Mercurial > repos > earlhaminst > gff3_to_json
changeset 0:be6cec883b02 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gff3_to_json commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty
| author | earlhaminst |
|---|---|
| date | Wed, 21 Dec 2016 10:02:59 -0500 |
| parents | |
| children | befe6021e476 |
| files | gff3_to_json.py gff3_to_json.xml test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.gff3 test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json test-data/ENSCAFT00000026349.gff test-data/ENSMUST00000005671.gff test-data/ENSMUST00000091291.gff test-data/ENSPTRT00000013802.gff test-data/ENSRNOT00000019267.gff test-data/test.json |
| diffstat | 10 files changed, 3260 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_to_json.py Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,255 @@ +from __future__ import print_function + +import json +import optparse +import sys + +cds_parent_dict = dict() +exon_parent_dict = dict() +five_prime_utr_parent_dict = dict() +gene_count = 0 +gene_dict = dict() +transcript_dict = dict() +three_prime_utr_parent_dict = dict() + + +def feature_to_json(cols): + d = { + 'end': int(cols[4]), + 'start': int(cols[3]), + } + for attr in cols[8].split(';'): + if '=' in attr: + (tag, value) = attr.split('=') + if tag == 'ID': + d['id'] = value + else: + d[tag] = value + if cols[6] == '+': + d['strand'] = 1 + elif cols[6] == '-': + d['strand'] = -1 + else: + raise Exception("Unrecognized strand '%s'" % cols[6]) + return d + + +def gene_to_json(cols, species): + global gene_count + gene = feature_to_json(cols) + gene.update({ + 'member_id': gene_count, + 'object_type': 'Gene', + 'seq_region_name': cols[0], + 'species': species, + 'Transcript': [], + }) + gene_dict[gene['id']] = gene + gene_count = gene_count + 1 + + +def transcript_to_json(cols, species): + transcript = feature_to_json(cols) + transcript.update({ + 'object_type': 'Transcript', + 'seq_region_name': cols[0], + 'species': species, + }) + transcript_dict[transcript['id']] = transcript + + +def exon_to_json(cols, species): + exon = feature_to_json(cols) + exon.update({ + 'length': int(cols[4]) - int(cols[3]) + 1, + 'object_type': 'Exon', + 'seq_region_name': cols[0], + 'species': species, + }) + if 'id' not in exon and 'Name' in exon: + exon['id'] = exon['Name'] + + if 'Parent' in exon: + for parent in exon['Parent'].split(','): + if parent not in exon_parent_dict: + exon_parent_dict[parent] = [exon] + else: + exon_parent_dict[parent].append(exon) + + +def five_prime_utr_to_json(cols): + five_prime_utr = feature_to_json(cols) + if 'Parent' in five_prime_utr: + for parent in five_prime_utr['Parent'].split(','): + # the 5' UTR can be split among multiple exons + if parent not in five_prime_utr_parent_dict: + five_prime_utr_parent_dict[parent] = [five_prime_utr] + else: + five_prime_utr_parent_dict[parent].append(five_prime_utr) + + +def three_prime_utr_to_json(cols): + three_prime_utr = feature_to_json(cols) + if 'Parent' in three_prime_utr: + for parent in three_prime_utr['Parent'].split(','): + # the 3' UTR can be split among multiple exons + if parent not in three_prime_utr_parent_dict: + three_prime_utr_parent_dict[parent] = [three_prime_utr] + else: + three_prime_utr_parent_dict[parent].append(three_prime_utr) + + +def cds_to_json(cols): + cds = feature_to_json(cols) + if 'id' not in cds: + if 'Name' in cds: + cds['id'] = cds['Name'] + elif 'Parent' in cds: + cds['id'] = cds['Parent'] + if 'Parent' in cds: + # At this point we are sure than 'id' is in cds + for parent in cds['Parent'].split(','): + if parent not in cds_parent_dict: + cds_parent_dict[parent] = [cds] + else: + cds_parent_dict[parent].append(cds) + + +def join_dicts(): + for parent, exon_list in exon_parent_dict.items(): + exon_list.sort(key=lambda _: _['start']) + if parent in transcript_dict: + transcript_dict[parent]['Exon'] = exon_list + + for transcript_id, transcript in transcript_dict.items(): + translation = { + 'CDS': [], + 'id': None, + 'end': transcript['end'], + 'object_type': 'Translation', + 'species': transcript['species'], + 'start': transcript['start'], + } + found_cds = False + derived_translation_start = None + derived_translation_end = None + if transcript_id in cds_parent_dict: + cds_list = cds_parent_dict[transcript_id] + cds_ids = set(_['id'] for _ in cds_list) + if len(cds_ids) > 1: + raise Exception("Transcript %s has multiple CDSs: this is not supported by Ensembl JSON format" % parent) + translation['id'] = cds_ids.pop() + cds_list.sort(key=lambda _: _['start']) + translation['CDS'] = cds_list + translation['start'] = cds_list[0]['start'] + translation['end'] = cds_list[-1]['end'] + found_cds = True + if transcript_id in five_prime_utr_parent_dict: + five_prime_utr_list = five_prime_utr_parent_dict[transcript_id] + five_prime_utr_list.sort(key=lambda _: _['start']) + if transcript['strand'] == 1: + derived_translation_start = five_prime_utr_list[-1]['end'] + 1 + else: + derived_translation_end = five_prime_utr_list[0]['start'] - 1 + if transcript_id in three_prime_utr_parent_dict: + three_prime_utr_list = three_prime_utr_parent_dict[transcript_id] + three_prime_utr_list.sort(key=lambda _: _['start']) + if transcript['strand'] == 1: + derived_translation_end = three_prime_utr_list[0]['start'] - 1 + else: + derived_translation_start = three_prime_utr_list[-1]['end'] + 1 + if derived_translation_start is not None: + if found_cds: + if derived_translation_start > translation['start']: + raise Exception("UTR overlaps with CDS") + else: + translation['start'] = derived_translation_start + if derived_translation_end is not None: + if found_cds: + if derived_translation_end < translation['end']: + raise Exception("UTR overlaps with CDS") + else: + translation['end'] = derived_translation_end + if found_cds or derived_translation_start is not None or derived_translation_end is not None: + transcript['Translation'] = translation + + for transcript in transcript_dict.values(): + if 'Parent' in transcript: + # A polycistronic transcript can have multiple parents + for parent in transcript['Parent'].split(','): + if parent in gene_dict: + gene_dict[parent]['Transcript'].append(transcript) + + +def merge_dicts(json_arg): + with open(json_arg) as f: + dict_from_json = json.load(f) + gene_intersection = set(gene_dict.keys()) & set(dict_from_json.keys()) + if gene_intersection: + raise Exception("JSON file '%s' contains information for genes '%s', which are also present in other files" % (json_arg, ', '.join(gene_intersection))) + gene_dict.update(dict_from_json) + + +def write_json(outfile=None, sort_keys=False): + if outfile: + with open(outfile, 'w') as f: + json.dump(gene_dict, f, sort_keys=sort_keys) + else: + print(json.dumps(gene_dict, indent=3, sort_keys=sort_keys)) + + +def __main__(): + parser = optparse.OptionParser() + parser.add_option('--gff3', action='append', default=[], help='GFF3 file to convert, in SPECIES:FILENAME format. Use multiple times to add more files') + parser.add_option('--json', action='append', default=[], help='JSON file to merge. Use multiple times to add more files') + parser.add_option('-s', '--sort', action='store_true', help='Sort the keys in the JSON output') + parser.add_option('-o', '--output', help='Path of the output file. If not specified, will print on the standard output') + options, args = parser.parse_args() + + if args: + raise Exception('Use options to provide inputs') + for gff3_arg in options.gff3: + try: + (species, filename) = gff3_arg.split(':') + except ValueError: + raise Exception("Argument for --gff3 '%s' is not in the SPECIES:FILENAME format" % gff3_arg) + with open(filename) as f: + for i, line in enumerate(f): + line = line.strip() + if not line: + # skip empty lines + continue + if line[0] == '#': + # skip comment lines + continue + cols = line.split('\t') + if len(cols) != 9: + raise Exception("Line %i in file '%s': '%s' does not have 9 columns" % (i, filename, line)) + feature_type = cols[2] + try: + if feature_type == 'gene': + gene_to_json(cols, species) + elif feature_type in ('mRNA', 'transcript'): + transcript_to_json(cols, species) + elif feature_type == 'exon': + exon_to_json(cols, species) + elif feature_type == 'five_prime_UTR': + five_prime_utr_to_json(cols) + elif feature_type == 'three_prime_UTR': + three_prime_utr_to_json(cols) + elif feature_type == 'CDS': + cds_to_json(cols) + else: + print("Line %i in file '%s': '%s' is not an implemented feature type" % (i, filename, feature_type), file=sys.stderr) + except Exception as e: + raise Exception("Line %i in file '%s': %s" % (i, filename, e)) + join_dicts() + + for json_arg in options.json: + merge_dicts(json_arg) + + write_json(options.output, options.sort) + + +if __name__ == '__main__': + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_to_json.xml Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,92 @@ +<tool id="gff3_to_json" name="GFF3 to JSON" version="0.1.1"> + <description>converter</description> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <command> +<![CDATA[ +python $__tool_directory__/gff3_to_json.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 +$sort +> "$output" +]]> + </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="JSON datasets to merge" /> + <param name="sort" type="boolean" truevalue="-s" falsevalue="" label="Sort the keys in the JSON output" help="Ensure reproducibility, but can slow down the JSON creation for big files" /> + </inputs> + + <outputs> + <data name="output" format="json" label="${tool.name} on ${on_string}" /> + </outputs> + + <tests> + <test> + <param name="gff3_input" ftype="gff3" value="ENSCAFT00000026349.gff" /> + <param name="genome" ftype="text" value="canisfamiliaris" /> + + <param name="gff3_input" ftype="gff3" value="ENSMUST00000005671.gff" /> + <param name="genome" ftype="text" value="musmusculus" /> + + <param name="gff3_input" ftype="gff3" value="ENSMUST00000091291.gff" /> + <param name="genome" ftype="text" value="musmusculus" /> + + <param name="gff3_input" ftype="gff3" value="ENSPTRT00000013802.gff" /> + <param name="genome" ftype="text" value="pantroglodytes" /> + + <param name="gff3_input" ftype="gff3" value="ENSRNOT00000019267.gff" /> + <param name="genome" value="rattusnorvegicus" /> + + <param name="sort" value="-s" /> + <output name="output" file="test.json" ftype="json" /> + </test> + <test> + <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.gff3" /> + <param name="genome" value="caenorhabditiselegans" /> + <param name="sort" value="-s" /> + <output name="output" file="Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json" ftype="json" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Simple tool to convert a set of GFF3 datasets into JSON format and to merge with other JSON files. + +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 + +Warning: **Gene**, **mRNA** and **exon** features are mandatory, UTR and CDS are optional. Also, **ID** and **Parent** tags are needed to create relations. +]]> + </help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.gff3 Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,41 @@ +##gff-version 3 +#!genome-build WormBase WBcel235 +#!genome-version WBcel235 +#!genome-date 2012-12 +#!genome-build-accession NCBI:GCA_000002985.3 +#!genebuild-last-updated 2014-10 +I WormBase chromosome 1 15072434 . . . ID=chromosome:I;Alias=BX284601.5,NC_003279.8 +I WormBase gene 10413 16842 . + . ID=gene:WBGene00022276;Name=nlp-40;biotype=protein_coding;description=Neuropeptide-Like Protein [Source:RefSeq peptide%3BAcc:NP_001293206];gene_id=WBGene00022276;logic_name=wormbase +I WormBase gene 17483 26781 . - . ID=gene:WBGene00022278;Name=rcor-1;biotype=protein_coding;description=RCOR (REST CO-Repressor) homolog [Source:RefSeq peptide%3BAcc:NP_001293207];gene_id=WBGene00022278;logic_name=wormbase +I WormBase miRNA_gene 6054951 6055002 . - . ID=gene:WBGene00219261;Name=mir-4926;biotype=miRNA;gene_id=WBGene00219261;logic_name=wormbase_non_coding +I WormBase mRNA 10413 16842 . + . ID=transcript:Y74C9A.2a.2;Name=Y74C9A.2a.2;Parent=gene:WBGene00022276;biotype=protein_coding;transcript_id=Y74C9A.2a.2 +I WormBase mRNA 17483 24796 . - . ID=transcript:Y74C9A.4d;Name=Y74C9A.4d;Parent=gene:WBGene00022278;biotype=protein_coding;transcript_id=Y74C9A.4d +I WormBase transcript 6054951 6055002 . - . ID=transcript:C27A12.13;Name=C27A12.13;Parent=gene:WBGene00219261;biotype=pre_miRNA;transcript_id=C27A12.13 +I WormBase miRNA 6054982 6055002 . - . ID=transcript:C27A12.13a;Name=C27A12.13a;Parent=gene:WBGene00219261;biotype=miRNA;transcript_id=C27A12.13a +I WormBase exon 10413 10585 . + . Name=Y74C9A.2a.2.e1;Parent=transcript:Y74C9A.2a.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Y74C9A.2a.2.e1;rank=1 +I WormBase exon 11618 11689 . + . Name=Y74C9A.2a.1.e1;Parent=transcript:Y74C9A.2a.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Y74C9A.2a.1.e1;rank=2 +I WormBase exon 14951 15160 . + . Name=Y74C9A.2a.1.e2;Parent=transcript:Y74C9A.2a.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=Y74C9A.2a.1.e2;rank=3 +I WormBase exon 16473 16842 . + . Name=Y74C9A.2a.1.e3;Parent=transcript:Y74C9A.2a.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=Y74C9A.2a.1.e3;rank=4 +I WormBase exon 24651 24796 . - . Name=Y74C9A.4d.e1;Parent=transcript:Y74C9A.4d;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Y74C9A.4d.e1;rank=1 +I WormBase exon 21013 21136 . - . Name=Y74C9A.4d.e2;Parent=transcript:Y74C9A.4d;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=Y74C9A.4d.e2;rank=2 +I WormBase exon 20848 20964 . - . Name=Y74C9A.4a.e8;Parent=transcript:Y74C9A.4d;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Y74C9A.4a.e8;rank=3 +I WormBase exon 20271 20478 . - . Name=Y74C9A.4a.e9;Parent=transcript:Y74C9A.4d;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=Y74C9A.4a.e9;rank=4 +I WormBase exon 19015 19241 . - . Name=Y74C9A.4a.e10;Parent=transcript:Y74C9A.4d;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Y74C9A.4a.e10;rank=5 +I WormBase exon 18006 18115 . - . Name=Y74C9A.4a.e11;Parent=transcript:Y74C9A.4d;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Y74C9A.4a.e11;rank=6 +I WormBase exon 17483 17958 . - . Name=Y74C9A.4a.e12;Parent=transcript:Y74C9A.4d;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Y74C9A.4a.e12;rank=7 +I WormBase exon 6054982 6055002 . - . Name=C27A12.13a.e1;Parent=transcript:C27A12.13a;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=C27A12.13a.e1;rank=1 +I WormBase CDS 11641 11689 . + 0 ID=CDS:Y74C9A.2a.2;Parent=transcript:Y74C9A.2a.2;protein_id=Y74C9A.2a.2 +I WormBase CDS 14951 15160 . + 2 ID=CDS:Y74C9A.2a.2;Parent=transcript:Y74C9A.2a.2;protein_id=Y74C9A.2a.2 +I WormBase CDS 16473 16585 . + 2 ID=CDS:Y74C9A.2a.2;Parent=transcript:Y74C9A.2a.2;protein_id=Y74C9A.2a.2 +I WormBase CDS 21013 21127 . - 0 ID=CDS:Y74C9A.4d;Parent=transcript:Y74C9A.4d;protein_id=Y74C9A.4d +I WormBase CDS 20848 20964 . - 2 ID=CDS:Y74C9A.4d;Parent=transcript:Y74C9A.4d;protein_id=Y74C9A.4d +I WormBase CDS 20271 20478 . - 2 ID=CDS:Y74C9A.4d;Parent=transcript:Y74C9A.4d;protein_id=Y74C9A.4d +I WormBase CDS 19015 19241 . - 1 ID=CDS:Y74C9A.4d;Parent=transcript:Y74C9A.4d;protein_id=Y74C9A.4d +I WormBase CDS 18006 18115 . - 2 ID=CDS:Y74C9A.4d;Parent=transcript:Y74C9A.4d;protein_id=Y74C9A.4d +I WormBase CDS 17911 17958 . - 0 ID=CDS:Y74C9A.4d;Parent=transcript:Y74C9A.4d;protein_id=Y74C9A.4d +I WormBase five_prime_UTR 10413 10585 . + . Parent=transcript:Y74C9A.2a.2 +I WormBase five_prime_UTR 11618 11640 . + . Parent=transcript:Y74C9A.2a.2 +I WormBase three_prime_UTR 16586 16842 . + . Parent=transcript:Y74C9A.2a.2 +I WormBase five_prime_UTR 24651 24796 . - . Parent=transcript:Y74C9A.4d +I WormBase five_prime_UTR 21128 21136 . - . Parent=transcript:Y74C9A.4d +I WormBase three_prime_UTR 17483 17910 . - . Parent=transcript:Y74C9A.4d
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,343 @@ +{ + "gene:WBGene00022276": { + "Name": "nlp-40", + "Transcript": [ + { + "Exon": [ + { + "Name": "Y74C9A.2a.2.e1", + "Parent": "transcript:Y74C9A.2a.2", + "constitutive": "0", + "end": 10585, + "ensembl_end_phase": "-1", + "ensembl_phase": "-1", + "exon_id": "Y74C9A.2a.2.e1", + "id": "Y74C9A.2a.2.e1", + "length": 173, + "object_type": "Exon", + "rank": "1", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 10413, + "strand": 1 + }, + { + "Name": "Y74C9A.2a.1.e1", + "Parent": "transcript:Y74C9A.2a.2", + "constitutive": "0", + "end": 11689, + "ensembl_end_phase": "1", + "ensembl_phase": "-1", + "exon_id": "Y74C9A.2a.1.e1", + "id": "Y74C9A.2a.1.e1", + "length": 72, + "object_type": "Exon", + "rank": "2", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 11618, + "strand": 1 + }, + { + "Name": "Y74C9A.2a.1.e2", + "Parent": "transcript:Y74C9A.2a.2", + "constitutive": "0", + "end": 15160, + "ensembl_end_phase": "1", + "ensembl_phase": "1", + "exon_id": "Y74C9A.2a.1.e2", + "id": "Y74C9A.2a.1.e2", + "length": 210, + "object_type": "Exon", + "rank": "3", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 14951, + "strand": 1 + }, + { + "Name": "Y74C9A.2a.1.e3", + "Parent": "transcript:Y74C9A.2a.2", + "constitutive": "0", + "end": 16842, + "ensembl_end_phase": "-1", + "ensembl_phase": "1", + "exon_id": "Y74C9A.2a.1.e3", + "id": "Y74C9A.2a.1.e3", + "length": 370, + "object_type": "Exon", + "rank": "4", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 16473, + "strand": 1 + } + ], + "Name": "Y74C9A.2a.2", + "Parent": "gene:WBGene00022276", + "Translation": { + "CDS": [ + { + "Parent": "transcript:Y74C9A.2a.2", + "end": 11689, + "id": "CDS:Y74C9A.2a.2", + "protein_id": "Y74C9A.2a.2", + "start": 11641, + "strand": 1 + }, + { + "Parent": "transcript:Y74C9A.2a.2", + "end": 15160, + "id": "CDS:Y74C9A.2a.2", + "protein_id": "Y74C9A.2a.2", + "start": 14951, + "strand": 1 + }, + { + "Parent": "transcript:Y74C9A.2a.2", + "end": 16585, + "id": "CDS:Y74C9A.2a.2", + "protein_id": "Y74C9A.2a.2", + "start": 16473, + "strand": 1 + } + ], + "end": 16585, + "id": "CDS:Y74C9A.2a.2", + "object_type": "Translation", + "species": "caenorhabditiselegans", + "start": 11641 + }, + "biotype": "protein_coding", + "end": 16842, + "id": "transcript:Y74C9A.2a.2", + "object_type": "Transcript", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 10413, + "strand": 1, + "transcript_id": "Y74C9A.2a.2" + } + ], + "biotype": "protein_coding", + "description": "Neuropeptide-Like Protein [Source:RefSeq peptide%3BAcc:NP_001293206]", + "end": 16842, + "gene_id": "WBGene00022276", + "id": "gene:WBGene00022276", + "logic_name": "wormbase", + "member_id": 0, + "object_type": "Gene", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 10413, + "strand": 1 + }, + "gene:WBGene00022278": { + "Name": "rcor-1", + "Transcript": [ + { + "Exon": [ + { + "Name": "Y74C9A.4a.e12", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "1", + "end": 17958, + "ensembl_end_phase": "-1", + "ensembl_phase": "0", + "exon_id": "Y74C9A.4a.e12", + "id": "Y74C9A.4a.e12", + "length": 476, + "object_type": "Exon", + "rank": "7", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 17483, + "strand": -1 + }, + { + "Name": "Y74C9A.4a.e11", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "1", + "end": 18115, + "ensembl_end_phase": "0", + "ensembl_phase": "1", + "exon_id": "Y74C9A.4a.e11", + "id": "Y74C9A.4a.e11", + "length": 110, + "object_type": "Exon", + "rank": "6", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 18006, + "strand": -1 + }, + { + "Name": "Y74C9A.4a.e10", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "1", + "end": 19241, + "ensembl_end_phase": "1", + "ensembl_phase": "2", + "exon_id": "Y74C9A.4a.e10", + "id": "Y74C9A.4a.e10", + "length": 227, + "object_type": "Exon", + "rank": "5", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 19015, + "strand": -1 + }, + { + "Name": "Y74C9A.4a.e9", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "1", + "end": 20478, + "ensembl_end_phase": "2", + "ensembl_phase": "1", + "exon_id": "Y74C9A.4a.e9", + "id": "Y74C9A.4a.e9", + "length": 208, + "object_type": "Exon", + "rank": "4", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 20271, + "strand": -1 + }, + { + "Name": "Y74C9A.4a.e8", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "1", + "end": 20964, + "ensembl_end_phase": "1", + "ensembl_phase": "1", + "exon_id": "Y74C9A.4a.e8", + "id": "Y74C9A.4a.e8", + "length": 117, + "object_type": "Exon", + "rank": "3", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 20848, + "strand": -1 + }, + { + "Name": "Y74C9A.4d.e2", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "0", + "end": 21136, + "ensembl_end_phase": "1", + "ensembl_phase": "-1", + "exon_id": "Y74C9A.4d.e2", + "id": "Y74C9A.4d.e2", + "length": 124, + "object_type": "Exon", + "rank": "2", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 21013, + "strand": -1 + }, + { + "Name": "Y74C9A.4d.e1", + "Parent": "transcript:Y74C9A.4d", + "constitutive": "0", + "end": 24796, + "ensembl_end_phase": "-1", + "ensembl_phase": "-1", + "exon_id": "Y74C9A.4d.e1", + "id": "Y74C9A.4d.e1", + "length": 146, + "object_type": "Exon", + "rank": "1", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 24651, + "strand": -1 + } + ], + "Name": "Y74C9A.4d", + "Parent": "gene:WBGene00022278", + "Translation": { + "CDS": [ + { + "Parent": "transcript:Y74C9A.4d", + "end": 17958, + "id": "CDS:Y74C9A.4d", + "protein_id": "Y74C9A.4d", + "start": 17911, + "strand": -1 + }, + { + "Parent": "transcript:Y74C9A.4d", + "end": 18115, + "id": "CDS:Y74C9A.4d", + "protein_id": "Y74C9A.4d", + "start": 18006, + "strand": -1 + }, + { + "Parent": "transcript:Y74C9A.4d", + "end": 19241, + "id": "CDS:Y74C9A.4d", + "protein_id": "Y74C9A.4d", + "start": 19015, + "strand": -1 + }, + { + "Parent": "transcript:Y74C9A.4d", + "end": 20478, + "id": "CDS:Y74C9A.4d", + "protein_id": "Y74C9A.4d", + "start": 20271, + "strand": -1 + }, + { + "Parent": "transcript:Y74C9A.4d", + "end": 20964, + "id": "CDS:Y74C9A.4d", + "protein_id": "Y74C9A.4d", + "start": 20848, + "strand": -1 + }, + { + "Parent": "transcript:Y74C9A.4d", + "end": 21127, + "id": "CDS:Y74C9A.4d", + "protein_id": "Y74C9A.4d", + "start": 21013, + "strand": -1 + } + ], + "end": 21127, + "id": "CDS:Y74C9A.4d", + "object_type": "Translation", + "species": "caenorhabditiselegans", + "start": 17911 + }, + "biotype": "protein_coding", + "end": 24796, + "id": "transcript:Y74C9A.4d", + "object_type": "Transcript", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 17483, + "strand": -1, + "transcript_id": "Y74C9A.4d" + } + ], + "biotype": "protein_coding", + "description": "RCOR (REST CO-Repressor) homolog [Source:RefSeq peptide%3BAcc:NP_001293207]", + "end": 26781, + "gene_id": "WBGene00022278", + "id": "gene:WBGene00022278", + "logic_name": "wormbase", + "member_id": 1, + "object_type": "Gene", + "seq_region_name": "I", + "species": "caenorhabditiselegans", + "start": 17483, + "strand": -1 + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENSCAFT00000026349.gff Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,46 @@ +7 Ensembl gene 41161397 41176758 . + . ID=ENSCAFG00000024151;Name=ENSCAFG00000024151;biotype=protein_coding +7 Ensembl transcript 41161397 41176758 . + . ID=ENSCAFT00000026349;Name=ENSCAFT00000026349;Parent=ENSCAFG00000024151;biotype=protein_coding +7 Ensembl exon 41161397 41161537 . + . Name=ENSCAFE00000180286;Parent=ENSCAFT00000026349 +7 Ensembl exon 41164527 41165078 . + 1 Name=ENSCAFE00000180288;Parent=ENSCAFT00000026349 +7 Ensembl exon 41166549 41166852 . + 1 Name=ENSCAFE00000180303;Parent=ENSCAFT00000026349 +7 Ensembl exon 41166945 41167087 . + 2 Name=ENSCAFE00000180319;Parent=ENSCAFT00000026349 +7 Ensembl exon 41167308 41167452 . + 1 Name=ENSCAFE00000180337;Parent=ENSCAFT00000026349 +7 Ensembl exon 41168280 41168494 . + 2 Name=ENSCAFE00000180353;Parent=ENSCAFT00000026349 +7 Ensembl exon 41168736 41168862 . + 1 Name=ENSCAFE00000180364;Parent=ENSCAFT00000026349 +7 Ensembl exon 41170224 41170462 . + 2 Name=ENSCAFE00000180374;Parent=ENSCAFT00000026349 +7 Ensembl exon 41170839 41171006 . + 1 Name=ENSCAFE00000180385;Parent=ENSCAFT00000026349 +7 Ensembl exon 41171100 41171295 . + 1 Name=ENSCAFE00000180394;Parent=ENSCAFT00000026349 +7 Ensembl exon 41171404 41171445 . + 2 Name=ENSCAFE00000180397;Parent=ENSCAFT00000026349 +7 Ensembl exon 41171521 41171741 . + 2 Name=ENSCAFE00000180399;Parent=ENSCAFT00000026349 +7 Ensembl exon 41171957 41172093 . + 1 Name=ENSCAFE00000180402;Parent=ENSCAFT00000026349 +7 Ensembl exon 41172179 41172341 . + 0 Name=ENSCAFE00000180416;Parent=ENSCAFT00000026349 +7 Ensembl exon 41172550 41172655 . + 1 Name=ENSCAFE00000180432;Parent=ENSCAFT00000026349 +7 Ensembl exon 41173257 41173309 . + 2 Name=ENSCAFE00000180442;Parent=ENSCAFT00000026349 +7 Ensembl exon 41173468 41173697 . + 1 Name=ENSCAFE00000180448;Parent=ENSCAFT00000026349 +7 Ensembl exon 41174196 41174306 . + 0 Name=ENSCAFE00000180452;Parent=ENSCAFT00000026349 +7 Ensembl exon 41174442 41174601 . + 0 Name=ENSCAFE00000180460;Parent=ENSCAFT00000026349 +7 Ensembl exon 41175094 41175223 . + 1 Name=ENSCAFE00000180475;Parent=ENSCAFT00000026349 +7 Ensembl exon 41175346 41175480 . + 2 Name=ENSCAFE00000180481;Parent=ENSCAFT00000026349 +7 Ensembl exon 41175700 41176758 . + 2 Name=ENSCAFE00000309098;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41161397 41161537 . + . Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41164527 41165078 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41166549 41166852 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41166945 41167087 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41167308 41167452 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41168280 41168494 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41168736 41168862 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41170224 41170462 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41170839 41171006 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41171100 41171295 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41171404 41171445 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41171521 41171741 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41171957 41172093 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41172179 41172341 . + 0 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41172550 41172655 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41173257 41173309 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41173468 41173697 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41174196 41174306 . + 0 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41174442 41174601 . + 0 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41175094 41175223 . + 1 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41175346 41175480 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349 +7 Ensembl CDS 41175700 41176758 . + 2 Name=ENSCAFP00000024471;Parent=ENSCAFT00000026349
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENSMUST00000005671.gff Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,44 @@ +7 Ensembl gene 67952859 68226780 . + . ID=ENSMUSG00000005533;Name=ENSMUSG00000005533;biotype=protein_coding +7 Ensembl transcript 67952859 68226780 . + . ID=ENSMUST00000005671;Name=ENSMUST00000005671;Parent=ENSMUSG00000005533;biotype=protein_coding +7 Ensembl exon 67952859 67952952 . + 0 Name=ENSMUSE00000261783;Parent=ENSMUST00000005671 +7 Ensembl exon 68003810 68004355 . + 1 Name=ENSMUSE00000261773;Parent=ENSMUST00000005671 +7 Ensembl exon 68164993 68165305 . + 1 Name=ENSMUSE00000261767;Parent=ENSMUST00000005671 +7 Ensembl exon 68169897 68170048 . + 2 Name=ENSMUSE00000261754;Parent=ENSMUST00000005671 +7 Ensembl exon 68173231 68173375 . + 1 Name=ENSMUSE00000261748;Parent=ENSMUST00000005671 +7 Ensembl exon 68183344 68183558 . + 2 Name=ENSMUSE00000261743;Parent=ENSMUST00000005671 +7 Ensembl exon 68184731 68184857 . + 1 Name=ENSMUSE00000261736;Parent=ENSMUST00000005671 +7 Ensembl exon 68186990 68187228 . + 2 Name=ENSMUSE00000261728;Parent=ENSMUST00000005671 +7 Ensembl exon 68189573 68189740 . + 1 Name=ENSMUSE00000261725;Parent=ENSMUST00000005671 +7 Ensembl exon 68189946 68190150 . + 1 Name=ENSMUSE00000261719;Parent=ENSMUST00000005671 +7 Ensembl exon 68193347 68193630 . + 2 Name=ENSMUSE00000261714;Parent=ENSMUST00000005671 +7 Ensembl exon 68194969 68195105 . + 1 Name=ENSMUSE00000200356;Parent=ENSMUST00000005671 +7 Ensembl exon 68195590 68195749 . + 0 Name=ENSMUSE00000200354;Parent=ENSMUST00000005671 +7 Ensembl exon 68201244 68201346 . + 1 Name=ENSMUSE00000200353;Parent=ENSMUST00000005671 +7 Ensembl exon 68201902 68201972 . + 2 Name=ENSMUSE00000200349;Parent=ENSMUST00000005671 +7 Ensembl exon 68207251 68207480 . + 1 Name=ENSMUSE00000200360;Parent=ENSMUST00000005671 +7 Ensembl exon 68207763 68207873 . + 0 Name=ENSMUSE00000530700;Parent=ENSMUST00000005671 +7 Ensembl exon 68211994 68212156 . + 0 Name=ENSMUSE00000261691;Parent=ENSMUST00000005671 +7 Ensembl exon 68214919 68215048 . + 1 Name=ENSMUSE00000530699;Parent=ENSMUST00000005671 +7 Ensembl exon 68218402 68218536 . + 2 Name=ENSMUSE00000200350;Parent=ENSMUST00000005671 +7 Ensembl exon 68226020 68226780 . + 2 Name=ENSMUSE00000331286;Parent=ENSMUST00000005671 +7 Ensembl CDS 67952859 67952952 . + 0 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68003810 68004355 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68164993 68165305 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68169897 68170048 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68173231 68173375 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68183344 68183558 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68184731 68184857 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68186990 68187228 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68189573 68189740 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68189946 68190150 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68193347 68193630 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68194969 68195105 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68195590 68195749 . + 0 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68201244 68201346 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68201902 68201972 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68207251 68207480 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68207763 68207873 . + 0 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68211994 68212156 . + 0 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68214919 68215048 . + 1 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68218402 68218536 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671 +7 Ensembl CDS 68226020 68226780 . + 2 Name=ENSMUSP00000005671;Parent=ENSMUST00000005671
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENSMUST00000091291.gff Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,44 @@ +8 Ensembl gene 3150922 3279617 . - . ID=ENSMUSG00000005534;Name=ENSMUSG00000005534;biotype=protein_coding +8 Ensembl transcript 3150922 3279617 . - . ID=ENSMUST00000091291;Name=ENSMUST00000091291;Parent=ENSMUSG00000005534;biotype=protein_coding +8 Ensembl exon 3279029 3279617 . - 1 Name=ENSMUSE00000771349;Parent=ENSMUST00000091291 +8 Ensembl exon 3258383 3258934 . - 1 Name=ENSMUSE00001230539;Parent=ENSMUST00000091291 +8 Ensembl exon 3211379 3211700 . - 2 Name=ENSMUSE00000611294;Parent=ENSMUST00000091291 +8 Ensembl exon 3204630 3204778 . - 1 Name=ENSMUSE00000611293;Parent=ENSMUST00000091291 +8 Ensembl exon 3202890 3203034 . - 2 Name=ENSMUSE00000611267;Parent=ENSMUST00000091291 +8 Ensembl exon 3198061 3198275 . - 1 Name=ENSMUSE00000638453;Parent=ENSMUST00000091291 +8 Ensembl exon 3194795 3194921 . - 2 Name=ENSMUSE00000611287;Parent=ENSMUST00000091291 +8 Ensembl exon 3192546 3192802 . - 1 Name=ENSMUSE00000611286;Parent=ENSMUST00000091291 +8 Ensembl exon 3189125 3189292 . - 1 Name=ENSMUSE00000611285;Parent=ENSMUST00000091291 +8 Ensembl exon 3184951 3185152 . - 2 Name=ENSMUSE00000611282;Parent=ENSMUST00000091291 +8 Ensembl exon 3174614 3174888 . - 1 Name=ENSMUSE00000233977;Parent=ENSMUST00000091291 +8 Ensembl exon 3173480 3173619 . - 0 Name=ENSMUSE00000233970;Parent=ENSMUST00000091291 +8 Ensembl exon 3169709 3169868 . - 1 Name=ENSMUSE00000611280;Parent=ENSMUST00000091291 +8 Ensembl exon 3167502 3167604 . - 2 Name=ENSMUSE00000611279;Parent=ENSMUST00000091291 +8 Ensembl exon 3165518 3165585 . - 1 Name=ENSMUSE00000611278;Parent=ENSMUST00000091291 +8 Ensembl exon 3163237 3163481 . - 0 Name=ENSMUSE00000611277;Parent=ENSMUST00000091291 +8 Ensembl exon 3161681 3161791 . - 0 Name=ENSMUSE00000611276;Parent=ENSMUST00000091291 +8 Ensembl exon 3161339 3161498 . - 1 Name=ENSMUSE00000611274;Parent=ENSMUST00000091291 +8 Ensembl exon 3159453 3159582 . - 2 Name=ENSMUSE00000611273;Parent=ENSMUST00000091291 +8 Ensembl exon 3158696 3158830 . - 2 Name=ENSMUSE00000611272;Parent=ENSMUST00000091291 +8 Ensembl exon 3150922 3156023 . - . Name=ENSMUSE00000569243;Parent=ENSMUST00000091291 +8 Ensembl CDS 3279029 3279617 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3258383 3258934 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3211379 3211700 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3204630 3204778 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3202890 3203034 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3198061 3198275 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3194795 3194921 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3192546 3192802 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3189125 3189292 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3184951 3185152 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3174614 3174888 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3173480 3173619 . - 0 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3169709 3169868 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3167502 3167604 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3165518 3165585 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3163237 3163481 . - 0 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3161681 3161791 . - 0 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3161339 3161498 . - 1 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3159453 3159582 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3158696 3158830 . - 2 Name=ENSMUSP00000088837;Parent=ENSMUST00000091291 +8 Ensembl CDS 3150922 3156023 . - . Name=ENSMUSP00000088837;Parent=ENSMUST00000091291
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENSPTRT00000013802.gff Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,44 @@ +15 Ensembl gene 96156951 96470984 . + . ID=ENSPTRG00000007489;Name=ENSPTRG00000007489;biotype=protein_coding +15 Ensembl transcript 96156951 96470984 . + . ID=ENSPTRT00000013802;Name=ENSPTRT00000013802;Parent=ENSPTRG00000007489;biotype=protein_coding +15 Ensembl exon 96156951 96157076 . + . Name=ENSPTRE00000075393;Parent=ENSPTRT00000013802 +15 Ensembl exon 96216402 96216947 . + 1 Name=ENSPTRE00000075406;Parent=ENSPTRT00000013802 +15 Ensembl exon 96403452 96403764 . + 1 Name=ENSPTRE00000075404;Parent=ENSPTRT00000013802 +15 Ensembl exon 96408876 96409024 . + 2 Name=ENSPTRE00000075400;Parent=ENSPTRT00000013802 +15 Ensembl exon 96411580 96411724 . + 1 Name=ENSPTRE00000075399;Parent=ENSPTRT00000013802 +15 Ensembl exon 96420797 96421011 . + 2 Name=ENSPTRE00000075389;Parent=ENSPTRT00000013802 +15 Ensembl exon 96423413 96423539 . + 1 Name=ENSPTRE00000075398;Parent=ENSPTRT00000013802 +15 Ensembl exon 96425147 96425385 . + 2 Name=ENSPTRE00000340876;Parent=ENSPTRT00000013802 +15 Ensembl exon 96428065 96428232 . + 1 Name=ENSPTRE00000075396;Parent=ENSPTRT00000013802 +15 Ensembl exon 96428770 96428974 . + 1 Name=ENSPTRE00000075392;Parent=ENSPTRT00000013802 +15 Ensembl exon 96434239 96434522 . + 2 Name=ENSPTRE00000075387;Parent=ENSPTRT00000013802 +15 Ensembl exon 96435965 96436101 . + 1 Name=ENSPTRE00000075390;Parent=ENSPTRT00000013802 +15 Ensembl exon 96436614 96436773 . + 0 Name=ENSPTRE00000075386;Parent=ENSPTRT00000013802 +15 Ensembl exon 96441658 96441760 . + 1 Name=ENSPTRE00000075407;Parent=ENSPTRT00000013802 +15 Ensembl exon 96442337 96442407 . + 2 Name=ENSPTRE00000075405;Parent=ENSPTRT00000013802 +15 Ensembl exon 96446912 96447141 . + 1 Name=ENSPTRE00000075403;Parent=ENSPTRT00000013802 +15 Ensembl exon 96447405 96447515 . + 0 Name=ENSPTRE00000075397;Parent=ENSPTRT00000013802 +15 Ensembl exon 96451284 96451443 . + 0 Name=ENSPTRE00000075394;Parent=ENSPTRT00000013802 +15 Ensembl exon 96455007 96455136 . + 1 Name=ENSPTRE00000423172;Parent=ENSPTRT00000013802 +15 Ensembl exon 96460655 96460789 . + 2 Name=ENSPTRE00000075402;Parent=ENSPTRT00000013802 +15 Ensembl exon 96469783 96470984 . + 2 Name=ENSPTRE00000075401;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96156951 96157076 . + . Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96216402 96216947 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96403452 96403764 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96408876 96409024 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96411580 96411724 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96420797 96421011 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96423413 96423539 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96425147 96425385 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96428065 96428232 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96428770 96428974 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96434239 96434522 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96435965 96436101 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96436614 96436773 . + 0 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96441658 96441760 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96442337 96442407 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96446912 96447141 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96447405 96447515 . + 0 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96451284 96451443 . + 0 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96455007 96455136 . + 1 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96460655 96460789 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802 +15 Ensembl CDS 96469783 96470984 . + 2 Name=ENSPTRP00000012792;Parent=ENSPTRT00000013802
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENSRNOT00000019267.gff Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,44 @@ +1 Ensembl gene 128924966 129206516 . + . ID=ENSRNOG00000014187;Name=ENSRNOG00000014187;biotype=protein_coding +1 Ensembl transcript 128924966 129206516 . + . ID=ENSRNOT00000019267;Name=ENSRNOT00000019267;Parent=ENSRNOG00000014187;biotype=protein_coding +1 Ensembl exon 128924966 128925059 . + 0 Name=ENSRNOE00000137027;Parent=ENSRNOT00000019267 +1 Ensembl exon 128978104 128978649 . + 1 Name=ENSRNOE00000135455;Parent=ENSRNOT00000019267 +1 Ensembl exon 129142521 129142833 . + 1 Name=ENSRNOE00000135507;Parent=ENSRNOT00000019267 +1 Ensembl exon 129147060 129147211 . + 2 Name=ENSRNOE00000135552;Parent=ENSRNOT00000019267 +1 Ensembl exon 129149693 129149837 . + 1 Name=ENSRNOE00000135606;Parent=ENSRNOT00000019267 +1 Ensembl exon 129159112 129159326 . + 2 Name=ENSRNOE00000135651;Parent=ENSRNOT00000019267 +1 Ensembl exon 129161168 129161294 . + 1 Name=ENSRNOE00000135775;Parent=ENSRNOT00000019267 +1 Ensembl exon 129162727 129162965 . + 2 Name=ENSRNOE00000137123;Parent=ENSRNOT00000019267 +1 Ensembl exon 129166863 129167030 . + 1 Name=ENSRNOE00000135864;Parent=ENSRNOT00000019267 +1 Ensembl exon 129167227 129167431 . + 1 Name=ENSRNOE00000137165;Parent=ENSRNOT00000019267 +1 Ensembl exon 129172248 129172531 . + 2 Name=ENSRNOE00000137211;Parent=ENSRNOT00000019267 +1 Ensembl exon 129174080 129174216 . + 1 Name=ENSRNOE00000136003;Parent=ENSRNOT00000019267 +1 Ensembl exon 129174682 129174841 . + 0 Name=ENSRNOE00000136044;Parent=ENSRNOT00000019267 +1 Ensembl exon 129180666 129180769 . + 1 Name=ENSRNOE00000136080;Parent=ENSRNOT00000019267 +1 Ensembl exon 129180773 129180803 . + 0 Name=ENSRNOE00000520956;Parent=ENSRNOT00000019267 +1 Ensembl exon 129186970 129187229 . + 1 Name=ENSRNOE00000136171;Parent=ENSRNOT00000019267 +1 Ensembl exon 129187512 129187622 . + 0 Name=ENSRNOE00000362520;Parent=ENSRNOT00000019267 +1 Ensembl exon 129191992 129192151 . + 0 Name=ENSRNOE00000136274;Parent=ENSRNOT00000019267 +1 Ensembl exon 129195281 129195410 . + 1 Name=ENSRNOE00000329647;Parent=ENSRNOT00000019267 +1 Ensembl exon 129198768 129198902 . + 2 Name=ENSRNOE00000136353;Parent=ENSRNOT00000019267 +1 Ensembl exon 129206132 129206516 . + 2 Name=ENSRNOE00000137303;Parent=ENSRNOT00000019267 +1 Ensembl CDS 128924966 128925059 . + 0 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 128978104 128978649 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129142521 129142833 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129147060 129147211 . + 2 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129149693 129149837 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129159112 129159326 . + 2 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129161168 129161294 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129162727 129162965 . + 2 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129166863 129167030 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129167227 129167431 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129172248 129172531 . + 2 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129174080 129174216 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129174682 129174841 . + 0 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129180666 129180769 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129180773 129180803 . + 0 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129186970 129187229 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129187512 129187622 . + 0 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129191992 129192151 . + 0 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129195281 129195410 . + 1 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129198768 129198902 . + 2 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267 +1 Ensembl CDS 129206132 129206516 . + 2 Name=ENSRNOP00000019267;Parent=ENSRNOT00000019267
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.json Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,2307 @@ +{ + "ENSCAFG00000024151": { + "Name": "ENSCAFG00000024151", + "Transcript": [ + { + "Exon": [ + { + "Name": "ENSCAFE00000180286", + "Parent": "ENSCAFT00000026349", + "end": 41161537, + "id": "ENSCAFE00000180286", + "length": 141, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41161397, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180288", + "Parent": "ENSCAFT00000026349", + "end": 41165078, + "id": "ENSCAFE00000180288", + "length": 552, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41164527, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180303", + "Parent": "ENSCAFT00000026349", + "end": 41166852, + "id": "ENSCAFE00000180303", + "length": 304, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41166549, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180319", + "Parent": "ENSCAFT00000026349", + "end": 41167087, + "id": "ENSCAFE00000180319", + "length": 143, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41166945, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180337", + "Parent": "ENSCAFT00000026349", + "end": 41167452, + "id": "ENSCAFE00000180337", + "length": 145, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41167308, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180353", + "Parent": "ENSCAFT00000026349", + "end": 41168494, + "id": "ENSCAFE00000180353", + "length": 215, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41168280, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180364", + "Parent": "ENSCAFT00000026349", + "end": 41168862, + "id": "ENSCAFE00000180364", + "length": 127, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41168736, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180374", + "Parent": "ENSCAFT00000026349", + "end": 41170462, + "id": "ENSCAFE00000180374", + "length": 239, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41170224, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180385", + "Parent": "ENSCAFT00000026349", + "end": 41171006, + "id": "ENSCAFE00000180385", + "length": 168, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41170839, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180394", + "Parent": "ENSCAFT00000026349", + "end": 41171295, + "id": "ENSCAFE00000180394", + "length": 196, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41171100, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180397", + "Parent": "ENSCAFT00000026349", + "end": 41171445, + "id": "ENSCAFE00000180397", + "length": 42, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41171404, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180399", + "Parent": "ENSCAFT00000026349", + "end": 41171741, + "id": "ENSCAFE00000180399", + "length": 221, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41171521, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180402", + "Parent": "ENSCAFT00000026349", + "end": 41172093, + "id": "ENSCAFE00000180402", + "length": 137, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41171957, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180416", + "Parent": "ENSCAFT00000026349", + "end": 41172341, + "id": "ENSCAFE00000180416", + "length": 163, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41172179, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180432", + "Parent": "ENSCAFT00000026349", + "end": 41172655, + "id": "ENSCAFE00000180432", + "length": 106, + "object_type": 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+ "length": 160, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41174442, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180475", + "Parent": "ENSCAFT00000026349", + "end": 41175223, + "id": "ENSCAFE00000180475", + "length": 130, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41175094, + "strand": 1 + }, + { + "Name": "ENSCAFE00000180481", + "Parent": "ENSCAFT00000026349", + "end": 41175480, + "id": "ENSCAFE00000180481", + "length": 135, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41175346, + "strand": 1 + }, + { + "Name": "ENSCAFE00000309098", + "Parent": "ENSCAFT00000026349", + "end": 41176758, + "id": "ENSCAFE00000309098", + "length": 1059, + "object_type": "Exon", + "seq_region_name": "7", + "species": "canisfamiliaris", + "start": 41175700, + "strand": 1 + } + ], + "Name": "ENSCAFT00000026349", + "Parent": "ENSCAFG00000024151", + "Translation": { + "CDS": [ + { + "Name": "ENSCAFP00000024471", + "Parent": "ENSCAFT00000026349", + "end": 41161537, + "id": "ENSCAFP00000024471", + "start": 41161397, + "strand": 1 + }, + { + "Name": "ENSCAFP00000024471", + "Parent": "ENSCAFT00000026349", + "end": 41165078, + "id": "ENSCAFP00000024471", + "start": 41164527, + "strand": 1 + }, + { + "Name": "ENSCAFP00000024471", + "Parent": "ENSCAFT00000026349", + "end": 41166852, + "id": "ENSCAFP00000024471", + "start": 41166549, + "strand": 1 + }, + { + "Name": "ENSCAFP00000024471", + "Parent": "ENSCAFT00000026349", + "end": 41167087, + "id": "ENSCAFP00000024471", + "start": 41166945, + "strand": 1 + }, + { + "Name": "ENSCAFP00000024471", + "Parent": "ENSCAFT00000026349", + "end": 41167452, + "id": "ENSCAFP00000024471", + "start": 41167308, + "strand": 1 + }, + { + "Name": "ENSCAFP00000024471", + "Parent": "ENSCAFT00000026349", + "end": 41168494, + "id": "ENSCAFP00000024471", + "start": 41168280, + "strand": 1 + }, + { + "Name": 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