74C9A.2a.2\n+I\tWormBase\texon\t11618\t11689\t.\t+\t.\tParent=transcript:Y74C9A.2a.2;Name=Y74C9A.2a.1.e1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Y74C9A.2a.1.e1;rank=2\n+I\tWormBase\tCDS\t11641\t11689\t.\t+\t0\tID=CDS:Y74C9A.2a.2;Parent=transcript:Y74C9A.2a.2;protein_id=Y74C9A.2a.2\n+I\tWormBase\texon\t14951\t15160\t.\t+\t.\tParent=transcript:Y74C9A.2a.2;Name=Y74C9A.2a.1.e2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=Y74C9A.2a.1.e2;rank=3\n+I\tWormBase\tCDS\t14951\t15160\t.\t+\t2\tID=CDS:Y74C9A.2a.2;Parent=transcript:Y74C9A.2a.2;protein_id=Y74C9A.2a.2\n+I\tWormBase\tCDS\t16473\t16585\t.\t+\t2\tID=CDS:Y74C9A.2a.2;Parent=transcript:Y74C9A.2a.2;protein_id=Y74C9A.2a.2\n+I\tWormBase\texon\t16473\t16842\t.\t+\t.\tParent=transcript:Y74C9A.2a.2;Name=Y74C9A.2a.1.e3;constitutive=0;ens'..b'.4b;Parent=transcript:Y74C9A.4b;protein_id=Y74C9A.4b\n+I\tWormBase\texon\t26590\t26690\t.\t-\t.\tParent=transcript:Y74C9A.4b;Name=Y74C9A.4b.e2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Y74C9A.4b.e2;rank=2\n+I\tWormBase\tCDS\t26590\t26690\t.\t-\t2\tID=CDS:Y74C9A.4b;Parent=transcript:Y74C9A.4b;protein_id=Y74C9A.4b\n+I\tWormBase\texon\t26733\t26778\t.\t-\t.\tParent=transcript:Y74C9A.4b;Name=Y74C9A.4b.e1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Y74C9A.4b.e1;rank=1\n+I\tWormBase\tCDS\t26733\t26778\t.\t-\t0\tID=CDS:Y74C9A.4b;Parent=transcript:Y74C9A.4b;protein_id=Y74C9A.4b\n+I\tWormBase\tmRNA\t17483\t26781\t.\t-\t.\tID=transcript:Y74C9A.4a;Parent=gene:WBGene00022278;Name=Y74C9A.4a;biotype=protein_coding;transcript_id=Y74C9A.4a\n+I\tWormBase\tthree_prime_UTR\t17483\t17910\t.\t-\t.\tParent=transcript:Y74C9A.4a\n+I\tWormBase\texon\t17483\t17958\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Y74C9A.4a.e12;rank=12\n+I\tWormBase\tCDS\t17911\t17958\t.\t-\t0\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t18006\t18115\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e11;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Y74C9A.4a.e11;rank=11\n+I\tWormBase\tCDS\t18006\t18115\t.\t-\t2\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t19015\t19241\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e10;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Y74C9A.4a.e10;rank=10\n+I\tWormBase\tCDS\t19015\t19241\t.\t-\t1\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t20271\t20478\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e9;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Y74C9A.4a.e9;rank=9\n+I\tWormBase\tCDS\t20271\t20478\t.\t-\t2\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t20848\t20964\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e8;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Y74C9A.4a.e8;rank=8\n+I\tWormBase\tCDS\t20848\t20964\t.\t-\t2\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t21013\t21139\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e7;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Y74C9A.4a.e7;rank=7\n+I\tWormBase\tCDS\t21013\t21139\t.\t-\t0\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t24651\t24845\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e6;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=Y74C9A.4a.e6;rank=6\n+I\tWormBase\tCDS\t24651\t24845\t.\t-\t0\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t24929\t25090\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=Y74C9A.4a.e5;rank=5\n+I\tWormBase\tCDS\t24929\t25090\t.\t-\t0\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t25273\t25472\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e4;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Y74C9A.4a.e4;rank=4\n+I\tWormBase\tCDS\t25273\t25472\t.\t-\t2\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t26371\t26524\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=Y74C9A.4a.e3;rank=3\n+I\tWormBase\tCDS\t26371\t26524\t.\t-\t0\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t26590\t26681\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=Y74C9A.4a.e2;rank=2\n+I\tWormBase\tCDS\t26590\t26681\t.\t-\t2\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\tCDS\t26733\t26778\t.\t-\t0\tID=CDS:Y74C9A.4a;Parent=transcript:Y74C9A.4a;protein_id=Y74C9A.4a\n+I\tWormBase\texon\t26733\t26781\t.\t-\t.\tParent=transcript:Y74C9A.4a;Name=Y74C9A.4a.e1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Y74C9A.4a.e1;rank=1\n+I\tWormBase\tfive_prime_UTR\t26779\t26781\t.\t-\t.\tParent=transcript:Y74C9A.4a\n' |
| b |
| diff -r 000000000000 -r 28879ca33b5f test-data/Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa Wed Mar 15 20:18:57 2017 -0400 |
| [ |
| b'@@ -0,0 +1,156 @@\n+>Y74C9A.3 cds chromosome:WBcel235:I:4119:10230:-1 gene:WBGene00022277 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:homt-1 description:Alpha N-terminal protein methyltransferase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9N4D9]\n+ATGAGCTCTTCATCATCTTCTAGAATTCACAATGGTGAAGATGTTTATGAAAAGGCGGAG\n+GAATACTGGAGCCGCGCGAGCCAGGACGTCAACGGAATGCTCGGCGGATTCGAAGCGCTT\n+CACGCGCCCGACATATCGGCGTCGAAACGATTTATTGAAGGACTGAAGAAAAAGAATCTA\n+TTCGGCTACTTTGACTATGCACTGGACTGCGGAGCGGGTATCGGACGTGTTACAAAGCAT\n+CTCTTAATGCCATTCTTCTCGAAAGTTGATATGGAAGACGTCGTCGAGGAGTTGATCACG\n+AAAAGTGATCAATATATTGGAAAACATCCACGAATTGGAGATAAATTCGTCGAAGGACTG\n+CAGACGTTTGCACCGCCCGAACGACGTTATGATTTGATATGGATTCAATGGGTTTCAGGG\n+CATTTGGTTGATGAGGATTTGGTTGATTTCTTTAAAAGATGTGCGAAAGGACTGAAACCT\n+GGTGGATGTATTGTGCTCAAGGATAATGTGACAAATCACGAGAAACGGTTATTCGACGAT\n+GATGATCATAGTTGGACGAGAACAGAGCCCGAGCTTCTTAAAGCGTTCGCCGATTCTCAA\n+CTGGACATGGTCTCGAAAGCACTGCAAACCGGATTCCCAAAGGAGATTTATCCAGTAAAA\n+ATGTATGCATTGAAGCCTCAACACACCGGATTCACCAATAATTGA\n+>Y74C9A.2a.1 cds chromosome:WBcel235:I:11618:16842:1 gene:WBGene00022276 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:nlp-40 description:Neuropeptide-Like Protein [Source:RefSeq peptide;Acc:NP_001293206]\n+ATGAAACTCGTAATTCTGCTATCTTTTGTTGCGACAGTTGCGGTTTTTGCGGCTCCATCG\n+GCTCCGGCAGGTCTCGAGGAGAAGCTGCGTGCTCTTCAGGAGCAACTGTACAGTCTGGAG\n+AAAGAGAACGGAGTTGATGTGAAGCAAAAGGAGCAACCAGCAGCAGCCGACACATTCCTT\n+GGATTTGTTCCACAGAAGAGAATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAAT\n+GAGGATTCTAGAGCTCCATTGCTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGA\n+GCCGGAGAACGCCTCGGAGTCAACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAAT\n+CAATTCCAATAA\n+>Y74C9A.2a.2 cds chromosome:WBcel235:I:10413:16842:1 gene:WBGene00022276 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:nlp-40 description:Neuropeptide-Like Protein [Source:RefSeq peptide;Acc:NP_001293206]\n+ATGAAACTCGTAATTCTGCTATCTTTTGTTGCGACAGTTGCGGTTTTTGCGGCTCCATCG\n+GCTCCGGCAGGTCTCGAGGAGAAGCTGCGTGCTCTTCAGGAGCAACTGTACAGTCTGGAG\n+AAAGAGAACGGAGTTGATGTGAAGCAAAAGGAGCAACCAGCAGCAGCCGACACATTCCTT\n+GGATTTGTTCCACAGAAGAGAATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAAT\n+GAGGATTCTAGAGCTCCATTGCTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGA\n+GCCGGAGAACGCCTCGGAGTCAACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAAT\n+CAATTCCAATAA\n+>Y74C9A.2a.3 cds chromosome:WBcel235:I:11505:16842:1 gene:WBGene00022276 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:nlp-40 description:Neuropeptide-Like Protein [Source:RefSeq peptide;Acc:NP_001293206]\n+ATGAAACTCGTAATTCTGCTATCTTTTGTTGCGACAGTTGCGGTTTTTGCGGCTCCATCG\n+GCTCCGGCAGGTCTCGAGGAGAAGCTGCGTGCTCTTCAGGAGCAACTGTACAGTCTGGAG\n+AAAGAGAACGGAGTTGATGTGAAGCAAAAGGAGCAACCAGCAGCAGCCGACACATTCCTT\n+GGATTTGTTCCACAGAAGAGAATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAAT\n+GAGGATTCTAGAGCTCCATTGCTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGA\n+GCCGGAGAACGCCTCGGAGTCAACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAAT\n+CAATTCCAATAA\n+>Y74C9A.2b.1 cds chromosome:WBcel235:I:11499:16842:1 gene:WBGene00022276 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:nlp-40 description:Neuropeptide-Like Protein [Source:RefSeq peptide;Acc:NP_001293206]\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGAGCCGGAGAACGCCTCGGAGTC\n+AACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAATCAATTCCAATAA\n+>Y74C9A.2b.2 cds chromosome:WBcel235:I:11495:16793:1 gene:WBGene00022276 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:nlp-40 description:Neuropeptide-Like Protein [Source:RefSeq peptide;Acc:NP_001293206]\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGAGCCGGAGAACGCCTCGGAGTC\n+AACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAATCAATTCCAATAA\n+>Y74C9A.2b.3 cds chromosome:WBcel235:I:11623:16842:1 gene:WBGene00022276 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:nlp-40 description:Neuropeptide-Like Protein [Source:RefSeq peptide;Acc:NP_001293206]\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAG'..b'CAAAACTATAAAACAATGATTAATGTGCATTTGAATGAAACCGACACTTATGATGAACTA\n+TTCAAAGAGGTCAATCATTTGGAGAGGGTTCCGTCGGGATATTGTGAGAATTGCAATGCA\n+AAAAGTGATCTGTTGATTCTAAATCGTGTAATGTCGCGTCACGAATGTAAACCGTGTATC\n+CTTTATTTCCGTTTGATGCGTGTTCCACGTCCGGCAAGCCTCCGTGCACTGACAAAACGA\n+CGGCAACGAGTTTTATGTCCAGAATACATGAAAATTTATGTATACGGATATCTTGAGCTC\n+ATGGAGCCAGCCAACGGAAAAGCGATCAAACGGCTTGGAATTGGAAAAGAAAAAGAAGAA\n+GACGATGATATTATGGTGGTCGACGACTGCCTTCTCCGTAAACCATCAGGCCCCTACATT\n+GTGGAGCAATCGATTGAAGCTGATCCAATCGATGAGAATACGTGCAGAATGACACGGTGC\n+TTCGATACACCGGCTGCACTGGCATTAATTGATAATATCAAGAGAAAACATCATATGTGT\n+GTTCCACTTGTTTGGAGAGTTAAACAAACGAAATGTATGGAGGAGAACGAAATTCTGAAT\n+GAAGAAGCCCGTCAACAAATGTTCCGTGCAACAATGACATACAGCCGTGTACCAAAAGGA\n+GAAATTGCAAATTGGAAGAAAGATATGATGGCGTTGAAGGGAAGATTCGAGAGATTTACT\n+CCTGAACTAGATACTACTGCAACAAATGGCAATCGATCTGGAAAAGTCAGGATAAATTAT\n+GGTTGGAGTCCTGAGGAAAAGAAGAATGCTATTAGATGTTTCCACTGGTACAAGGACAAT\n+TTCGAGTTGATCGCCGAGTTGATGGCCACAAAAACTGTGGAACAAATCAAAAAGTTCTAT\n+ATGGACAATGAAAAGCTAATTTTGGAGTCAATCGACACGTATCGCGCCGAGCTCAAGTCA\n+AAACTCGGCAAATAA\n+>Y74C9A.4c cds chromosome:WBcel235:I:17483:26643:-1 gene:WBGene00022278 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:rcor-1 description:RCOR (REST CO-Repressor) homolog [Source:RefSeq peptide;Acc:NP_001293207]\n+ATGGAGGAAGATGATCCAGAGGAGCAGGCGGAACAAGAAGAAGAAACCAGCAGAATGGCT\n+CGTCCTATAAGATCCATGAGAAAACGCGAAACAACGTCTGGGGAATCAATGGGCGATGAG\n+GATGAAGATTTGGAGGATGAAGAGGACGAAGATGAAGAAGCTGAAGCTCGTGAGCATCAT\n+GAAAGTGGTGCTCATGACACATCTTTCTCAAATCCACTTTCCAACGTCGACAATCTAATC\n+CACGTGGGAACCGAATATCAGGCGATTATACAGCCAACTGCAGAGCAATTGGAAAAAGAA\n+CCGTGCAGAGATCAACAAATTTGGGCGTTTCCAGACGAAATGAACGAGAATCGGCTTACA\n+GAATACATTTCAGAAGCTACTGGACGATATCAATTACCTATAGATAGGGCTCTGTTCATT\n+CTGAACAAACAGTCAAATGATTTCGACGCTGCGATGGTTCAAGCGATGAGAAGAAAAGAA\n+ATTCATGATGATTGGACGGCAGAAGAAATTAGTCTTTTCTCCACTTGCTTCTTTCATTTC\n+GGAAAACGGTTCAAGAAGATTCATGCGGCTATGCCCCAACGCTCGCTTTCTTCCATTATC\n+CAATACTATTACAACACGAAAAAAGTGCAAAACTATAAAACAATGATTAATGTGCATTTG\n+AATGAAACCGACACTTATGATGAACTATTCAAAGAGGTCAATCATTTGGAGAGGGTTCCG\n+TCGGGATATTGTGAGAATTGCAATGCAAAAAGTGATCTGTTGATTCTAAATCGTGTAATG\n+TCGCGTCACGAATGTAAACCGTGTATCCTTTATTTCCGTTTGATGCGTGTTCCACGTCCG\n+GCAAGCCTCCGTGCACTGACAAAACGACGGCAACGAGTTTTATGTCCAGAATACATGAAA\n+ATTTATGTATACGGATATCTTGAGCTCATGGAGCCAGCCAACGGAAAAGCGATCAAACGG\n+CTTGGAATTGGAAAAGAAAAAGAAGAAGACGATGATATTATGGTGGTCGACGACTGCCTT\n+CTCCGTAAACCATCAGGCCCCTACATTGTGGAGCAATCGATTGAAGCTGATCCAATCGAT\n+GAGAATACGTGCAGAATGACACGGTGCTTCGATACACCGGCTGCACTGGCATTAATTGAT\n+AATATCAAGAGAAAACATCATATGTGTGTTCCACTTGTTTGGAGAGTTAAACAAACGAAA\n+TGTATGGAGGAGAACGAAATTCTGAATGAAGAAGCCCGTCAACAAATGTTCCGTGCAACA\n+ATGACATACAGCCGTGTACCAAAAGGAGAAATTGCAAATTGGAAGAAAGATATGATGGCG\n+TTGAAGGGAAGATTCGAGAGATTTACTCCTGAACTAGATACTACTGCAACAAATGGCAAT\n+CGATCTGGAAAAGTCAGGATAAATTATGGTTGGAGTCCTGAGGAAAAGAAGAATGCTATT\n+AGATGTTTCCACTGGTACAAGGACAATTTCGAGTTGATCGCCGAGTTGATGGCCACAAAA\n+ACTGTGGAACAAATCAAAAAGTTCTATATGGACAATGAAAAGCTAATTTTGGAGTCAATC\n+GACACGTATCGCGCCGAGCTCAAGTCAAAACTCGGCAAATAA\n+>Y74C9A.4d cds chromosome:WBcel235:I:17483:24796:-1 gene:WBGene00022278 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:rcor-1 description:RCOR (REST CO-Repressor) homolog [Source:RefSeq peptide;Acc:NP_001293207]\n+ATGTCGCGTCACGAATGTAAACCGTGTATCCTTTATTTCCGTTTGATGCGTGTTCCACGT\n+CCGGCAAGCCTCCGTGCACTGACAAAACGACGGCAACGAGTTTTATGTCCAGAATACATG\n+AAAATTTATGTATACGGATATCTTGAGCTCATGGAGCCAGCCAACGGAAAAGCGATCAAA\n+CGGCTTGGAATTGGAAAAGAAAAAGAAGAAGACGATGATATTATGGTGGTCGACGACTGC\n+CTTCTCCGTAAACCATCAGGCCCCTACATTGTGGAGCAATCGATTGAAGCTGATCCAATC\n+GATGAGAATACGTGCAGAATGACACGGTGCTTCGATACACCGGCTGCACTGGCATTAATT\n+GATAATATCAAGAGAAAACATCATATGTGTGTTCCACTTGTTTGGAGAGTTAAACAAACG\n+AAATGTATGGAGGAGAACGAAATTCTGAATGAAGAAGCCCGTCAACAAATGTTCCGTGCA\n+ACAATGACATACAGCCGTGTACCAAAAGGAGAAATTGCAAATTGGAAGAAAGATATGATG\n+GCGTTGAAGGGAAGATTCGAGAGATTTACTCCTGAACTAGATACTACTGCAACAAATGGC\n+AATCGATCTGGAAAAGTCAGGATAAATTATGGTTGGAGTCCTGAGGAAAAGAAGAATGCT\n+ATTAGATGTTTCCACTGGTACAAGGACAATTTCGAGTTGATCGCCGAGTTGATGGCCACA\n+AAAACTGTGGAACAAATCAAAAAGTTCTATATGGACAATGAAAAGCTAATTTTGGAGTCA\n+ATCGACACGTATCGCGCCGAGCTCAAGTCAAAACTCGGCAAATAA\n' |
| b |
| diff -r 000000000000 -r 28879ca33b5f test-data/gene.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene.json Wed Mar 15 20:18:57 2017 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"ENSSSCG00000012257":{"source":"ensembl_havana","object_type":"Gene","logic_name":"ensembl_havana_gene","version":3,"species":"sus_scrofa","description":"monoamine oxidase A [Source:HGNC Symbol;Acc:HGNC:6833]","display_name":"MAOA","assembly_name":"Sscrofa10.2","biotype":"protein_coding","end":43209051,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCG00000012257","Transcript":[{"source":"ensembl_havana","object_type":"Transcript","logic_name":"ensembl_havana_transcript","Exon":[{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43209051,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000253366","start":43208580},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43189968,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000256152","start":43189874},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43179405,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000251395","start":43179268},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43161209,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000255769","start":43161105},{"object_type":"Exon","version":2,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43160068,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108039","start":43159977},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43155057,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108051","start":43154916},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43151715,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000198047","start":43151566},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43151271,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108042","start":43151112},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43149487,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108043","start":43149391},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43144966,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108044","start":43144913},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43139851,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108045","start":43139794},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43138092,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000185275","start":43137995},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43134262,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108052","start":43134151},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43133522,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108053","start":43133460},{"object_type":"Exon","version":3,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":43133148,"seq_region_name":"X","db_type":"core","strand":-1,"id":"ENSSSCE00000108054","start":43132739}],"Parent":"ENSSSCG00000012257","seq_region_name":"X","db_type":"core","is_canonical":"1","strand":-1,"id":"ENSSSCT00000013404","version":3,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","display_name":"MAOA-001","end":43209051,"biotype":"protein_coding","Translation":{"object_type":"Translation","species":"sus_scrofa","Parent":"ENSSSCT00000013404","end":43208652,"length":527,"db_type":"core","id":"ENSSSCP00000013044","start":43133002},"start":43132739},{"source":"havana","object_type":"Transcript","logic_name":"havan'..b'iens","assembly_name":"GRCh38","display_name":"BRAT1-005","end":2554448,"biotype":"nonsense_mediated_decay","Translation":{"object_type":"Translation","species":"homo_sapiens","Parent":"ENST00000421712","end":2554431,"length":168,"db_type":"core","id":"ENSP00000409209","start":2543738},"start":2542181}],"start":2537877},"ENSSSCG00000007563":{"source":"ensembl","object_type":"Gene","logic_name":"ensembl","version":2,"species":"sus_scrofa","description":"BRCA1 associated ATM activator 1 [Source:HGNC Symbol;Acc:HGNC:21701]","display_name":"BRAT1","assembly_name":"Sscrofa10.2","biotype":"protein_coding","end":2121143,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCG00000007563","Transcript":[{"source":"ensembl","object_type":"Transcript","logic_name":"ensembl","Exon":[{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2121143,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000175882","start":2121017},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2117944,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000244655","start":2117790},{"object_type":"Exon","version":2,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2115860,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000064688","start":2115713},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2115267,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000064689","start":2114895},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2114646,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000064690","start":2114530},{"object_type":"Exon","version":2,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2113541,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000064691","start":2113372},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2113310,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000238316","start":2113266},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2113163,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000201914","start":2113108},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2113090,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000233250","start":2112985},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2112773,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000208084","start":2112700},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2112009,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000224350","start":2111907},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2111805,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000173794","start":2111707},{"object_type":"Exon","version":1,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2111547,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000173250","start":2111372},{"object_type":"Exon","version":2,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","end":2111015,"seq_region_name":"3","db_type":"core","strand":-1,"id":"ENSSSCE00000064713","start":2109137}],"Parent":"ENSSSCG00000007563","seq_region_name":"3","db_type":"core","is_canonical":"1","strand":-1,"id":"ENSSSCT00000008295","version":2,"species":"sus_scrofa","assembly_name":"Sscrofa10.2","display_name":"BRAT1-201","end":2121143,"biotype":"protein_coding","Translation":{"object_type":"Translation","species":"sus_scrofa","Parent":"ENSSSCT00000008295","end":2121143,"length":815,"db_type":"core","id":"ENSSSCP00000008076","start":2110317},"start":2109137}],"start":2109137}}\n' |
| b |
| diff -r 000000000000 -r 28879ca33b5f test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fasta Wed Mar 15 20:18:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,156 @@\n+>Y74C9A.3_caenorhabditiselegans\n+ATGAGCTCTTCATCATCTTCTAGAATTCACAATGGTGAAGATGTTTATGAAAAGGCGGAG\n+GAATACTGGAGCCGCGCGAGCCAGGACGTCAACGGAATGCTCGGCGGATTCGAAGCGCTT\n+CACGCGCCCGACATATCGGCGTCGAAACGATTTATTGAAGGACTGAAGAAAAAGAATCTA\n+TTCGGCTACTTTGACTATGCACTGGACTGCGGAGCGGGTATCGGACGTGTTACAAAGCAT\n+CTCTTAATGCCATTCTTCTCGAAAGTTGATATGGAAGACGTCGTCGAGGAGTTGATCACG\n+AAAAGTGATCAATATATTGGAAAACATCCACGAATTGGAGATAAATTCGTCGAAGGACTG\n+CAGACGTTTGCACCGCCCGAACGACGTTATGATTTGATATGGATTCAATGGGTTTCAGGG\n+CATTTGGTTGATGAGGATTTGGTTGATTTCTTTAAAAGATGTGCGAAAGGACTGAAACCT\n+GGTGGATGTATTGTGCTCAAGGATAATGTGACAAATCACGAGAAACGGTTATTCGACGAT\n+GATGATCATAGTTGGACGAGAACAGAGCCCGAGCTTCTTAAAGCGTTCGCCGATTCTCAA\n+CTGGACATGGTCTCGAAAGCACTGCAAACCGGATTCCCAAAGGAGATTTATCCAGTAAAA\n+ATGTATGCATTGAAGCCTCAACACACCGGATTCACCAATAATTGA\n+>Y74C9A.2a.1_caenorhabditiselegans\n+ATGAAACTCGTAATTCTGCTATCTTTTGTTGCGACAGTTGCGGTTTTTGCGGCTCCATCG\n+GCTCCGGCAGGTCTCGAGGAGAAGCTGCGTGCTCTTCAGGAGCAACTGTACAGTCTGGAG\n+AAAGAGAACGGAGTTGATGTGAAGCAAAAGGAGCAACCAGCAGCAGCCGACACATTCCTT\n+GGATTTGTTCCACAGAAGAGAATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAAT\n+GAGGATTCTAGAGCTCCATTGCTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGA\n+GCCGGAGAACGCCTCGGAGTCAACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAAT\n+CAATTCCAATAA\n+>Y74C9A.2a.2_caenorhabditiselegans\n+ATGAAACTCGTAATTCTGCTATCTTTTGTTGCGACAGTTGCGGTTTTTGCGGCTCCATCG\n+GCTCCGGCAGGTCTCGAGGAGAAGCTGCGTGCTCTTCAGGAGCAACTGTACAGTCTGGAG\n+AAAGAGAACGGAGTTGATGTGAAGCAAAAGGAGCAACCAGCAGCAGCCGACACATTCCTT\n+GGATTTGTTCCACAGAAGAGAATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAAT\n+GAGGATTCTAGAGCTCCATTGCTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGA\n+GCCGGAGAACGCCTCGGAGTCAACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAAT\n+CAATTCCAATAA\n+>Y74C9A.2a.3_caenorhabditiselegans\n+ATGAAACTCGTAATTCTGCTATCTTTTGTTGCGACAGTTGCGGTTTTTGCGGCTCCATCG\n+GCTCCGGCAGGTCTCGAGGAGAAGCTGCGTGCTCTTCAGGAGCAACTGTACAGTCTGGAG\n+AAAGAGAACGGAGTTGATGTGAAGCAAAAGGAGCAACCAGCAGCAGCCGACACATTCCTT\n+GGATTTGTTCCACAGAAGAGAATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAAT\n+GAGGATTCTAGAGCTCCATTGCTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGA\n+GCCGGAGAACGCCTCGGAGTCAACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAAT\n+CAATTCCAATAA\n+>Y74C9A.2b.1_caenorhabditiselegans\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGAGCCGGAGAACGCCTCGGAGTC\n+AACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAATCAATTCCAATAA\n+>Y74C9A.2b.2_caenorhabditiselegans\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGAGCCGGAGAACGCCTCGGAGTC\n+AACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAATCAATTCCAATAA\n+>Y74C9A.2b.3_caenorhabditiselegans\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGAGCCGGAGAACGCCTCGGAGTC\n+AACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAATCAATTCCAATAA\n+>Y74C9A.2b.4_caenorhabditiselegans\n+ATGGTCGCGTGGCAGCCGATGAAGCGGTCGATGATCAATGAGGATTCTAGAGCTCCATTG\n+CTCCACGCAATCGAAGCCCGCTTGGCCGAAGTGTTGAGAGCCGGAGAACGCCTCGGAGTC\n+AACCCGGAGGAAGTTTTGGCGGATCTTCGTGCTCGTAATCAATTCCAATAA\n+>Y74C9A.4a_caenorhabditiselegans\n+ATGGATTCGTACACGTCATCTGACGAAGACGCCTCTCGAAAAGAAAACGAAGGCTTGAAT\n+ATGTTGAATGCATCGCCGGAGCCAATGGAGGAAGATGATCCAGAGGAGCAGGCGGAACAA\n+GAAGAAGAAACCAGCAGAATGGCTCGTCCTATAAGATCCATGAGAAAACGCGAAACAACG\n+TCTGGGGAATCAATGGGCGATGAGGATGAAGATTTGGAGGATGAAGAGGACGAAGATGAA\n+GAAGCTGAAGCTCGTGAGCATCATGAAAGTGGTGCTCATGACACATCTTTCTCAAATCCA\n+CTTTCCAACGTCGACAATCTAATCCACGTGGGAACCGAATATCAGGCGATTATACAGCCA\n+ACTGCAGAGCAATTGGAAAAAGAACCGTGCAGAGATCAACAAATTTGGGCGTTTCCAGAC\n+GAAATGAACGAGAATCGGCTTACAGAATACATTTCAGAAGCTACTGGACGATATCAATTA\n+CCTATAGATAGGGCTCTGTTCATTCTGAACAAACAGTCAAATGATTTCGACGCTGCGATG\n+GTTCAAGCGATGAGAAGAAAAGAAATTCATGATGATTGGACGGCAGAAGAAATTAGTCTT\n+TTCTCCACTTGCTTCTTTCATTTCGGAAAACGGTTCAAGAAGATTCATGCGGCTATGCCC\n+CAACGCTCGCTTTCTTCCATTATCCAATACTATTACAACACGAAAAAAGTGCAAAACTAT\n+AAAACAATGATTAATGTGCATTTGAATGAAACCGACACTTATGATGAACTATTCAAAGAG\n+GTCAATCATTTGGAGAGGGTTCCGTCGGGATATTGTGAGAATTGCAATGCAAAAAGTGAT\n+CTGTTGATTCTAAATCGTGTAATGTCGCGTCACGAATGTAAACCGTGTATCCTTTATTTC\n+CGTTTGATGCGTGTTCCACGTCCGGCAAGCCTCCGTGCACTGACAAAACGACGGCAACGA\n+GTTTTATGTCCAGAATACATGAAAATTTATGTATACGGATATCTTGAGCTCATGGAGCCA\n+GCCAACGGAAAA'..b'CGACAATCTAATCCACGTGGGAACCGAATATCAGGCGATT\n+ATACAGCCAACTGCAGAGCAATTGGAAAAAGAACCGTGCAGAGATCAACAAATTTGGGCG\n+TTTCCAGACGAAATGAACGAGAATCGGCTTACAGAATACATTTCAGAAGCTACTGGACGA\n+TATCAATTACCTATAGATAGGGCTCTGTTCATTCTGAACAAACAGTCAAATGATTTCGAC\n+GCTGCGATGGTTCAAGCGATGAGAAGAAAAGAAATTCATGATGATTGGACGGCAGAAGAA\n+ATTAGTCTTTTCTCCACTTGCTTCTTTCATTTCGGAAAACGGTTCAAGAAGATTCATGCG\n+GCTATGCCCCAACGCTCGCTTTCTTCCATTATCCAATACTATTACAACACGAAAAAAGTG\n+CAAAACTATAAAACAATGATTAATGTGCATTTGAATGAAACCGACACTTATGATGAACTA\n+TTCAAAGAGGTCAATCATTTGGAGAGGGTTCCGTCGGGATATTGTGAGAATTGCAATGCA\n+AAAAGTGATCTGTTGATTCTAAATCGTGTAATGTCGCGTCACGAATGTAAACCGTGTATC\n+CTTTATTTCCGTTTGATGCGTGTTCCACGTCCGGCAAGCCTCCGTGCACTGACAAAACGA\n+CGGCAACGAGTTTTATGTCCAGAATACATGAAAATTTATGTATACGGATATCTTGAGCTC\n+ATGGAGCCAGCCAACGGAAAAGCGATCAAACGGCTTGGAATTGGAAAAGAAAAAGAAGAA\n+GACGATGATATTATGGTGGTCGACGACTGCCTTCTCCGTAAACCATCAGGCCCCTACATT\n+GTGGAGCAATCGATTGAAGCTGATCCAATCGATGAGAATACGTGCAGAATGACACGGTGC\n+TTCGATACACCGGCTGCACTGGCATTAATTGATAATATCAAGAGAAAACATCATATGTGT\n+GTTCCACTTGTTTGGAGAGTTAAACAAACGAAATGTATGGAGGAGAACGAAATTCTGAAT\n+GAAGAAGCCCGTCAACAAATGTTCCGTGCAACAATGACATACAGCCGTGTACCAAAAGGA\n+GAAATTGCAAATTGGAAGAAAGATATGATGGCGTTGAAGGGAAGATTCGAGAGATTTACT\n+CCTGAACTAGATACTACTGCAACAAATGGCAATCGATCTGGAAAAGTCAGGATAAATTAT\n+GGTTGGAGTCCTGAGGAAAAGAAGAATGCTATTAGATGTTTCCACTGGTACAAGGACAAT\n+TTCGAGTTGATCGCCGAGTTGATGGCCACAAAAACTGTGGAACAAATCAAAAAGTTCTAT\n+ATGGACAATGAAAAGCTAATTTTGGAGTCAATCGACACGTATCGCGCCGAGCTCAAGTCA\n+AAACTCGGCAAATAA\n+>Y74C9A.4c_caenorhabditiselegans\n+ATGGAGGAAGATGATCCAGAGGAGCAGGCGGAACAAGAAGAAGAAACCAGCAGAATGGCT\n+CGTCCTATAAGATCCATGAGAAAACGCGAAACAACGTCTGGGGAATCAATGGGCGATGAG\n+GATGAAGATTTGGAGGATGAAGAGGACGAAGATGAAGAAGCTGAAGCTCGTGAGCATCAT\n+GAAAGTGGTGCTCATGACACATCTTTCTCAAATCCACTTTCCAACGTCGACAATCTAATC\n+CACGTGGGAACCGAATATCAGGCGATTATACAGCCAACTGCAGAGCAATTGGAAAAAGAA\n+CCGTGCAGAGATCAACAAATTTGGGCGTTTCCAGACGAAATGAACGAGAATCGGCTTACA\n+GAATACATTTCAGAAGCTACTGGACGATATCAATTACCTATAGATAGGGCTCTGTTCATT\n+CTGAACAAACAGTCAAATGATTTCGACGCTGCGATGGTTCAAGCGATGAGAAGAAAAGAA\n+ATTCATGATGATTGGACGGCAGAAGAAATTAGTCTTTTCTCCACTTGCTTCTTTCATTTC\n+GGAAAACGGTTCAAGAAGATTCATGCGGCTATGCCCCAACGCTCGCTTTCTTCCATTATC\n+CAATACTATTACAACACGAAAAAAGTGCAAAACTATAAAACAATGATTAATGTGCATTTG\n+AATGAAACCGACACTTATGATGAACTATTCAAAGAGGTCAATCATTTGGAGAGGGTTCCG\n+TCGGGATATTGTGAGAATTGCAATGCAAAAAGTGATCTGTTGATTCTAAATCGTGTAATG\n+TCGCGTCACGAATGTAAACCGTGTATCCTTTATTTCCGTTTGATGCGTGTTCCACGTCCG\n+GCAAGCCTCCGTGCACTGACAAAACGACGGCAACGAGTTTTATGTCCAGAATACATGAAA\n+ATTTATGTATACGGATATCTTGAGCTCATGGAGCCAGCCAACGGAAAAGCGATCAAACGG\n+CTTGGAATTGGAAAAGAAAAAGAAGAAGACGATGATATTATGGTGGTCGACGACTGCCTT\n+CTCCGTAAACCATCAGGCCCCTACATTGTGGAGCAATCGATTGAAGCTGATCCAATCGAT\n+GAGAATACGTGCAGAATGACACGGTGCTTCGATACACCGGCTGCACTGGCATTAATTGAT\n+AATATCAAGAGAAAACATCATATGTGTGTTCCACTTGTTTGGAGAGTTAAACAAACGAAA\n+TGTATGGAGGAGAACGAAATTCTGAATGAAGAAGCCCGTCAACAAATGTTCCGTGCAACA\n+ATGACATACAGCCGTGTACCAAAAGGAGAAATTGCAAATTGGAAGAAAGATATGATGGCG\n+TTGAAGGGAAGATTCGAGAGATTTACTCCTGAACTAGATACTACTGCAACAAATGGCAAT\n+CGATCTGGAAAAGTCAGGATAAATTATGGTTGGAGTCCTGAGGAAAAGAAGAATGCTATT\n+AGATGTTTCCACTGGTACAAGGACAATTTCGAGTTGATCGCCGAGTTGATGGCCACAAAA\n+ACTGTGGAACAAATCAAAAAGTTCTATATGGACAATGAAAAGCTAATTTTGGAGTCAATC\n+GACACGTATCGCGCCGAGCTCAAGTCAAAACTCGGCAAATAA\n+>Y74C9A.4d_caenorhabditiselegans\n+ATGTCGCGTCACGAATGTAAACCGTGTATCCTTTATTTCCGTTTGATGCGTGTTCCACGT\n+CCGGCAAGCCTCCGTGCACTGACAAAACGACGGCAACGAGTTTTATGTCCAGAATACATG\n+AAAATTTATGTATACGGATATCTTGAGCTCATGGAGCCAGCCAACGGAAAAGCGATCAAA\n+CGGCTTGGAATTGGAAAAGAAAAAGAAGAAGACGATGATATTATGGTGGTCGACGACTGC\n+CTTCTCCGTAAACCATCAGGCCCCTACATTGTGGAGCAATCGATTGAAGCTGATCCAATC\n+GATGAGAATACGTGCAGAATGACACGGTGCTTCGATACACCGGCTGCACTGGCATTAATT\n+GATAATATCAAGAGAAAACATCATATGTGTGTTCCACTTGTTTGGAGAGTTAAACAAACG\n+AAATGTATGGAGGAGAACGAAATTCTGAATGAAGAAGCCCGTCAACAAATGTTCCGTGCA\n+ACAATGACATACAGCCGTGTACCAAAAGGAGAAATTGCAAATTGGAAGAAAGATATGATG\n+GCGTTGAAGGGAAGATTCGAGAGATTTACTCCTGAACTAGATACTACTGCAACAAATGGC\n+AATCGATCTGGAAAAGTCAGGATAAATTATGGTTGGAGTCCTGAGGAAAAGAAGAATGCT\n+ATTAGATGTTTCCACTGGTACAAGGACAATTTCGAGTTGATCGCCGAGTTGATGGCCACA\n+AAAACTGTGGAACAAATCAAAAAGTTCTATATGGACAATGAAAAGCTAATTTTGGAGTCA\n+ATCGACACGTATCGCGCCGAGCTCAAGTCAAAACTCGGCAAATAA\n' |
| b |
| diff -r 000000000000 -r 28879ca33b5f test-data/test1.sqlite |
| b |
| Binary file test-data/test1.sqlite has changed |
| b |
| diff -r 000000000000 -r 28879ca33b5f test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.fasta Wed Mar 15 20:18:57 2017 -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 000000000000 -r 28879ca33b5f test-data/test2.sqlite |
| b |
| Binary file test-data/test2.sqlite has changed |
