| Previous changeset 0:af9f72ddf7f9 (2016-12-21) Next changeset 2:0c2f9172334a (2017-02-20) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 81a1e79dda127d1afc16c7e456bbec16093a3c3f-dirty |
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modified:
GAFA.py GAFA.xml test-data/gene.json test-data/test.gafa.sqlite |
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added:
test-data/align1.fasta test-data/align2.fasta test-data/align3.fasta test-data/align4.fasta test-data/tree1.nhx test-data/tree2.nhx test-data/tree3.nhx test-data/tree4.nhx |
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removed:
test-data/cigar.tabular test-data/tree.nhx |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 GAFA.py --- a/GAFA.py Wed Dec 21 07:31:50 2016 -0500 +++ b/GAFA.py Mon Feb 20 06:25:33 2017 -0500 |
| [ |
| @@ -1,10 +1,51 @@ from __future__ import print_function +import collections import json import optparse +import re import sqlite3 -version = "0.1.0" +version = "0.2.0" + +Sequence = collections.namedtuple('Sequence', ['header', 'sequence']) + + +def FASTAReader_gen(fasta_filename): + fasta_file = open(fasta_filename) + line = fasta_file.readline() + while True: + if not line: + return + assert line.startswith('>'), "FASTA headers must start with >" + header = line.rstrip() + sequence_parts = [] + line = fasta_file.readline() + while line and line[0] != '>': + sequence_parts.append(line.rstrip()) + line = fasta_file.readline() + sequence = "".join(sequence_parts) + yield Sequence(header, sequence) + + +FASTA_MATCH_RE = re.compile(r'[^-]') + + +def fasta_aln2cigar(sequence): + # Converts each match into M and each gap into D + tmp_seq = FASTA_MATCH_RE.sub('M', sequence) + tmp_seq = tmp_seq.replace('-', 'D') + # Split the sequence in substrings composed by the same letter + tmp_seq = tmp_seq.replace('DM', 'D,M') + tmp_seq = tmp_seq.replace('MD', 'M,D') + cigar_list = tmp_seq.split(',') + # Condense each substring, e.g. DDDD in 4D, and concatenate them again + cigar = '' + for s in cigar_list: + if len(s) > 1: + cigar += str(len(s)) + cigar += s[0] + return cigar def create_tables(conn): @@ -29,38 +70,41 @@ cur.execute('''CREATE TABLE transcript ( transcript_id VARCHAR PRIMARY KEY NOT NULL, protein_id VARCHAR UNIQUE, + protein_sequence VARCHAR, gene_id VARCHAR NOT NULL REFERENCES gene(gene_id))''') cur.execute('''CREATE TABLE gene_family_member ( gene_family_id INTEGER NOT NULL REFERENCES gene_family(gene_family_id), protein_id VARCHAR KEY NOT NULL REFERENCES transcript(protein_id), - alignment VARCHAR NOT NULL, + protein_alignment VARCHAR NOT NULL, PRIMARY KEY (gene_family_id, protein_id))''') conn.commit() -def cigar_to_db(conn, i, fname): +def align_to_db(conn, i, fname): cur = conn.cursor() - with open(fname) as f: - for element in f.readlines(): - seq_id, cigar = element.rstrip('\n').split('\t') - # Trim seq_id by removing everything from the first underscore - seq_id = seq_id.split('_', 1)[0] + for fasta_seq_align in FASTAReader_gen(fname): + seq_id = fasta_seq_align.header[1:] + # Trim seq_id by removing everything from the first underscore + seq_id = seq_id.split('_', 1)[0] - cur.execute('SELECT transcript_id, protein_id FROM transcript WHERE transcript_id=? OR protein_id=?', - (seq_id, seq_id)) - results = cur.fetchall() - if len(results) == 0: - raise Exception("Sequence id '%s' could not be found among the transcript and protein ids" % seq_id) - elif len(results) > 1: - raise Exception("Searching sequence id '%s' among the transcript and protein ids returned multiple results" % seq_id) - transcript_id, protein_id = results[0] - if protein_id is None: - print("Skipping transcript '%s' with no protein id" % transcript_id) - else: - cur.execute('INSERT INTO gene_family_member (gene_family_id, protein_id, alignment) VALUES (?, ?, ?)', - (i, protein_id, cigar)) - conn.commit() + cur.execute('SELECT transcript_id, protein_id FROM transcript WHERE transcript_id=? OR protein_id=?', + (seq_id, seq_id)) + results = cur.fetchall() + if len(results) == 0: + raise Exception("Sequence id '%s' could not be found among the transcript and protein ids" % seq_id) + elif len(results) > 1: + raise Exception("Searching sequence id '%s' among the transcript and protein ids returned multiple results" % seq_id) + transcript_id, protein_id = results[0] + if protein_id is None: + print("Skipping transcript '%s' with no protein id" % transcript_id) + else: + cigar = fasta_aln2cigar(fasta_seq_align.sequence) + cur.execute('INSERT INTO gene_family_member (gene_family_id, protein_id, protein_alignment) VALUES (?, ?, ?)', + (i, protein_id, cigar)) + protein_sequence = fasta_seq_align.sequence.replace('-', '') + cur.execute('UPDATE transcript SET protein_sequence=? WHERE protein_id=?', (protein_sequence, protein_id)) + conn.commit() def newicktree_to_db(conn, i, fname): @@ -99,7 +143,7 @@ def __main__(): parser = optparse.OptionParser() parser.add_option('-t', '--tree', action='append', help='Gene tree files') - parser.add_option('-c', '--cigar', action='append', help='CIGAR alignments of CDS files in tabular format') + parser.add_option('-a', '--align', action='append', help='Protein alignments in fasta_aln format') parser.add_option('-g', '--gene', help='Gene features file in JSON format') parser.add_option('-o', '--output', help='Path of the output file') options, args = parser.parse_args() @@ -111,9 +155,11 @@ gene_json_to_db(conn, options.gene) - for i, (tree, cigar) in enumerate(zip(options.tree, options.cigar), start=1): + for i, (tree, align) in enumerate(zip(options.tree, options.align), start=1): newicktree_to_db(conn, i, tree) - cigar_to_db(conn, i, cigar) + align_to_db(conn, i, align) + + conn.close() if __name__ == '__main__': |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 GAFA.xml --- a/GAFA.xml Wed Dec 21 07:31:50 2016 -0500 +++ b/GAFA.xml Mon Feb 20 06:25:33 2017 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="gafa" name="Gene Align and Family Aggregator" version="0.1.0"> +<tool id="gafa" name="Gene Align and Family Aggregator" version="0.2.0"> <description>generates an SQLite database that can be visualised with Aequatus</description> <command> <![CDATA[ @@ -7,7 +7,7 @@ -t '$dataset' #end for #for $dataset in $alignmentFile: - -c '$dataset' + -a '$dataset' #end for -g '$genesFile' -o '$outputFile' @@ -15,16 +15,16 @@ </command> <inputs> <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" /> - <param name="alignmentFile" type="data" format="tabular" multiple="true" label="CDS alignments" help="CDS alignments in tabular format generated by 'T-Coffee to CIGAR' tool" /> - <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get Ensembl features by ID' tool" /> + <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" /> + <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get features by Ensembl ID' tool" /> </inputs> <outputs> <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> - <param name="treeFile" ftype="nhx" value="tree.nhx" /> - <param name="alignmentFile" ftype="tabular" value="cigar.tabular" /> + <param name="treeFile" ftype="nhx" value="tree1.nhx,tree2.nhx,tree3.nhx,tree4.nhx" /> + <param name="alignmentFile" ftype="fasta" value="align1.fasta,align2.fasta,align3.fasta,align4.fasta" /> <param name="genesFile" ftype="json" value="gene.json" /> <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" /> </test> @@ -35,7 +35,7 @@ Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures. -N.B.: The tool will modify the sequence identifiers found in the "CDS alignments" dataset by removing everything from the first underscore to the end of the string. +N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string. .. _Aequatus: http://aequatus.earlham.ac.uk ]]> |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/align1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align1.fasta Mon Feb 20 06:25:33 2017 -0500 |
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| @@ -0,0 +1,108 @@ +>ENST00000338702_homosapiens_1 +MENQEKASIAGHMFDVVVIGGGISGLSAAKLLTEYGVSVLVLEARDRVGG +RTYTIRNEHVDYVDVGGAYVGPTQNRILRLSKELGIETYKVNVSERLVQY +VKGKTYPFRGAFPPVWNPIAYLDYNNLWRTIDNMGKEIPTDAPWEAQHAD +KWDKMTMKELIDKICWTKTARRFAYLFVNINVTSEPHEVSALWFLWYVKQ +CGGTTRIFSVTNGGQERKFVGGSGQVSERIMDLLGDQVKLNHPVTHVDQS +SDNIIIETLNHEHYECKYVINAIPPTLTAKIHFRPELPAERNQLIQRLPM +GAVIKCMMYYKEAFWKKKDYCGCMIIEDEDAPISITLDDTKPDGSLPAIM +GFILARKADRLAKLHKEIRKKKICELYAKVLGSQEALHPVHYEEKNWCEE +QYSGGCYTAYFPPGIMTQYGRVIRQPVGRIFFAGTETATKWSGYMEGAVE +AGERAAREVLNGLGKVTEKDIWVQEPESKDVPAVEITHTFWERNLPSVSG +LLKIIGFSTSVTALGFVLYKYKLLPRS +>ENST00000542639_homosapiens_1 +MGKEIPTDAPWEAQHADKWDKMTMKELIDKICWTKTARRFAYLFVNINVT +SEPHEVSALWFLWYVKQCGGTTRIFSVTNGGQERKFVGGSGQVSERIMDL +LGDQVKLNHPVTHVDQSSDNIIIETLNHEHYECKYVINAIPPTLTAKIHF +RPELPAERNQLIQRLPMGAVIKCMMYYKEAFWKKKDYCGCMIIEDEDAPI +SITLDDTKPDGSLPAIMGFILARKADRLAKLHKEIRKKKICELYAKVLGS +QEALHPVHYEEKNWCEEQYSGGCYTAYFPPGIMTQYGRVIRQPVGRIFFA +GTETATKWSGYMEGAVEAGERAAREVLNGLGKVTEKDIWVQEPESKDVPA +VEITHTFWERNLPSVSGLLKIIGFSTSVTALGFVLYKYKLLPRS------ +-------------------------------------------------- +-------------------------------------------------- +--------------------------- +>ENSPTRT00000040520_pantroglodytes_1 +MENQEKASIAGHMFDVVVIGGGISGLSAAKLLTEYGVSVLVLEARDRVGG +RTYTIRNEHVDYVDVGGAYVGPTQNRILRLSKELGIETYKVNVSERLVQY +VKGKTYPFRGAFPPVWNPIAYLDYNNLWRTIDNMGKEIPNDAPWEAQHAD +EWDKMTMKELIDKICWTKTARRFAYLFVNINVTSEPHEVSALWFLWYVKQ +CGGTTRIFSVTNGGQERKFVGGSGQVSERIMDLLGDQVKLNHPVTHVDQS +SDNIIIETLNHEHYECKYVINAIPPTLTAKIHFRPELPAERNQLIQRLPM +GAIIKCMMYYKEAFWKKKDYCGCMIIEDEDAPISITLDDTKPDGSLPAIM +GFILARKADRLAKLHKEIRKKKICELYAKVLGSQEALHPVHYEEKNWCEE +QYSGGCYTAYFPPGIMTQYGRVIRQPVGRIFFAGTETATKWSGYMEGAVE +AGERAAREVLNGLGKVTEKDIWVQEPESKDVPAVEITHTFWERNLPSVSG +LLKIIGFSTSVTTLGFVLYKYKLLPRS +>ENSSSCT00000013404_susscrofa_1 +MERQEKANNAGHMVDVVVIGGGISGLSAAKLLNEYGINVLVLEARDRVGG +RTYTVRNENVDYVDVGGAYVGPTQNRILRLSKELGLETYKVNVNECLVQY +VKGKSYPFRGAFPPVWNPIAYLDYNNLWRTMDDMGKKIPADAPWESPHAE +EWDKMTMKDLIDKICWTKTAKRFASLFVNINVTSEPHEVSALWFLWYVKQ +CGGTTRIFSVTNGGQERKFVGGSGQVSERIMHLLGDRVKLRCPVTYVDQS +GDNIIVETLNHELYECQYVISAIPPTLTAKIHFRPELPSERNQLIQRLPM +GAIIKCMMYYKEAFWKKKNYCGCMIIEDEEAPISITLDDTKPDGSLPAIM +GFILARKADRLAKVHKEIRKRKICELYAKVLGSQEALHPVHYEEKNWCEE +QYSGGCYTAYFPPGIMTQYGRVIRQPVGRIFFAGTETATQWSGYMEGAVE +AGERAAREILNALGKVSKKDIWLREPESEDVPAFEITRTFWERNLPSVTG +LLKIIGFSTSVTALWLAVYKFRLLTRS +>ENSSSCT00000035258_susscrofa_1 +SLPAIMGFILARKADRLAKVHKEIRKRKICELYAKVLGSQEALHPVHYEE +KNWCEEQYSGGCYTAYFPPGIMTQYGRVIRQPVGRIFFAGTETATQWSGY +MEGAVEAGERAAREDVPAFEITRTFWERNLPSVTGLLKIIGFSX------ +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +--------------------------- +>ENSSSCT00000032764_susscrofa_1 +MDDMGKKIPADAPWESPHAEEWDKMTMKDLIDKICWTKTAKRFASLFVNI +NVTSEPHEVSALWFLWYVKQCGGTTRIFSVTNGGQERKFVGGSGQVSERI +MHLLGDRVKLRCPVTYVDQSGDNIIVETLNHELYECQYVISAIPPTL--- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +--------------------------- +>ENSCAFT00000022939_canisfamiliaris_1 +MASREKTSIEGHMFDVVVIGGGISGLSAAKLLAEHEVDVLVLEARDRVGG +RTYTVRNEHVDYVDVGGAYVGPTQNRILRLSKELGLETYKVNVNERLVQY +VKGKTYPFRGAFPPVWNPIAYLDYNNLWRTMDNMGKEIPADAPWEAPHAE +EWDKMTMKDLIDKICWTKTARRFASLFVNINVTSEPHEVSALWFLWYVKQ +CGGTTRIFSVTNGGQERKFVGGSGQVSERIMERLGDRVKLKRPVTYVDQS +DDNIIIETLNHELYECKYVISAIPPTLTAKIHFRPELPSERNQLIQRLPM +GAIIKCMMYYKEAFWKKKDYCGCMIIEDEEAPISITLDDTKPDGSLPAIM +GFILARKADRLAKLHKEIRKRKICELYAKVLGSQEALQPVHYEEKNWCEE +QYSGGCYTAYFPPGIMTHYGRVIRQPFGRIYFAGTETATHWSGYMEGAVE +AGERTAREVLNALGRVAEKDLKTQEPESKDVPAMEITHTFWERNLPSVTG +LLKLIGFTTSVTALWIVAYKFRLLRRS +>ENSMUST00000026013_musmusculus_1 +MTDLEKPSITGHMFDVVVIGGGISGLAAAKLLSEYKINVLVLEARDRVGG +RTYTVRNEHVKWVDVGGAYVGPTQNRILRLSKELGIETYKVNVNERLVQY +VKGKTYPFRGAFPPVWNPLAYLDYNNLWRTMDDMGKEIPVDAPWQARHAE +EWDKITMKDLIDKICWTKTAREFAYLFVNINVTSEPHEVSALWFLWYVRQ +CGGTSRIFSVTNGGQERKFVGGSGQISEQIMVLLGDKVKLSSPVTYIDQT +DDNIIIETLNHEHYECKYVISAIPPVLTAKIHFKPELPPERNQLIQRLPM +GAVIKCMVYYKEAFWKKKDYCGCMIIEDEEAPISITLDDTKPDGSMPAIM +GFILARKAERLAKLHKDIRKRKICELYAKVLGSQEALSPVHYEEKNWCEE +QYSGGCYTAYFPPGIMTLYGRVIRQPVGRIYFAGTETATQWSGYMEGAVE +AGERAAREVLNALGKVAKKDIWVQEPESKDVPALEITHTFLERNLPSVPG +LLKITGFSTSVALLCFVLYKFKQPQS- +>ENSRNOT00000066674_rattusnorvegicus_1 +MTDLEKPNLAGHMFDVVVIGGGISGLAAAKLLSEYKINVLVLEARDRVGG +RTYTVRNEHVKWVDVGGAYVGPTQNRILRLSKELGIETYKVNVNERLVQY +VKGKTYPFRGAFPPVWNPLAYLDYNNLWRTMDEMGKEIPVDAPWQARHAQ +EWDKMTMKDLIDKICWTKTAREFAYLFVNINVTSEPHEVSALWFLWYVRQ +CGGTARIFSVTNGGQERKFVGGSGQVSEQIMGLLGDKVKLSSPVTYIDQT +DDNIIVETLNHEHYECKYVISAIPPILTAKIHFKPELPPERNQLIQRLPM +GAVIKCMVYYKEAFWKKKDYCGCMIIEDEEAPIAITLDDTKPDGSLPAIM +GFILARKADRLAKLHKDIRKRKICELYAKVLGSQEALYPVHYEEKNWCEE +QYSGGCYTAYFPPGIMTQYGRVIRQPVGRIYFAGTETATQWSGYMEGAVE +AGERAAREVLNALGKVAKKDIWVEEPESKDVPAIEITHTFLERNLPSVPG +LLKITGVSTSVALLCFVLYKIKKLPC- |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/align2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align2.fasta Mon Feb 20 06:25:33 2017 -0500 |
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| @@ -0,0 +1,108 @@ +>ENSPTRT00000040521_pantroglodytes_1 +MSNKCDVVVVGGGISGKAAAKLLHDSGLNVVVLEARDRVGGRTYTLRNQK +VKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHHVKGKSYPFR +GPFPPVWNPITYLDHNNFWRTMDDMGREIPSDAPWKAPLAEEWDNMTMKE +LLDKLCWTESAKQLATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIIS +TTNGGQERKFVGGSGQVSERIMDLLGDRVKLERPVIYIDQTRENVLVETL +NHEMYEAKYVISAIPPTLGMKIHFNPPLPMMRNQMITRVPLGSVIKCIVY +YKEPFWRKKDYCGTMIIDGEEAPVAYTLDDTKPEGNYAAIMGFILAHKAR +KLARLTKEERLKKLCELYAKVLGSPEALEPVHYEEKNWCEEQYSGGCYTT +YFPPGILTQYGRVLRQPVDRIYFAGTETATHWSGYMEGAVEAGERAAREI +LHAMGKIPEDEIWQSEPESVDVPAQPITTTFLERHLPSVPGLLRLIGLTT +IFSATALGFLAHKRGLLVRV +>ENST00000378069_homosapiens_1 +MSNKCDVVVVGGGISGMAAAKLLHDSGLNVVVLEARDRVGGRTYTLRNQK +VKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHHVKGKSYPFR +GPFPPVWNPITYLDHNNFWRTMDDMGREIPSDAPWKAPLAEEWDNMTMKE +LLDKLCWTESAKQLATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIIS +TTNGGQERKFVGGSGQVSERIMDLLGDRVKLERPVIYIDQTRENVLVETL +NHEMYEAKYVISAIPPTLGMKIHFNPPLPMMRNQMITRVPLGSVIKCIVY +YKEPFWRKKDYCGTMIIDGEEAPVAYTLDDTKPEGNYAAIMGFILAHKAR +KLARLTKEERLKKLCELYAKVLGSLEALEPVHYEEKNWCEEQYSGGCYTT +YFPPGILTQYGRVLRQPVDRIYFAGTETATHWSGYMEGAVEAGERAAREI +LHAMGKIPEDEIWQSEPESVDVPAQPITTTFLERHLPSVPGLLRLIGLTT +IFSATALGFLAHKRGLLVRV +>ENSRNOT00000044009_rattusnorvegicus_1 +MSNKCDVIVVGGGISGMAAAKLLHDCGLSVVVLEARDRVGGRTYTIRNKN +VKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHFVKGKSYAFR +GPFPPVWNPITYLDYNNLWRTMDEMGQEIPSDAPWKAPLAEEWDYMTMKE +LLDKICWTNSTKQIATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIIS +TTNGGQERKFIGGSGQVSERIKDILGDRVKLERPVIHIDQTGENVVVKTL +NHEIYEAKYVISAIPPVLGMKIHHSPPLPILRNQLITRVPLGSVIKCMVY +YKEPFWRKKDFCGTMVIEGEEAPIAYTLDDTKPDGSCAAIMGFILAHKAR +KLVRLTKEERLRKLCELYAKVLNSQEALQPVHYEEKNWCEEQYSGGCYTA +YFPPGILTQYGRVLRQPVGKIFFAGTETASHWSGYMEGAVEAGERAAREI +LHAIGKIPEDEIWQPEPESVDVPARPITNTFLERHLPSVPGLLKLLGLTT +ILSATALGFLAHKKGLFVRF +>ENSMUST00000040820_musmusculus_1 +MSNKSDVIVVGGGISGMAAAKLLHDCGLSVVVLEARDRVGGRTYTIRNKN +VKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHFVKGKSYAFR +GPFPPVWNPITYLDNNNLWRTMDEMGQEIPSDAPWKAPLAEEWDYMTMKE +LLDKICWTKSTKQIATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIIS +TTNGGQERKFIGGSGQVSERIKDILGDRVKLERPVIHIDQTGENVIVKTL +NHEIYEAKYVISAIPPALGMKIHYSPPLPMLRNQLISRVPLGSVIKCMVY +YKEPFWRKKDFCGTMVIEGEEAPIAYTLDDTKPDGTYAAIMGFILAHKAR +KLVRLTKEERLRKLCELYAKVLNSQEALQPVHYEEKNWCEEQYSGGCYTT +YFPPGILTQYGRVLRQPVGKIFFAGTETASHWSGYMEGAVEAGERAAREI +LHAIGKIPEDEIWQPEPESLDVPARPITSTFLERHLPSVPGLLKLFGLTT +ILSATALGFLAHKRGLFVHF +>ENSMUST00000168613_musmusculus_1 +MSNKSDVIVVGGGISGMAAAKLLHDCGLSVVVLEARDRVGGRTYTIRNKN +VKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHFVKGKSYAFR +GPFPPVWNPITYLDNNNLWRTMDEMGQEIPSDAPWKAPLAEEWDYMTMKE +LLDKICWTKSTKQIATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIIS +TTNGGQGKMLL--------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------- +>ENSMUST00000163344_musmusculus_1 +MSNKSDVIVVGGGISGMAAAKLLHDCGLSVVVLEARDRVGGRTYTIRNKN +VKYVDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHFVKIYKADCH +ALCEPVCNCRDP-------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------- +>ENSSSCT00000033745_susscrofa_1 +MAAAKLLHDSGLSVIVLEARDRVGGRTYTVRNQQVKYVDLGGSYVGPTQN +RILRLSKELGLETYKVNEVERLIHYVKGKSYPFRGPLPPVRNPITFLDLN +NLWRTVDDMGREIPSDAPWKAPLAEQWDQMTMKELLDKLCWTESSKQLAT +LFVNLCVTAETHEVSALWFLWYVKQCGGTTRIISTTNGGQERKFVGGSGQ +VTERIKDLLGDRVKLERPVVHIDQTGENVLVETLNHEVYEAKYVISAIPP +VLGMKIHFSPPLPMMRNQLITRVPLGSVIKCIVYYKEPFWRHKDYCGSMI +IEGEEAPIAYTLDDSKPDGSCAAIIGFILAHKARKLARLTKEERLKKLCD +LYAKVLGSKEALNPVHYEEKNWCEEQYSAGCYTTYFPPGIMTQYGRVLRQ +PVGRIYFAGTETATHWSGYMEGAVEAGERAAREILHAMGKIPEDEIWQSE +PESVDVPAKPITTTFLERHLPSVPGLLRLIGLTAIFSATALGYLAHKRGL +LVRV---------------- +>ENSSSCT00000023183_susscrofa_1 +MAAAKLLHDSGLSVIVLEARDRVGGRTYTVRNQQVKYVDLGGSYVGPTQN +RILRLSKELGLETYKVNEVERLIHYIKGKSYPFRGPLPPVRNPITFLDLN +NLWRTVDDMGREIPSDAPWKAPLAEQWDQMTMKELLDKLCWTESSKQLAT +LFVNLCVTAETHEVSALWFLWYVKQCGGTTRIISTTNGGQERKFVGGSGQ +VTERIKDLLGDRVKLERPVVHIDQTGENVLVETLNHEVYEAKYVISAIPP +VLGMKIHFSPPLPMMRNQLITRVPLGSVIKCIVYYKEPFWRHKDYCGSMI +IEGEEAPIAYTLDDSKPDGSCAAIIGFILAHKARKLARLTKEERLKKLCD +LYAKVLGSKEALNPVHYEEKNWCEEQYSAGCYTTYFPPGIMTQYGRVLRQ +PVGRIYFAGTETATHWSGYMEGAVEAGERAAREILHAMGKIPEDEIWQSE +PESVDVPAKPITTTFLERHLPSVPGLLRLIGLTAIFSATALGYLAHKRGL +LVRV---------------- +>ENSCAFT00000022963_canisfamiliaris_1 +MSGKCDVVMVGGGISGMAAAKLLHDFGLNVVVLEARDRVGGRTYTIRNQK +VKYLDLGGSYVGPTQNCILRLAKELGLETYKVNEVERLIHHVKGKSYPFR +GPFPPVWNPIAYLDHNNLWRTMDDMGREIPSDAPWKAPLAEEWDHMTMKE +LLDKICWTESAKQLATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIIS +TTNGGQERKFVGGSGQVSERIMDLLGDQVKLERPVTHIDQTGENVLVETL +NHEVYEAKYVISAIPPTLGMKIHFNPPLPMMRNQLITRVPLGSVIKCIVY +YKEPFWRKKDYCGTMIIEGEEAPIAYTLDDTKPDGNYAAIMGFILAHKAR +KLARLTKDERMKKLCELYAKVLGSQEALQPVHYEEKNWCEEQYSGGCYTT +YFPPGIMTQYGRVLRQPVGRIYFAGTETATHWSGYMEGAVEAGERAAREI +LHAMGKIPEDEIWQSEPESVDVPAQPITTTFLERHLPSVPGLLRLIGLTA +IFSATALGVLAHKRGLLVRV |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/align3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align3.fasta Mon Feb 20 06:25:33 2017 -0500 |
| b |
| b'@@ -0,0 +1,171 @@\n+>ENSPTRT00000034846_pantroglodytes_1\n+MDPECAQLLPALCAVLVDPRQPVADDTCLEKLLDWFKTVTEGESSVVLLQ\n+EHPCLVELLSHVLKVQDLSSGVLSFSLRLAGTFAAQENCFQYLQQGELLP\n+GLFGEAGPLGRAAWAVPTVRSGWIQGLRSLAQHPSALRFLADHGAVDTIF\n+SLQGDSSLFVASAASQLLVHVLALSMQGGAEGQPCLPGGDWPACAQRIMD\n+HVEESLCSAATPKVTQALNVLTTTFGRCQSPWTEALWVRLSPRVACLLER\n+DPIPAAHSFVDLLLCVARSPVFSSSDGSLWETVARALSCLGPTHMGPLAL\n+GILKLEHCPQALRTQAFQVLLQPLACVLKATVQAPGPPGLLDGTADDATT\n+VDTLLASKSSCAGLLCRTLAHLEELQPLPQRPSPWPQASLLGATVTVLRL\n+CDGSAAPASSVGGHLCGTLAGCVRVQRAALDFLGTLSQGTGPQELVTQAL\n+AVLLECLESPGSSPTVLKKAFQATLRWLLSSPKTPGCSDLGPLIPQFLRE\n+LFPVLQKRLCHPCWEVRDSALEFLTQLSRHWGGQADFRCALLASEVPELA\n+LQLLQDPESYVRASAVTAMGQLSSQGLHAPTSPEHAEARQSLFPELLHIL\n+SVDSEGFPRRAVMQVFTEWLRDGHADAARDTEQFVATVLQVASRDLDWEV\n+RAQGLELALVFLGQTLGPPRTHCPYAVALPEVAPAQPLTEALRALCHVGL\n+FDFAFCALFDCDRPVAQKSCDLLLFLRDKIASYSSLREARGGPNTASAEA\n+TLPRWRAGEQAQPPGDQEPEAVLAMLRSLDLEGLRSTLAESSDHVEKSPQ\n+SLLQDMLATGGFLQGD----------------------------------\n+---------EADCY---\n+>ENST00000340611_homosapiens_1\n+MDPECAQLLPALCAVLVDPRQPVADDTCLEKLLDWFKTVTEGESSVVLLQ\n+EHPCLVELLSHVLKVQDLSSGVLSFSLRLAGTFAAQENCFQYLQQGELLP\n+GLFGEPGPLGRATWAVPTVRSGWIQGLRSLAQHPSALRFLADHGAVDTIF\n+SLQGDSSLFVASAASQLLVHVLALSMRGGAEGQPCLPGGDWPACAQKIMD\n+HVEESLCSAATPKVTQALNVLTTTFGRCQSPWTEALWVRLSPRVACLLER\n+DPIPAAHSFVDLLLCVARSPVFSSSDGSLWETVARALSCLGPTHMGPLAL\n+GILKLEHCPQALRTQAFQVLLQPLACVLKATVQAPGPPGLLDGTADDATT\n+VDTLLASKSSCAGLLCRTLAHLEELQPLPQRPSPWPQASLLGATVTVLRL\n+CDGSAAPASSVGGHLCGTLAGCVRVQRAALDFLGTLSQGTGPQELVTQAL\n+AVLLECLESPGSSPTVLKKAFQATLRWLLSSPKTPGCSDLGPLIPQFLRE\n+LFPVLQKRLCHPCWEVRDSALEFLTQLSRHWGGQADFRCALLASEVPQLA\n+LQLLQDPESYVRASAVTAMGQLSSQGLHAPTSPEHAEARQSLFLELLHIL\n+SVDSEGFPRRAVMQVFTEWLRDGHADAAQDTEQFVATVLQAASRDLDWEV\n+RAQGLELALVFLGQTLGPPRTHCPYAVALPEVAPAQPLTEALRALCHVGL\n+FDFAFCALFDCDRPVAQKSCDLLLFLRDKIASYSSLREARGSPNTASAEA\n+TLPRWRAGEQAQPPGDQEPEAVLAMLRSLDLEGLRSTLAESSDHVEKSPQ\n+SLLQDMLATGGFLQGD----------------------------------\n+---------EADCY---\n+>ENSRNOT00000064726_rattusnorvegicus_1\n+MDAECSRLLPALCAVLADPRQLVADDTCLEKLLDWFKTVTEAEPSLQLLQ\n+DHPCLMELLSHVLKPQDVSPRVLSFALRLVGVFAAQEDCFQYLQQGELLL\n+GLFGETGALSWAAWSIPSVRSGWIQGLCSLAHHPSALHFLADSGAVDTIF\n+SLQGDPSLFVASAASQLLVHILALSMQGGAPGSPVPEAVAWPVCAQKIMN\n+HVEESLHSKATPQVTQALNVLTTTFGRCHNPWTGVLWERLSPPVARLFER\n+DPIPATHSLMDLLLSVARSPVLNFAACGLWEMLAQTLSRLSPTQAGPLAL\n+GTLKLQHCPQELRTQAFRVLLQPLACILKATTQAPGPPGLLDGTAGSLLT\n+VDALLSSKSACVGLLCQTLAHLEELQMLPQCPSPWPQVPLLQAAVTILRL\n+SDGSADPSSSAGGRLCGALGGCVRVQRAALDFLGTLSLGTSPLELVLEVF\n+AVLLKTLESPESSPMVLKKAFQATLRWLQSPHKTPSGSDLSPDALLFLGE\n+LFPILQKRLCSPCWEVRDSALEFLTHLIRDWGGQADFREALHSSEVPTLA\n+RQLLQDPESYVRASAVGAAGQLSSQGLQATPANQQGLLMDLMHILSTDSE\n+GFPRRAVLRVFTEWLRDGHADVVRDTEWFVATVLQAVSRDLDWEVRVQGL\n+ELAQVFLIQAMGQPRLHCPYTVGLPGATSSRPHLEFLQTLCRLPLFEFAF\n+CALLDCDRPVAQKACDLLLFLRDKTVSCSNPQEAGDSPNSASVEAALQRW\n+REGEQAQPLGDLEPEAMLAILRSLDLEGLQGRLAKSSDHVEKSPQSLLQD\n+MLATVGVLEENEADCY----------------------------------\n+-----------------\n+>ENSMUST00000041588_musmusculus_1\n+MDPECSRLLPALCAVLADPRQLVADDTCLEKLLDWFKTVTEAESSLQLLQ\n+DHPCLMELLSHVLKPQDVSPRVLSFALRLVGVFAAQEDCFEYLQQGELLL\n+GLFGESGAPGWAAWSIPSVRSGWIQGLCYLAHHPSALHFLADSGAVDTLF\n+SLQGDPSLFVASAASQLLVHILALSMQGGAPGSPVPEAAAWPMCAQKIVN\n+HVDESLHAKATPQVTQALNVLTTTFGRCHNPWTGVLWERLSPPVARLFER\n+DPIPAVHALMDLLLSVARSPVLNFAACGLWEMLAQTLSRLSPIQAGPLAL\n+GTLKLQHCPQELRTQAFGVLLQPLACILKATTQAPGPPGLLDGTVGSLLT\n+VDILLASKSACVGLLCQTLAHLEELQMLPQCPSPWPQVHLLQAALTILHL\n+CDGSADPSSSAGGRLCGTLGGCVRVQRAALDFLGTLSQGTSPLELVLEVF\n+AVLLKTLESPESSPMVLKKAFQATLRWLQNPHKTPSSSDLSSDALLFLGE\n+LFPILQKRLCSPCWEVRDSALEFLTHLIRHWGGQADFREALRSSEVPTLA\n+LQLLQDPESYVRASAVGAAGQLSSQGLQAAPASPENSQAQQGLLMDLMHI\n+LSTDSEGFPRRAVLRVFTDWLRDGHADVVRDTEWFVATVLQAVSRDLDWE\n+VRVQGLELARVFLTQALGQPSLHCPYTVGLPRASSPRPHPEFLQTLCRLP\n+LFEFAFCALLDCDRPVAQKACDLLLFLRDKTVPCSSPREAGDSPNSASVE\n+AALQRWREGEQAQPLGDLDPEAMLAILRALDLEGLQGRLAKSSDHVEKSP\n+QSLLQDMLATVGVLEENEADCY----------------------------\n+-----------------\n+>ENSMUST00000153440_musmusculus_1\n+MDPECSRLLPALCAVLADPRQLVADDTCLEKLLDWFKTVTEAESSLQLLQ\n+DHPCLMELLSHVLKPQDVSPRVLSFALRLVGVFAAQEDCFEYLQQGELLL\n+GLFGESGAPGWAAWSIPSVRSGWIQGLCYLAHHPSALHFLADSGAVDTLF\n+SLQGDPSLFVASAASQLLVHILALSMQGGAPG'..b'-----------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------\n+>ENSMUST00000110806_musmusculus_1\n+MDPECSRLLPALCAVLADPRQLVADDTCLEKLLDWFKTVTEAESSLQLLQ\n+DHPCLMELLSHVLKPQDVSPRVLSFALRLVGVFAAQEDCFEYLQQGELLL\n+GLFGESGAPGWAAWSIPSVRSGWIQGLCYLAHHPSALHFLADSGAVDTLF\n+SLQGDPSLFVASAASQLLVHILALSMQGGAPGSPVPEAAAWPMCAQKIVN\n+HVDESLHAKATPQVTQALNVLTTTFGRCHNPWTGVLWERLSPPVARLFER\n+DPIPAVHALMDLLLSVARSPVLNFAACGLWEMLAQTLSRLSPIQAGPLAL\n+GTLKLQHCPQELRTQAFGVLLQPLACILKATTQAPGPPGLLDGTVGSLLT\n+VDILLASKSACVGLLCQTLAHLEELQMLPQCPSPWPQVHLLQAALTILHL\n+CDGSADPSSSAGGRLCGTLGGCVRVQRAALDFLGTLSQGTSPLELVLEVF\n+AVLLKTLESPESSPMVLKKAFQATLRWLQNPHKTPSSSDLSSDALLFLGE\n+LFPILQKRLCSPCWEVRDSALEFLTHLIRHWGGQADFREALRSSEVPTLA\n+LQLLQDPESYVRASAVGAAGQLSSQGLQAAPASPENSQAQQVDTGSW---\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+-----------------\n+>ENSMUST00000100505_musmusculus_1\n+MVHFALSGLIPVAEGCGGGIRTPRLTRSRRERTSYPDLGGTACLIMDPEC\n+SRLLPALCAVLADPRQLVADDTCLEKLLDWFKTVTEAESSLQLLQDHPCL\n+MELLSHVLKPQDVSPRVLSFALRLVGVFAAQEDCFEYLQQGELLLGLFGE\n+SGAPGWAAWSIPSVRSGWIQGLCYLAHHPSALHFLADSGAVDTLFSLQGD\n+PSLFVASAASQLLVHILALSMQGGAPGSPVPEAAAWPMCAQKIVNHVDES\n+LHAKATPQVTQALNVLTTTFGRCHNPWTGVLWERLSPPVARLFERDPIPA\n+VHALMDLLLSVARSPVLNFAACGLWEMLAQTLSRLSPIQAGPLALGTLKL\n+QHCPQELRTQAFGVLLQPLACILKATTQAPGPPGLLDGTVGSLLTVDILL\n+ASKSACVGLLCQTLAHLEELQMLPQCPSPWPQVHLLQAALTILHLCDGSA\n+DPSSSAGGRLCGTLGGCVRVQRAALDFLGTLSQGTSPLELVLEVFAVLLK\n+TLESPESSPMVLKKAFQATLRWLQNPHKTPSSSDLSSDALLFLGELFPIL\n+QKRLCSPCWEVRDSALEFLTHLIRHWGGQADFREALRSSEVPTLALQLLQ\n+DPESYVRASAVGAAGQLSSQGLQAAPASPENSQAQQGLLMDLMHILSTDS\n+EGFPRRAVLRVFTDWLRDGHADVVRDTEWFVATVLQAVSRDLDWEVRVQG\n+LELARVFLTQALGQPSLHCPYTVGLPRASSPRPHPEFLQTLCRLPLFEFA\n+FCALLDCDRPVAQKACDLLLFLRDKTVPCSSPREAGDSPNSASVEAALQR\n+WREGEQAQPLGDLDPEAMLAILRALDLEGLQGRLAKSSDHVEKSPQSLLQ\n+DMLATVGVLEENEADCY\n+>ENSCAFT00000025950_canisfamiliaris_1\n+MDPECSQLLPALCAVLADPRQPVADDTCLEKLLDWFKTITKAGSSLLLLQ\n+ENPCLVELLCHVLKPQDLSSRVLSFSLRLAGVFAAQEDCFQYLQQGELLP\n+RLFGEPGPLGGAAWTAPSVRSGWIQGLRSLAQHPSALHFLADCGAVDTIF\n+SLQGDSSLFVASAAGQLLVHILGLSMQGLAEGHPSLQAGDWPVCAQKIVG\n+HIEESLHSTAVPQITQALNVLTTTFGHCHDPWTQVLWVRLSPLVGSLLEK\n+DPVPAAHSLVDLLLSVARSPGLSSSSCGLWETLAQTLNHLSPTQAGPLAL\n+GILKLQDCPQVLRAQAFVILLQPLACVLKATGQDPGPSGVLDSATGDSLT\n+VDVLLSSKAACVGLLCRTLAHLELLQPLPQRPCPWPQEPLLGAAVTLLQL\n+CRGSASPASDVGRHLCALLLGCVRVQRAALDFLGTLSQGTGPQELVTEVF\n+AVLLEYLRSPDSSPTVLKKAFQATFRWLLSSPKTPGCCDLEPHALLVLRE\n+LLPVLQKRLCSPCWEVRDSGLEFLTQMTRHWGGQAGFRHALLASEVPKLT\n+EQLLRDPESYVRASAVTVMGQLSSQGLHVTPVSPEHPGGQQKSLLVELLH\n+ILSTDSEGFPRRAVMQVFTQWLRDHHADVAGDTEQFMARVLQVASQDLDW\n+EVRAQGLELALVFLEQTLGQFHSHCPYAVTPPVAAPAGSLAQALQPLCRV\n+RLFEFAFRALFDCDRPVAQKSCDLLLFLRAKTASSSGSLEESRSGPDVAS\n+VEAALQRWQAGDQGQPLGDLEPEVVLAVLRSVDLEGLRGALAEGSDHMEK\n+SPQSLLQDMLATVGVL----------------------------------\n+---------GENEADCY\n+>ENSSSCT00000008295_susscrofa_1\n+MDPECSRLLPALCAVLADPRQPVADDTCLEKLLDWFKTITEAGSSLLVLQ\n+ENPCLVELLFDVLKPQDLSPRVLSFSLRLAGMFAAQEDCFQYLQQGELLP\n+RLFGEAGPLGGAAWTAPTVRSGWIQGLRSLAQHPRALPFLADCGAVDTIF\n+SLQGDSSLFVASAAGQLLVHILDLAMRAPPRGHPGPQACDGPACAQKIVC\n+HLEDSLRAAAAPQLTQALNVLTTTFGHCHGLWTPGLWGRLSPLVGHLLEK\n+DPVPASHALVDLLLSVARSPVLSSESGPWETLALTLSRLSPMQAGPLALG\n+ILKLQDCPQALRTQASGVLLQPLACVLKAAVQGPGRPGRLLGKGGRCRMA\n+GPWGPERILGAGAGCHPRCDCCSCCHPGXSALGLAQEARLRLCDNAAIPR\n+SDLGGQFCGHLVACVRVQRAALDFLGTLSQRAGPQELVTQVSAVLLEYLS\n+GPDSSPTVLKKAFQASLGWLLSSPKTPGCCDLDPHAQQFLRELLPVLQKR\n+LCSPCWEVRDSGLEFLTQMARHWGGQAAFRQVLLASEVPRLTRQLLQDPE\n+SYVRASAVTATGQLSSWGLHAAPAGPEHPGVQQKSLLSELLHVLATDSEG\n+FPRRAVMQVFTEWLRGGHADVAEDPEQFVAGVLQAASRDLDWEVRAQGLE\n+LALVFLEQLLGPPGVRCPYAVALPKAAPPGTLAQALQALCRVQLFEFAFR\n+ALFDCDRPVAQKSCDLLLFLKAKATSCGTPQEERDSPDVSSVEATLQKWQ\n+AGEHGHPLGDLEPAAVVAVLRSMDLEGLQDTLAESSDHVERSPQSLLQDM\n+LATVGVLGENEADCY-----------------------------------\n+-----------------\n' |
| b |
| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/align4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align4.fasta Mon Feb 20 06:25:33 2017 -0500 |
| b |
| b'@@ -0,0 +1,290 @@\n+>ENSPTRT00000019089_pantroglodytes_1\n+IGTGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHEL\n+ENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLK\n+DLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNN\n+ELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATV\n+INGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPT\n+KCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG\n+CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDS\n+VTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS\n+YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQ\n+GKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELL\n+KFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDA\n+CGSNSWTVVDIDPPLRSNDPKSQNHP--GWLMRGLKPWTQYAIFVKTLVT\n+FSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDP\n+NGNITHYLVFWERQAEDSELFELDYCLKWCVWCVCVVVCLWSVCEYEDSA\n+GECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPR\n+PSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKES\n+LVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGP\n+VTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFA\n+LERGCRLRGLSPGNYSVRVRATSLAGNGSWTEPTYFYVTDYLDVPSNIAK\n+IIIGPLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVF\n+PCSVYVPDEWEVPREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAV\n+KTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELM\n+AHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFV\n+HRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPVRWMAPE\n+SLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLD\n+QPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHS\n+EENKAPESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYE\n+EHIPYTHMNGGKKNGRILTLPRSNPS----------\n+>ENST00000341500_homosapiens_1\n+MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHEL\n+ENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLK\n+DLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNN\n+ELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATV\n+INGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPT\n+KCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG\n+CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDS\n+VTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS\n+YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQ\n+GKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELL\n+KFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDA\n+CGSNSWTVVDIDPPLRSNDPKSQNHP--GWLMRGLKPWTQYAIFVKTLVT\n+FSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDP\n+NGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHN\n+QSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRPSRK\n+RRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVIS\n+GLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHE\n+IFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERG\n+CRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG\n+PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSV\n+YVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVN\n+ESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGD\n+LKSYLRSLRPEAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDL\n+AARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPVRWMAPESLKD\n+GVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN\n+CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENK\n+APESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIP\n+YTHMNGGKKNGRILTLPRSNPS--------------\n+>ENST00000302850_homosapiens_1\n+MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHEL\n+ENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLK\n+DLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNN\n+ELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATV\n+INGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPT\n+KCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG\n+CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDS\n+VTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS\n+YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQ\n+GKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELL\n+KFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDA\n+CGSNSWTVVDIDPPLRSNDPKSQNHP--GWLMRGLKPWTQYAIFVKTLVT\n+FSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDP\n+NGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHN\n+QSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSS\n+GTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPF\n+EKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEA\n+KADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHL\n+CVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYL\n+DVPSNI'..b'GLIEEISGFLKIRRS\n+YALVSLSFFRKLHLIRGETLEIGNYSFYALDNQNLRQLWDWNKHNLTITQ\n+GKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELL\n+KFSFIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDA\n+CGSNSWTVVDIDPPQRSNDPKSQTPS--HPGWLMRGLKPWTQYAIFVKTL\n+VTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPS\n+DPNGNITHYLVYWERQAEDSELFELDYCLKGLKLPSRTWSPPFESDDSQK\n+HNQSEYDDSASECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKT\n+SSGNGAEDTRPSRKRRSLEEVGNVTATTPTLPDFPNISSTIAPTSHEEHR\n+PFEKVVNKESLVISGLRHFTGYRIELQACNQDSPEERCSVAAYVSARTMP\n+EAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEEL\n+HLCVSRKHFALERGCRLRGLSPGNYSVRVRATSLAGNGSWTEPTYFYVTD\n+YLDVPSNIAKIIIGPLIFVFLFSVVIGSIYLFLRKRQPDGPMGPLYASSN\n+PEYLSASDVFPSSVYVPDEWEVPREKITLLRELGQGSFGMVYEGNAKDII\n+KGEVETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKG\n+QPTLVVMELMAHGDLKSHLRSLRPDAENNPGRPPPTLQEMIQMTAEIADG\n+MAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKG\n+LLPVRWMSPESLKDGVFTASSDMWSFGVVLWEITSLAEQPYQGLSNEQVL\n+KFVMDGGYLDPPDNCPERLTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHP\n+SFPEVSFFYSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGCREGG\n+SSLSIKRTYDEHIPYTHMNGGKKNGRVLTLPRSNPS\n+>ENSRNOT00000067448_rattusnorvegicus_1\n+MGSGRGCETTAVPLLMAVAVAGGTAGHLYPGEVCPGMDIRNNLTRLHELE\n+NCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKD\n+LFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNE\n+LCYLATIDWSRILDSVEDNYIVLNKDDNEECGDVCPGTAKGKTNCPATVI\n+NGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHKECLGNCSEPDDPTK\n+CVACRNFYLDGQCVETCPPPYYHFQDWRCVNFSFCQDLHYKCRNSRKPGC\n+HQYVIHNNKCIPECPSGYTMNSSNLMCTPCLGPCPKVCQILEGEKTIDSV\n+TSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGFLKIRRSY\n+ALVSLSFFRKLHLIRGETLEIGNYSFYALDNQNLRQLWDWNKHNLTITQG\n+KLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLK\n+FSFIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDAC\n+GSNSWTVVDIDPPQRSNDPKSQTPSH--PGWLMRGLKPWTQYAIFVKTLV\n+TFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSD\n+PNGNITHYLVYWERQAEDSELFELDYCLKGLKLPSRTWSPPFESDDSQKH\n+NQSEYDDSASECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTS\n+SGNGAEDTRPSRKRRSLEEVGNVTATTPTLPDFPNISSTIAPTSHEEHRP\n+FEKVVNKESLVISGLRHFTGYRIELQACNQDSPEERCSVAAYVSARTMPE\n+AKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELH\n+LCVSRKHFALERGCRLRGLSPGNYSVRVRATSLAGNGSWTEPTYFYVTDY\n+LDVPSNIAKIIIGPLIFVFLFSVVIGSIYLFLRKRQPDGPMGPLYASSNP\n+EYLSASDVFPSSVYVPDEWEVPREKITLLRELGQGSFGMVYEGNAKDIIK\n+GEVETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQ\n+PTLVVMELMAHGDLKSHLRSLRPDAENNPGRPPPTLQEMIQMTAEIADGM\n+AYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGL\n+LPVRWMSPESLKDGVFTASSDMWSFGVVLWEITSLAEQPYQGLSNEQVLK\n+FVMDGGYLDPPDNCPERLTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPS\n+FPEVSFFYSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGCREGGS\n+SLSIKRTYDEHIPYTHMNGGKKNGRVLTLPRSNPS-\n+>ENSSSCT00000014817_susscrofa_1\n+VCPGMDIRNNLTRLHELANCSVIEGHLQILLMFKTRPEDFRDLSFPKLIM\n+ITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGL\n+YNLMNITRGAVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECG\n+DICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGL\n+CCHSECLGNCSEPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNF\n+SFCQDLHNKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLMCTPCLG\n+PCPKVCHLLEGEKTIDSVTSAQELRGCTIINGSLIINIRGGNNLAAELEA\n+NLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQ\n+NLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERND\n+IALKTNGDQASCENELLKFSYIRTSYDKILLKWEPYWPPDFRDLLGFMLF\n+YKEAPYQNVTEFDGQDACGSNSWTVVDIDPPTRSNDPKSQNHPGWLMRGL\n+KPWTQYAIFVKTLVTFSDERRTYGAK--SDIIYVQTDATSKHV-------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+--------------------------------------------------\n+------------------------------------\n' |
| b |
| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/cigar.tabular --- a/test-data/cigar.tabular Wed Dec 21 07:31:50 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,64 +0,0 @@\n-ENSLACP00000008815\t477DM4D2M2795D18M6D16M4D2MD17M8D14MD68MD28M2D32M2D13M27DM3D13M6D10M6D5M3D36MD139MD43M5D96M2D83MD16M2D27M2D66M5D102M12D49M4D124M7D6M3D16MD23MD26M12D68M4D85M\n-ENSXETP00000060681\t4D22MD23M3D43MD3MD17M5D19M4D5MD3M3D42M2D3M2D28M2D6M6D17MD2M3D14M11D23M4D4M3D15M3DM6D37MD7MD11M3D3MD24M4D8M3D19M4D9MD10M4D16M8D18MD14M82D17M12DM9D23M15D70M5D4M2D22M4D28M4D35MD44M29D2MD10M115D5M8D7M4D3M5D23M4D24MD8M7D103MD2M2D5MD21M2D44M5D42MDM3D64M6D11M2D75M8D34M5D9MD6M4D8MD33M8D7M7D14M11D15M15D3M12D8MD25M14D6M15D3M21D25M81DM5D10M5D16M162DM4D11M5D12MD21MD25M6D5M6D18M23D8MD5MD24M2D25M9D9M5D4M2D30M4D23M10D4M26D31M2D14M28DM10D10M38D13M59D17MD3M2D3M5D6M20D28M2D3M2D18M4D10MD27M5D19M4D31MD28M7D38M13D2M66D33M27D74MD24M2D5M10D31M6D16MD5MD17M8D13M8D2MD35M22D8MD11MD10M2D32M2D13M27DM3D14MD14M4D7M3D36MD139MD43M5D7M3D86M2D83MD16M2D27M2D67M4D102M12D49M4D37MD20M4D17M16D15MD13M7D6MD8M3D7MD23MD13MD3MD8M12D4MD11MD33MD9M17D41M19D4M16D\n-ENSOANP00000032170\t3946D47M2D14M2D27M497D6M113D\n-ENSOANP00000024376\t4D46M3D47MD18MD22M4D8M4D19M11D12M2D3MD38MD14M2D25M11D11M3D9M4D4M3D6MD16MD8MD28M10D11M3D3MD19M10D12MD17MD11MD10M4D15M9D18MD14M82D21M3D6M9D23MD2MD62M3D17M2D6M2D24M2D16MD2MD36MD10MD17MD26M29D2MD10M115D12MD7M4D4M4D24M3D18M8D7M7D2MD21M4D34M3D27M3D6MDMD9MD21M2D29MD47M14D2M3D42M4D17M7D11M2D7M30DM6D31M8D34M5D9MD6MD32MD12M8D7M8D13M11D14M16D3M12D8MD25M5D15M2D10M3D4M4D21M3D21M53D12MD12M2D13MD20M162DM4D11MD64M6D16MD13M13D17MD5MD24M2D25MD26M2D14MD113M2D6M2D14M8D3M8D3M2D57M4D22M39D22MD3M2D24M10D6M2D16M3DM2D26MD10MD6M2D19M5D10MD25M2D43MDM7D37M82D33MD17M4D37MD21M8D23M6D8M2D14MD13MD11MD5M6D16MD5MD17M8D14MD8MD37MD16M3D2MD17MD10M2D32M2D37M3DM3D14MD17M2D6M3D36MD139MD43M5D7M3D86M2D84M2D14M2D27M2D66M5D102M12D25M4D20M4D36MD40M10D3M2D45MD18MD23MD13MD3MD6M19D56M16D35M3D3M39D\n-ENSMEUP00000009812\t122D20M4D9M3D19M11D12M2D3MD37MD15M2D5MD2M3D14M11D13MD9M4D4M3D6MD11M6D8MD10M2D17MD7MD6MD4M3D3M5D20M4D13MD17MD11MD10M4D42M97D21M8DM9D23M15D51M2D18M2D6M2D22M4D16M16D35MD44M29D2MD10M115D12M20D23M4D24MD8M7D2M9D13M176D14M14DM4D41M19DM9D11M2D8M36D31M8D34M2DM3D6M3D6M4D9MD12M11D8M9D7M8D13M11D10MD4M15D3M12D8MD25M5D15M4D8M3D3M5D6MD14MD19M2D2M53D6MD5MD12M6D9MD20M166D25M5D47M6D21M6D3M11D9M4D6MD30M2D25M3D24M2D30M2D9MD11M6D18M3D48M2D6M2D7M29D19MD9M5D61M24D31M2D2M32D29M2D64M5D19M4D60M7D37M82D33MD17M4D104M2D46M6D22MD17M8D15MD7M3D52M6D17MD11M2D57M6D7M3DM3D15MD16M6D2M3D36MD139MD43M5D7M3D86M2D55MD21MD5M3D15M2D94M8D99M12D25M4D20M4D37MD41M7D4M2D13M6D13M7D6MD18MD23MD13MD3MD8M12D4MD11MD28M2D2MD10M17D16M3D16M4D3M19D3M16D\n-ENSSHAP00000012162\t4D4M19D23M3D47MD18MD22M4D9M3D19M11D12M2D3MD38MD14M2D5MD2M3D14M11D23M4D4M3D6MD12M6D7MD10M3D16MD7MD5MD5M3D3M2D23M4D13MD17MD11MD10M4D16MD6MD8M17D8M82D21M3D6M9D23MD2M3D29MD30M2D18M2D6M2D42M4D6MDM4D32MD2MD26M7D11M29D2MD10M115D6M7D13M6D23M4D42M2D20M4D34M3D27M3D8MD8M2D21M7D17MD13MD37M14D5M3D42M5D33M3D7M30DM6D31M8D34M5D7M3D18MD17M4D12M8D7M8D13M16D10M15D3M12D8MD25M5D15M2D10M3D4M4D44M54D6M7D12M5D10MD20M162DM4D28MD47M6D30M11D9M4D6MD30M2D25M3D24M2D4M2D24M2D9MD15M5D13M2D51M2D6M2D6M28DM10D19M18D36M4D9M24D31M2D2M32D28M2D4MD21MD17M2D19M5D19M4D12M3D7M3D33MDM7D38M13D4M57D40MD17M4D55M2D9MD12MD18M2D4M2D14MD13MD17M6D16MD5MD17M8D14MD8MD37MD16M3D2MD17M2D9M2D32M2D25M5D7M3DM3D14MD3MD13MD7M3D36MD139MD43M5D7M3D86M2D83MD16M2D95M5D102M12D25M4D20M4D37MD41M5D4M9D14MD12M7D6MD18MD23MD12MD13M12D4MD11MD27M113D\n-ENSMODP00000033276\t4D22MD23M3D47MD18MD22M4D9M3D19M11D12M2D3MD38MD14M2D5MD2M3D14M11D23M4D4M3D6MD11M7D7MD11M2D16MD7MD5MD5M3D3MD24M4D13MD17MD11MD10M4D23M2D7M17D8M82D21M3D6M9D23MD34MD30M2D18M2D6M2D24M2D16MDMD7MDM4D32MD2MD27MD16M29D2MD10M115D12MD13M6D23M4D42MD21M4D34M3D27M3D8MD9MD21M7D17MD13MD37M14D5M3D42M6D42M30DM6D31M8D34M5D9MD6M3D9MD20MD12M8D7M8D13M11D12M18D3M12D8MD25M5D15M2D10M3D5M3D11M4D31M52D12MD12M6D9MD5MD14M162DM4D28MD47M6D30M11D9M2D4M2D2MD5MD24M2D25M3D24M2D30M3D8MD15M10D61M2D6M2D6M46D12M18D35M5D9M24D31M2D2M32D28M2D4MD21MD8M3D28M4D19M4D13M2D12M3D28MDM7D8M3D26M14D4M57D40MD17M7D9MD42M2D9MD12MD18M2D4M2D14MD13MD17M6D16MD5MD17M8D14MD8MD37MD16M3D2MD17M2D9M2D59M5D7M3DM3D14MD3MD13MDMD5M3D36MD1'..b'3M9D35M3D3M19D20M\n-ENSLOCP00000009962\t3570DM9D3M3D36MD139MD42MDM3D97M2D83M3D14M2D19M2D6M2D68M4D101M12D49M4D36MD23M2D62M12DMD18MD18M3D2MD13MD3MD12MD6M21D18M119D\n-ENSDARP00000099674\t14D11M2D18M8D25MD17M5D17M22D2M4D9M6D20M7D15M3D53M2D8M3D13M7D28M4D4M3D6M19D18MD18MD13M17D20M4D8M3DM3D5M12D10M84D57M140D2M3D17M2D4M5D21M36D35MD11M5D28M29D13M115D4M28D23M4D24MD8M7D24M20D18M23D7M22D21M3D16M43DM3D13M14DM6D40M28D11M2D8M45D22M8D34M6D15M2D24M8D11M6D10M8D13M11D19M11D5M10D8MD17M2D94M53D61M162D16MD100M11D19MD5MD24M2D84M18D35M15D30M104D16M4D7MD9M24D25M42D27M3D32M6D27M5D19M4D8M7D43M8D16M108D29MD17M12D4M2D22M4D39MD24M2D14M2D12MD45MD17M8D14MD8MD37M4D7M3DM9D27M22D51M6D16MD16MD7M3D36MD139MD41M6D8M3D86M2D84M2D14M2D18M3D6M2D68M4D101M12D48M5D36MD42M15D14M3D13M19D13MD23MD12M6D12MD4M20D28M112D\n-ENSAMXP00000013440\t10D12M5D23M3D89M4D9M35D15MD53M2D8M3D13M11D14MD9M4D6MD6M19D18MD18MD13M9D28M4D5M13D2M12D11MD5M65D14M4D47M145DM3D17M2D6M2D22M4D17MDMD6M6D10M4D21MD21M10D13M29D13M115D4M37D14M4D15MD8MD8M7D4M7D13M20D3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|
| b |
| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/gene.json --- a/test-data/gene.json Wed Dec 21 07:31:50 2016 -0500 +++ b/test-data/gene.json Mon Feb 20 06:25:33 2017 -0500 |
| [ |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/test.gafa.sqlite |
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| Binary file test-data/test.gafa.sqlite has changed |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/tree.nhx --- a/test-data/tree.nhx Wed Dec 21 07:31:50 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/tree1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1.nhx Mon Feb 20 06:25:33 2017 -0500 |
| [ |
| @@ -0,0 +1,13 @@ +((((ENSPTRT00000040520_pantroglodytes:0.003426[&&NHX:S=pantroglodytes], +ENST00000338702_homosapiens:0.005715[&&NHX:S=homosapiens] +):0.056362[&&NHX:D=N:S=prim:T=31:B=97], +ENST00000542639_homosapiens:100000[&&NHX:E=$-pantroglodytes:S=homosapiens] +):4e-06[&&NHX:D=Y:SIS=50:DCS=0.5000:S=prim:T=8:B=43], +(ENSRNOT00000066674_rattusnorvegicus:0.024708[&&NHX:S=rattusnorvegicus], +ENSMUST00000026013_musmusculus:0.020534[&&NHX:S=musmusculus] +):0.126977[&&NHX:D=N:S=rod:T=31:B=100] +):0[&&NHX:D=N:S=euarc:T=8:B=46], +(ENSCAFT00000022939_canisfamiliaris:0.078848[&&NHX:S=canisfamiliaris], +ENSSSCT00000013404_susscrofa:0.084278[&&NHX:S=susscrofa] +):0.037628[&&NHX:D=N:S=laur:T=31:B=100] +)[&&NHX:D=N:S=mamm:B=0]; |
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| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/tree2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree2.nhx Mon Feb 20 06:25:33 2017 -0500 |
| [ |
| @@ -0,0 +1,17 @@ +(((ENSPTRT00000040521_pantroglodytes:0.003576[&&NHX:S=pantroglodytes], +ENST00000378069_homosapiens:0.00314[&&NHX:S=homosapiens] +):0.033582[&&NHX:D=N:E=$-rod:S=prim:T=31:B=100], +ENSCAFT00000022963_canisfamiliaris:0.05575[&&NHX:E=$-susscrofa:S=canisfamiliaris] +):0.036438[&&NHX:D=N:S=mamm:T=31:B=81], +((ENSRNOT00000044009_rattusnorvegicus:0.033002[&&NHX:S=rattusnorvegicus], +((ENSMUST00000040820_musmusculus:0[&&NHX:S=musmusculus], +ENSMUST00000168613_musmusculus:0.012852[&&NHX:S=musmusculus] +):0[&&NHX:D=Y:SIS=100:DCS=1.0000:S=musmusculus:T=18:B=100], +ENSMUST00000163344_musmusculus:0.139009[&&NHX:S=musmusculus] +):0.023529[&&NHX:D=Y:SIS=100:DCS=1.0000:S=musmusculus:T=2:B=96] +):0.059746[&&NHX:D=N:E=$-prim:S=rod:T=7:B=96], +(ENSSSCT00000023183_susscrofa:0.002007[&&NHX:S=susscrofa], +ENSSSCT00000033745_susscrofa:0[&&NHX:S=susscrofa] +):556.372[&&NHX:D=Y:SIS=100:DCS=1.0000:E=$-canisfamiliaris:S=susscrofa:T=31:B=100] +):0[&&NHX:D=N:S=mamm:T=7:B=81] +)[&&NHX:D=Y:SIS=0:DCS=0.0000:DD=Y:S=mamm:B=0]; |
| b |
| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/tree3.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree3.nhx Mon Feb 20 06:25:33 2017 -0500 |
| [ |
| @@ -0,0 +1,17 @@ +((((ENSPTRT00000034846_pantroglodytes:0.008941[&&NHX:S=pantroglodytes], +ENST00000340611_homosapiens:0.002566[&&NHX:S=homosapiens] +):0.14728[&&NHX:D=N:S=prim:T=31:B=100], +(ENSRNOT00000064726_rattusnorvegicus:0.05607[&&NHX:S=rattusnorvegicus], +((ENSMUST00000041588_musmusculus:0.005599[&&NHX:S=musmusculus], +ENSMUST00000110806_musmusculus:0.003481[&&NHX:S=musmusculus] +):0[&&NHX:D=Y:SIS=100:DCS=1.0000:S=musmusculus:T=24:B=98], +ENSMUST00000153440_musmusculus:0.020275[&&NHX:S=musmusculus] +):0.076743[&&NHX:D=Y:SIS=100:DCS=1.0000:S=musmusculus:T=24:B=98] +):0.21386[&&NHX:D=N:S=rod:T=31:B=100] +):0.103346[&&NHX:D=N:S=euarc:T=31:B=72], +ENSCAFT00000025950_canisfamiliaris:0.111975[&&NHX:E=$-susscrofa:S=canisfamiliaris] +):0.210884[&&NHX:D=N:S=mamm:T=31:B=54], +(ENSMUST00000100505_musmusculus:13.5088[&&NHX:E=$-rattusnorvegicus-prim:S=musmusculus], +ENSSSCT00000008295_susscrofa:0.206967[&&NHX:E=$-canisfamiliaris:S=susscrofa] +):0[&&NHX:D=N:S=mamm:T=31:B=55] +)[&&NHX:D=Y:SIS=17:DCS=0.1667:S=mamm:B=0]; |
| b |
| diff -r af9f72ddf7f9 -r fc8ca4ade638 test-data/tree4.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree4.nhx Mon Feb 20 06:25:33 2017 -0500 |
| [ |
| @@ -0,0 +1,19 @@ +((((ENSPTRT00000019089_pantroglodytes:0.004346[&&NHX:S=pantroglodytes], +(ENST00000302850_homosapiens:0[&&NHX:S=homosapiens], +ENST00000341500_homosapiens:0[&&NHX:S=homosapiens] +):0.001483[&&NHX:D=Y:SIS=100:DCS=1.0000:S=homosapiens:T=7:B=100] +):0.130609[&&NHX:D=N:S=prim:T=7:B=100], +(ENSRNOT00000041155_rattusnorvegicus:0.025292[&&NHX:S=rattusnorvegicus], +ENSMUST00000091291_musmusculus:0.023349[&&NHX:S=musmusculus] +):0[&&NHX:D=N:S=rod:T=27:B=100] +):1.86081[&&NHX:D=N:S=euarc:T=19:B=96], +((ENST00000600492_homosapiens:4.08746[&&NHX:E=$-pantroglodytes:S=homosapiens], +ENSMUST00000207100_musmusculus:0[&&NHX:E=$-rattusnorvegicus:S=musmusculus] +):5.88981[&&NHX:D=N:S=euarc:T=1:B=1], +(ENSRNOT00000067448_rattusnorvegicus:0[&&NHX:S=rattusnorvegicus], +ENSMUST00000208839_musmusculus:100000[&&NHX:S=musmusculus] +):0[&&NHX:D=N:E=$-prim:S=rod:T=1:B=0] +):2.09131[&&NHX:D=Y:SIS=33:DCS=0.3333:S=euarc:T=1:B=0] +):0[&&NHX:D=Y:SIS=75:DCS=0.7500:S=euarc:T=3:B=39], +ENSSSCT00000014817_susscrofa:4.61035[&&NHX:E=$-canisfamiliaris:S=susscrofa] +)[&&NHX:D=N:S=mamm:B=0]; |