| Next changeset 1:fd85bf67c4bb (2016-12-20) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty |
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added:
TreeBest_best_wrapper.xml fasta_header_converter.py fasta_header_converter.xml test-data/dna_alignment.fasta test-data/genetree.nhx test-data/out.fasta test-data/species.nhx test-data/test.fasta test-data/test.json |
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| diff -r 000000000000 -r 4f9e5110914b TreeBest_best_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TreeBest_best_wrapper.xml Tue Dec 20 16:32:25 2016 -0500 |
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| @@ -0,0 +1,117 @@ +<tool id="treebest_best_wrapper" name="TreeBeST best" version="1.9.2"> + <description>Generate a phylogenetic tree using CDS alignment and species tree</description> + <requirements> + <requirement type="package" version="1.9.2_ep78">treebest</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <command> +<![CDATA[ +treebest best +-f $species_tree +$P +$S +$A +#if $C + -C $C +#end if +$s +$g +$N +-c $c +-d $d +-l $l +-L $L +-b $b +#if $k.k_selector == 'yes' + -k e +#else + -k $k.k_value +#end if +#if $a.a_selector == 'yes' + -a e +#else + -a $a.a_value +#end if +-F $F +-p "Galaxy_TreeBest_Best" +$aln +> $output +]]> + </command> + + <inputs> + <param name="species_tree" type="data" format="nhx" label="Species file in Newick format" help="-f"/> + <param name="aln" type="data" format="fasta" label="CDS alignment in FASTA format"/> + <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip PHYML" help="(-P)" /> + <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Ignore the probability of gene evolution (NOT recommended)" help="(-S)" /> + <param name="A" type="boolean" truevalue="-A" falsevalue="" label="Apply constraint to PHYML" help="(-A)" /> + <param name="r" type="boolean" truevalue="-r" falsevalue="" label="Discard species that do not appear at all" help="(-r)" /> + <param name="C" type="data" format="nhx" optional="true" label="Constraining tree" help="Optional (-C)" /> + <param name="s" type="boolean" truevalue="-s" falsevalue="" label="Only build tree for genes from sequenced species" help="(-s)" /> + <param name="g" type="boolean" truevalue="-g" falsevalue="" label="Collapse alternative splicing forms" help="(-g)" /> + <param name="N" type="boolean" truevalue="-N" falsevalue="" label="Do not mask low-scoring segments" help="(-N)" /> + <param name="F" type="integer" min="1" value="11" label="Quality cut-off" help="(-F)" /> + <param name="c" type="integer" min="1" value="2" label="Number of rate categories for PHYML-HKY" help="(-c)" /> + <conditional name="k"> + <param name="k_selector" type="select" label="tv/ts ratio (kappa)" help="(-k)"> + <option value="yes">Estimate (e)</option> + <option value="no">Specify value</option> + </param> + <when value="yes" /> + <when value="no"> + <param name="k_value" type="float" value="0.0" label="tv/ts ratio (kappa)" /> + </when> + </conditional> + <conditional name="a"> + <param name="a_selector" type="select" label="Alpha parameter for Gamma distribution" help="(-a)"> + <option value="yes">Estimate (e)</option> + <option value="no">Specify value</option> + </param> + <when value="yes" /> + <when value="no"> + <param name="a_value" type="float" value="0.0" label="Alpha parameter for Gamma distribution" /> + </when> + </conditional> + <param name="d" type="float" min="0" value="0.15" label="Duplication probability" help="(-d)" /> + <param name="l" type="float" min="0" value="0.10" label="Probability of a loss following a speciation" help="(-l)" /> + <param name="L" type="float" min="0" value="0.20" label="Probability of a loss following a duplication" help="(-L)" /> + <param name="b" type="float" min="0" value="0.01" label="Probability of the presence of an inconsistent branch" help="(-b)" /> + </inputs> + + <outputs> + <data name="output" format="nhx" label="$tool.name on ${on_string}" /> + </outputs> + + <tests> + <test> + <param name="species_tree" ftype="nhx" value="species.nhx" /> + <param name="aln" ftype="fasta" value="dna_alignment.fasta" /> + <param name="F" value="11" /> + <param name="k_selector" value="yes" /> + <param name="a_selector" value="yes" /> + <param name="d" value="0.15" /> + <param name="l" value="0.10" /> + <param name="L" value="0.20" /> + <param name="b" value="0.01" /> + <output name="output" file="genetree.nhx" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +`TreeBeST`_ (gene Tree Building guided by Species Tree) is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate. + +The 'best' command builds the best gene tree from a species tree and a CDS alignment. The resultant tree will be bootstrapped for 100 times, reconciled with the species tree and rooted by minimizing with the number of duplications and losses. Duplications and losses are also stored in the NHX format. + +Note that TreeBeST first determines the topology of resultant tree with a complex procedure, and then performs a hundred times of resampling with an improved neighbour-joining algorithm. Branch lengths are finally estimated with the standard ML method under the HKY model. + +.. _TreeBeST: http://treesoft.sourceforge.net/treebest.shtml +]]> + </help> + <citations> + <citation type="doi">10.1080/10635150390235520</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 4f9e5110914b fasta_header_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_header_converter.py Tue Dec 20 16:32:25 2016 -0500 |
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| @@ -0,0 +1,39 @@ +from __future__ import print_function + +import json +import optparse + + +def read_gene_info(gene_info): + transcript_species_dict = dict() + for gene_dict in gene_info.values(): + for transcript in gene_dict['Transcript']: + transcript_species_dict[transcript['id']] = transcript['species'].replace("_", "") + return transcript_species_dict + + +parser = optparse.OptionParser() +parser.add_option('-j', '--json', dest="input_gene_filename", + help='Gene feature information in JSON format') +parser.add_option('-f', '--fasta', dest="input_fasta_filename", + help='Sequences in FASTA format') +options, args = parser.parse_args() + +if options.input_gene_filename is None: + raise Exception('-j option must be specified') + +if options.input_fasta_filename is None: + raise Exception('-f option must be specified') + +with open(options.input_gene_filename) as json_fh: + gene_info = json.load(json_fh) +transcript_species_dict = read_gene_info(gene_info) + +with open(options.input_fasta_filename) as fasta_fh: + for line in fasta_fh: + line = line.rstrip() + if line.startswith(">"): + name = line[1:].lstrip() + print(">" + name + "_" + transcript_species_dict[name]) + else: + print(line) |
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| diff -r 000000000000 -r 4f9e5110914b fasta_header_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_header_converter.xml Tue Dec 20 16:32:25 2016 -0500 |
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| @@ -0,0 +1,32 @@ +<tool id="fasta_header_converter" name="FASTA header converter" version="0.1.1"> + <description>to append species information</description> + <command> +<![CDATA[ +python '$__tool_directory__/fasta_header_converter.py' +-f '$fastaFile' +-j '$genesFile' +> '$outputFile' +]]> + </command> + <inputs> + <param name="fastaFile" type="data" format="fasta" label="FASTA file" help="FASTA file with transcript ID as FASTA ID" /> + <param name="genesFile" type="data" format="json" label="Gene feature information" help="In JSON format" /> + </inputs> + <outputs> + <data format="fasta" name="outputFile" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="fastaFile" ftype="nhx" value="test.fasta" /> + <param name="genesFile" ftype="json" value="test.json" /> + <output name="outputFile" file="out.fasta" /> + </test> + </tests> + <help> + <![CDATA[ +Simple converter for FASTA files, which appends the species name to the FASTA header for usage in TreeBeST. It uses gene feature information in JSON format (similar to the result of Ensembl REST API - lookup/id). + ]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 4f9e5110914b test-data/dna_alignment.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_alignment.fasta Tue Dec 20 16:32:25 2016 -0500 |
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| b'@@ -0,0 +1,168 @@\n+>ENSLOCT00000017020_lepisosteusoculatus\n+ATGGACAAAGGGCAGAAACCCGAAATTGAGAAGAAAGATGTAATTGTCATTGGGGGTGGT\n+TTATCTGGCTTGTCTGCTGCTAAACTGCTGAAAGAGTCTGGATTGAATGTCCTGGTTCTG\n+GAAGCACGTGATCGTGTGGGTGGGAGAACGTTGACTGTAAAAGGGCCTGAATTCCAATAT\n+GTGGATCTTGGAGGTGCTTATGTTGGTCCAACTCAGAACAGCATTCTGAGACTTGCAAAA\n+GAACTGGGGGTGAAGACTCATTTAGTAAACGAGAAAGAGCGACTCATTCATTATTATAAG\n+GGTAAGACGTATCCATTTCGAGGGCCATTTCCTCCAGCATGGAACCCCATCGTCTACCTG\n+GATTACAACAACCTCTGGAGGACTCTGGACCGAATGGGAAAGGAGATCCCAGCAGATGCT\n+CCATGGACTGCTCAACATGCCACACAGTGGGACAATATGACGATGAAAGAACTAATTGAC\n+AAACATTGCTGGACAAGGACTGCAAAAAACTTTGCAACTCTCTTCGTCAATGTCAATGTG\n+ACCTCTGAACCTCATGAAGTCTCAGCGCTCTGGTTTCTTTGGTATGTGAAGCAGTGTGGA\n+GGGACAAAAAGGATATTTTCAACATCTAATGGAGGACAGGAAAGAAAATTCATGGGGGGA\n+TCAGGGCAGATTAGTGAACGGATCGCAGACCGGCTGAAGGGCAACGTCCACCTAAACCAG\n+CCTGTGATTAAGCTCTTGCAGACTCCAGCTGGTGTGTGTGTCGAAACACTAACTGGAAAT\n+AAGTATGAGGCAGCCTATGCCATCAGTGCTATTCCACCAGGGCTGAGCATGAGTTTGCAT\n+TATGAGCCCCAGCTGCCTCCAGTGAGAAACCAAATGATCCAAAGAGTCCCAATGGGGTCC\n+ATCATTAAATGCATGATGTACTACAAGAGGACCTTCTGGAGAGAGAAGGGGTACTGCGGA\n+ACAATGATGATCGAAGATGAGGACTCTCCCATTTCAATGACCCTAGATGACACCAAACCA\n+GATGGATCGTATCCCTGTATTATGGGGTTTGTTTTAGCAAGAAAAGCAAGAGATCTTATC\n+AATTTGACTAAGGATGAGAGG---AAAAAACGTATCTGTCAGATTTATGCAAAAGTGCTG\n+GGAACAAATGAAGCATTGCATCCTGTTCACTATGAAGAAAAAGACTGGTGTGAAGAACAA\n+TATTCAGGAGGCTGTTATACTGCCTATTTTCCTCCAGGTACCTTCTGCCAGTTCAGCAGA\n+GTTCTAAGGGAGCCTTTTGGTAGGCTCTTCTTCGCAGGCACAGAGACAGCAACCAGATGG\n+AGTGGATATATGGATGGTGCTGTTCAAGCTGGTGAGAGAGCTGGAAGAGAGGTACTGCAT\n+---GCAATGGGTAAAGTATCCCAGTCAAAAATCTGGAAGGAAGACGTAGAATCACAGGAA\n+GTTCCAGCTGAACCAATTACAACAAGTTTCTTAGAAGAGCATCTGCCTTCTGTCCCTGCA\n+TTTCTGACAATGATCGGAGTCTCTTTTGCATTTATCACAACAGCCGCAGCCCTTGGGTCG\n+GGCATCTTAAAGACAAATTCACGTTTACGTCTCTTTCAT\n+>ENSLACT00000014274_latimeriachalumnae\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+---------------------------------------TTTTTTCTTTTTTTCTCCCAG\n+GGTAAGTCGTATCCCTTTAGGGGTCCTTTCCCTCCTATGTGGAACCCCATTGCCTATATG\n+GATTACAACAACCTGTGGAGAACAATGGACGAAATGGGGAAGGAGATCCCCAAGGAAGCC\n+CCGTGGAAGGCCCCACATGCTGAAGAATGGGATAAAATTACCATGAAGGATCTGATTGAC\n+AAAATCTGCTGGACAGGTGTTGCCAAGCAGTTTGCCACGCTGTTTGTGAATGTCAACGTT\n+ACTTCTGAACCCCATGAGGTCTCTGCTCTCTGGTTCCTGTGGTATGTGAAGCAGTGCGGT\n+GGAACGACCAGGATCTTTTCAACAACCAATGGTGGACAGGAGCGTAAGTTTGTTGGCGGT\n+TCAAGCCAGATCAGTGAGAAGATGATGGATCTCCTTGGAGATCAGGTGAAACTGCAGAGA\n+CCTGTAGTCGGCATTGATCAGTCTGGGGAGGATGTGGTCGTGGAGACTCTAAACCGTGAG\n+AAGTATGAGGCCAAATATGTCATTAGTGCCATTCCTCCAACCCTTAGTGTGAAGATTCAC\n+TACAACCCACCTTTGCCGCCTTTGAGAAACCAGTTAATCCATCGTGTTCCTTTGGGATCC\n+GTTATCAAGTGCATGGTGTATTACAAGGACTCATTTTGGAGAAAGCAGGATTACTGTGGC\n+AGCATGATAATTGAAGAAGAGGATGCTCCAATTGGGCTGACACTGGATGACACCAAACCA\n+GATGGCAGTGTGCCTGCCATTATGGGATTCATTCTTGCCCGAAAAGCCAGAAGACTAGCA\n+CATTTCACCAAAGAAGAGCGA---AAGAAGAAAATCTGTGAACTTTATGCAAGAGTTCTT\n+GGATCACAGGAAGCTTTACAGCCTGTACACTATGAAGAGAAGAACTGGTGTGAGGAGGAG\n+TACTCGGGCGGGTGTTACACTGCTTACTTCCCACCAGGAATAATGACCCAGTTTGGCAAG\n+GTAATCCGTCAGCCAGTTGGCAGAATTTTCTTTGCCGGCACTGAGACGGCTACCGAGTGG\n+AGCGGCTACATGGAGGGGGCAGTGCAGGCTGGAGAGAGAGCAGCCAGAGAGATCTTATGT\n+---TCAATGAGAAGAATTCCTGAAAGTGAAATCTGGAAGCCTGAGCCAGAGTGTCTGGAT\n+GTCCCAGCTTCTCCGATCACCACCGCGTTCTGGGAGAGGAACCTTCCATCTGTCCCTGGG\n+TTTCTGAGGCTGCTTGGATTCTCC---GCGTTTCTCACCTCGACAGCGGCAGTAGGGCTC\n+TTT------GCCTACAAGAGGGGACTGCTGATTAAGAAC\n+>ENSLACT00000009516_latimeriachalumnae\n+ATGTCTGTT------------------GAGAAAAGAGATGTGATCATTGTTGGAGGTGGT\n+CTATCAGGTCTGTCAGCTGCAAAATTGCTAGCAGAGGCGGGGCTGAACGTCTTGGTTCTG\n+GAGGCCAGGAACCGTGTTGGTGGAAGAACGTACACAGTTCAAGGCCCAGAGTTCCAGTAC\n+GTAGACCTTGGGGGAGCATATGTTGGACCCACCCAGAATCGCATACTAAGAGTCGCAAAG\n+GAGTTTGGGGTTAAGACTTACCTGGTAAATGAAAAGGAGCAACTGATTCATTATGTCAAG\n+GGAAAGTCATACCCCTTCCAAGGGCCTTTCCCTCCTGCATGGAACCCAATTGTCTATCTG\n+GATTACAACAATCTCTGGAGGACTTTAGATGAGATGGGACGAGAGATTCCTGCAGAAGCT\n+CCTTGGAAGGCACCCTGTGCTGAAGCGTGGGACAACATGACAATGAAGCAGCTGATTGAT\n+AAACTCTGCTGGACGAGGGTAGCCAAGGACTTTGCAACGCTATTTGTCAACGTGAAT'..b'TGACACCAAGCCC\n+GATGGCACTGTTCCTGCTATTATGGGTTTCATCCTTGCCCGAAAAGCTAGGAGGCTGGCA\n+CATATCACAAAAGAAGAAAGG---AAAACGAAAATCTGTGAACTTTATGCAAGGGTTCTT\n+GGATCAGAGGAAGCTTTACATCCAGTACACTATGAAGAGAAGAACTGGTGCGAGGAGGAG\n+TACTCGGGCGGGTGTTACGCTGCTTACTTCCCACCAGGAATAATGACCCAGTTTGGCAAG\n+GTAATCCGTCAGCCAGTTGGCAGAATTTTCTTTGCTGGCACTGAGACGGCTACCGAGTGG\n+AGCGGCTACATGGAGGGGGCAGTGCAGGCTGGAGAGAGAGCAGCCAGAGAGGTACGGTGC\n+---AGAAATGTGATC---------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------ATAACATACCTACTG\n+>ENSLACT00000014695_latimeriachalumnae\n+---------------------------------AATTTTCTACTTCTCCAAAGAAACTTT\n+CTTTTAGGTCTGTCGGCCGCCAAGCTGCTGACTGAGTCTGGGCTGAATGTGGTTGTGTTG\n+GAGGCCCGTGACAGGGTTGGAGGAAGAACCTTCACCACCAGGAATAAGCATGTTAAGTAT\n+GTGGACCTTGGCGGAGCCTATGTGGGGCCGACGCAGAATCGCATTCTACGCCTGTCGAAG\n+GAGCTGGGCATTGAGACGTATAAAGTGAATGAAGTGGAGCGCTTCATCCATCACATAAAG\n+GGAAAATCATATCCTTTCCAGGGACCATTCCCTCCAATGTGGAATCCACTTGCCTTCCTG\n+GATTATAATAACCTCTGGAGAACACTGGATGAAATGGGAAAAGAGATCCCCAGGGAAGCC\n+CCGTGGAAGGCCCCACATGCCGAAGAATGGGACAAAATGACCATGAAGGATCTGATTGAC\n+AAAATCTGCTGGACAGAAGCTGCCAAGCAGTTTGCCACGCTGTTTGTGAATGTCAACGTT\n+ACTTCTGAGCCCTGTGAGGTCTCTGCTCTCTGGTTCCTGTGGTACGTGAAGCAGTGCGGT\n+GGAACGACCAGGATCTTTTCAATTGGTAATGGTGGGCAGGAGCGCAAGTTTGTCGGAGGT\n+TCAGGTCAGATCAGTGAGAAGATGATGGAGATCCTTGGAGATCGGGTGAAACTACAGGGA\n+CCTGTAATCAGCATTGATCAGTCCGGAGACGGTGTGGTCGTGGAAACTCTGAACCATGAG\n+AAGTATGAGGCCAAATATGTCATTAGTGCCATTCCCCCATCCCTTAGCATGAAGATTCAT\n+TACAAGCCACCTTTGCCACCAATACGAAACCAGTTTATCTATCGAGTTCCGATTGGATCT\n+GTTATCAAGTGTATGGTCTATTACAAGGAAGCCTTTTGGAAAAAGAAGGATTTCTGTGGC\n+TGTATGATGATTGAAGATGAAGAAGCTCCTATCGGTGTGACTCTGGATGACACCAAGCCC\n+GATGGCACTGTTCCTGCTATTATGGGTTTCATCCTTGCCCGAAAAGCTAGGAGGCTGGCA\n+CATATCACAAAAGAAGAAAGG---AAAACGAAAATCTGTGAACTTTATGCAAGGGTTCTT\n+GGATCAGAGGAAGCTTTACATCCAGTACACTATGAAGAGAAGAACTGGTGCGAGGAGGAG\n+TACTCGGGCGGGTGTTACGCTGCTTACTTCCCACCAGGAATAATGACCCAGTTTGGCAAG\n+GTAATCCGTCAGCCAGTTGGCAGAATTTTCTTTGCTGGCACTGAGACGGCTACCGAGTGG\n+AGCGGCTACATGGAGGGGGCAGTGCAGGCTGGAGAGAGAGCAGCCAGAGAGAGTAGACGC\n+CATGCAGCATCATCAAAGACCAGGGAGAAGCCGGGGGGAACAAAGCCTGACAAACACGAT\n+GTCCCAGCTTCTCCGATCACCACCGCGTTCTGGGAGAGGAACCTTCCATCTGTCCCTGGG\n+TTTCTGAGGCTGCTTGGATTCTCC---GCGTTTCTCACCTCGACAGCGGCAGTAGGGCTC\n+TTT------GCCTACAAGAGGGGACTGCTGATTAAGAAC\n+>ENSLACT00000026689_latimeriachalumnae\n+ATGACCAGC------------------AATAAATATGATGTAATTGTCATTGGAGCAGGC\n+ATCTCAGGTCTGTCGGCTGCCAAGCTGCTGACTGAGTCTGGGCTGAATGTGGTTGTGTTG\n+GAGGCCCGTGACAGGGTTGGAGGAAGAACCTTCACCACCAGGAATAAGCATGTTAAGTAT\n+GTGGACCTTGGCGGAGCCTATGTGGGGCCAACGCAGAATCGCATTCTACGCCTGTCGAAG\n+GAGCTGGGCATTGAGACGTATAAAGTGAATGAAGTGGAACGCCTCATCCATCATGTCAAG\n+GGTAAGTCGTATCCCTTTAGGGGTCCTTTCCCTCCTATGTGGAACCCCATTGCCTATATG\n+GATTACAACAACCTGTGGAGAACAATGGACGAAATGGGGAAGGAGATCCCCAAGGAAGCC\n+CCGTGGAAGGCCCCACATGCTGAAGAATGGGATAAAATTACCATGAAGGATCTGATTGAC\n+AAAATCTGCTGGACAGGTGTTGCCAAGCAGTTTGCCACGCTGTTTGTGAATGTCAACGTT\n+ACTTCTGAACCCCATGAGGTCTCTGCTCTCTGGTTCCTGTGGTATGTGAAGCAGTGCGGT\n+GGAACGACCAGGATCTTTTCAACAACCAATGGTGGACAGGAGCGTAAGTTTGTTGGCGGT\n+TCAAGCCAGATCAGTGAGAAGATGATGGATCTCCTTGGAGATCAGGTGAAACTGCAGAGA\n+CCTGTAGTCGGCATTGATCAGTCTGGGGAGGATGTGGTCGTGGAGACTCTAAACCGTGAG\n+AAGTATGAGGCCAAATATGTCATTAGTGCCATTCCTCCAACCCTTAGTGTGAAGATTCAC\n+TACAACCCACCTTTGCCGCCTTTGAGAAACCAGTTAATCCATCGTGTTCCTTTGGGATCC\n+GTTATCAAGTGCATGGTGTATTACAAGGACTCATTTTGGAGAAAGCAGGATTACTGTGGC\n+AGCATGATAATTGAAGAAGAGGATGCTCCAATTGGGCTGACACTGGATGACACCAAACCA\n+GATGGCAGTGTGCCTGCCATTATGGGATTCATTCTTGCCCGAAAAGCCAGAAGACTAGCA\n+CATTTCACCAAAGAAGAGCGA---AAGAAGAAAATCTGTGAACTTTATGCAAGAGTTCTT\n+GGATCACAGGAAGCTTTACAGCCTGTACACTATGAAGAGAAGAACTGGTGTGAGGAGGAG\n+TACTCGGGCGGGTGTTACACTGCTTACTTCCCACCAGGAATAATGACCCAGTTTGGCAAG\n+GTAATCCGTCAGCCAGTTGGCAGAATTTTCTTTGCCGGCACTGAGACGGCTACCGAGTGG\n+AGCGGCTACATGGAGGGGGCAGTGCAGGCTGGAGAGAGAGCAGCCAGAGAGATCTTATGT\n+---TCAATGAGAAGAATTCCTGAAAGTGAAATCTGGAAGCCTGAGCCAGAGTGTCTGGAT\n+GTCCCAGCTTCTCCGATCACCACCGCGTTCTGGGAGAGGAACCTTCCATCTGTCCCTGGG\n+TTTCTGAGGCTGCTTGGATTCTCC---GCGTTTCTCACCTCGACAGCGGCAGTAGGGCTC\n+TTT------GCCTACAAGAGGGGACTGCTGATTAAGAAC\n' 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| diff -r 000000000000 -r 4f9e5110914b test-data/genetree.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetree.nhx Tue Dec 20 16:32:25 2016 -0500 |
| [ |
| @@ -0,0 +1,11 @@ +(ENSLOCT00000017020_lepisosteusoculatus:0.258673[&&NHX:E=$-186625:S=lepisosteusoculatus], +(ENSLACT00000009516_latimeriachalumnae:0.149849[&&NHX:S=latimeriachalumnae], +((ENSLACT00000014274_latimeriachalumnae:0.011979[&&NHX:S=latimeriachalumnae], +ENSLACT00000026689_latimeriachalumnae:0[&&NHX:S=latimeriachalumnae] +):0.040268[&&NHX:D=Y:SIS=100:DCS=1.0000:S=latimeriachalumnae:T=31:B=100], +(ENSLACT00000014694_latimeriachalumnae:0.022411[&&NHX:S=latimeriachalumnae], +ENSLACT00000014695_latimeriachalumnae:0.019166[&&NHX:S=latimeriachalumnae] +):0.074979[&&NHX:D=Y:SIS=100:DCS=1.0000:S=latimeriachalumnae:T=31:B=100] +):0.296006[&&NHX:D=Y:SIS=100:DCS=1.0000:S=latimeriachalumnae:T=31:B=100] +):0[&&NHX:D=Y:SIS=100:DCS=1.0000:E=$-32523:S=latimeriachalumnae:T=31:B=100] +)[&&NHX:D=N:S=117571:B=0]; |
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| diff -r 000000000000 -r 4f9e5110914b test-data/out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.fasta Tue Dec 20 16:32:25 2016 -0500 |
| b |
| b'@@ -0,0 +1,11171 @@\n+>ENSLACT00000008884_latimeriachalumnae\n+ATGGAATGGGAAGCAGTTGAAAGTGTCAAAGCTTTAATGCGAGATGATGAGCTTACAGAT\n+GCAGGACTAGATGCAAGCAAAGACAGTTTGAACCGTGCATGCAGGAGACAGTCAGGTGGA\n+AATTTCCGAGCTAGGAAGCGGATGAGACTTGAACAAGTGTCGGCTGATGAGCCACCAGTT\n+AAGAGGCAACTCTTGGCTGAATTTGACAGGACGGTTGAAAATGGCCATAAGTCACTTCAG\n+AAGCCTTTAATATGCACTCCAAATGGTACGCTGAAAGACAGAAGGAAGTTTATGTATAGT\n+GTTCCCCTTAAGCCTGTAGTGTGTGGTCCATGGAGCAACAACTCCAAAACTGGGCAACAG\n+GTCACAAAACCCAGCATTACTTTGCCTGGCAGAGGAGTAGAAACATTTCAACCCAAGAAC\n+CACATTGCTCCCAGTCCAGTTTATGATCCACCTTCAAATAGACGAGGCCCAGTCTTTGCT\n+CCACCATTTCATGGGGCCACGTTTCGGGGACTGCAGAAACCAAGTGCTTCACACACATCA\n+AGCAAAACTGCTAAAACTTTTGTTCCTCCATTTAAAATGAAAGCCAGTGCCTCCCACACA\n+GTACATTTCAGTAGCAAAGTTATCAACACTTGTGAAAAGATTTTAGAAAATCTAGTCTAC\n+TTGAAGCCTAGTTTAGCCTCTTGTAATATTTTTCAAAGTTTGGAAGAGATGACTGCTAAC\n+CTTCAGTGTGCCAGAGACCTACAGGAAATGAGGCTGAGAAAGAAGCAAAGGCAAAATATC\n+CGGCCGCAGCCAGGCAGCCTTTACCTTGCTAAAACATCTGGTGTTGCTAGGGTCTCCCTG\n+AAGGCAGCTACAGGAAATCAGTGCCCATCCTCCTACTCCACAGAGCAGTTATATGTTCAT\n+GGTGTAGGAAAAAGCACCTTGAAAGTACGCAGTGAGAATGCAGAATCTTTTCAGTTCAGT\n+TGCAGTGATTATTTTGGTAAAGATGTTCTCCTAGCTGGAAATGGCTTGAAGCTGGCAGAT\n+GGAGGGTGGCTTATACCCAGTGATAAAGGAATGGTAGGAAAAGAAGAATTTTACAGGGCA\n+CTGTGCGATACACCTGGTGTGGCCCCAAAGCTTATTAGTGAATCTTGGGTCTACAATCAT\n+TACAGATGGATTGTATGGAAGCTTGCAGCGATGGAGGCAGCTTTTCCAAAAGAATTTGGC\n+AACCGGTGTCTAACACCAGAGAGGGTGCTGCTACAGCTTAAATACAGGTATGACATTGAA\n+GTTGACAAGTGTCGAAGATCTACTGTAAAGAAGATAATGGAAAGAGATGACACTGCCGCC\n+AAGACACTTGTGCTGTGCATTTCGAAACTTATATCCGTGGAGGACCGTTTTAAACAAACC\n+AAAAATAAGAATGAAAAGGGTGCTGAAGAAGCTAGGAAAGAAGCAGTAGCTGGAGTCATT\n+GAAACTACGGATGGGTGGTATGGGATTAAGGTACTCTTGGATCCTCCCCTTACAGTGCTG\n+GTACAGAGAGGAAGGCTGTCAGTTGGCTGTAAAATTATAACACATGGAGCTGAAATAATT\n+GGCTCCCAGGATGCCTGTACACCACTGGAAGCTCCGGAGTGTCTCATGCTAAAGATTTCT\n+GCGAACAGTACTCGACCTGCTTGCTGGAGTGCTAAACTTGGGTTTCATCGAGATCCCCGA\n+CCTTTTCCTCTCCCATTAGCATCGCTTTTTAATGATGGTGGATTAGTTGGCTGTGTTGAT\n+GTTGTTGTAGTGCGACTGTACCCCATACAGTGGATGGAAAAGAAATCAGATGGGATTTTT\n+GTGTTTCGTAATGATCGAGCAGAAGAAAGAGAGGCTCAAAGGCAAGTTGAGAATCAGCAA\n+AGAAAAATGGAAAGTTTGTTTGCAAAGATTCAAACTGAATTTGAACAGAAATATGAAGCC\n+AAAAGCAAAAGGAGAGGCCAAAAGGCACAGAAATTCAGCAAGCAGGAAATCCAGGCTCTT\n+CAAGATGGTGCAGAACTGAATGAAGCAATTGAGAATTCAATGGATCCGGGTTACTTTGAG\n+GCTTGCTTAAGAGAGGAGCAGTTAAAAGTCCTGCATGGCCACAGACAAATGTTAAATGAA\n+AAGAAACAAGCAGAGTTCCAGGCAGAGTTCAAGAAGGCACTGGAGTCTGCTGAACAGGAG\n+GGGAAGAGCTGCTGCAAGCGAGGTGTAACCCCTGTTTGGAAACTACGCATTGTGGACTAT\n+AGAAAACCAAGTGCTGCAGAATATATATTAAATATTTGGCGACCATTGGCTGATCTGCAT\n+TCCCTGTTAAAGGAAGGTAACCGGTACAGAATTTACCAGTTACTTGCATCACAATCCAAA\n+GGAAGAACCACTACTGCTGACATACAGCTAACAGCTACAAAGAAAACCCAGTATCAGCAG\n+TTCCAGTCTTTCCCAGAATTGATATCAGAGCTGTACAGTCCAAGAAAAGCTGTTAAATTC\n+AACATGTTGATGGATCCAACTTTCCGACCAGCCTATGCAGAAGTAGACCTGGTAGGATAT\n+ACCATCTCTATAGAAGGAAAGCCAGGTGTTGCTCCAGTGGTGTACCTATCTGATGAAAGT\n+CATAACTTTGTGGCAATAAAAGTTTGGACTGCCCTAAATCAGCTTGCTGTTGAAGACATT\n+GTGAAGCCATTTTCACTGATTGCTGCAAGTAACTTACAGTGGAGATCAGACAGCAGATCA\n+ATAATTCCTATGTTGTATGCTGGGGACCTTTCAATATTTTCATCAAATCCAAAAGAAGGG\n+CATCTTCAAGAGGCTTTTAATCAAAGAAGGACTGCTATACAAGAGAACATTTCTGGTACA\n+TACCTCCCCCCAGAAAAAAAAAATCTGCATCAGGAGTCTTATAAATCATGTCAATACAAC\n+ACATTGAATGTTTTGATGAATGGAAACATACACACACAGAGCCCAGTGCTGTCCAGGGTT\n+CATATGGGTACATCCTGTGCTTTTCTCTTTCTACTGCCTTCACCCTACCCTGAAAGTAAA\n+CACACTAGTCCTTTGATAACTATGAAGGCAGGAGTCAAATCTATGACTTTCCCAGGCTCT\n+GCAAAACTAATGCCACAAGCAAGTGAAAATCAAGAACTGGATACTCCCAAGAATCGTAAA\n+AAGAAGGCAGCTTTAGACTATCTTTGCCGCATTCCTTCCCCACCTGCACTTACTCCTATT\n+CGCAGTTTTGTGTCTTCCTCCTTGCAAAAGGCTTTTCACCCACCAAGGAGCTGCGTCAAA\n+CTACAAAGCGGCGAAAACCCAGTCGTCCCCACAGTTGGCAATAACGCTGTCCTAGGGATT\n+CAGTCAAAAAAAGATGAAGGGCCTGCTGCTTTTAATGAAGAGGATTCAGTAGCAGACGAG\n+GAACTAGCAATGATCAATACACAGGCATTCTTAGTCGGCTTAAGAAGGGACAAAAGACCA\n+AGTTTACTGGACAAAACTGCCAGTTTAAAGGGGCATGTTCCCTCAGAAAGATTTCTTGAA\n+GAGAAGCTCTTGTCAGTACTAAAAGAGCAGGCAAGCTCTAATTCTGAGAGAAACGCCACA\n+TCATTGGAAAATAAGAGCTGTGATAAAAGCAGGACATGTGTGAAACCATGTGAACATTCT\n+AATGACAGCATTGCAGAGGAAACTTCAGAAATCATCCCAGGCTGTCATGGTGGAGAATCT\n+GCTGTGGAAAACCAAAGTAAAAATTCCTCATTGTGCCACAAAAAACTGCAACAGAAGAAA\n+AGACGGAAGTATTACTAA\n+>ENSXETT00000064180_xenopustropicalis\n+ATGGCTGCACCGCAACTTGGAAAATCTGTCTTCTA'..b'ATTCATGGTGCTCAGCTAGTCGGTTCACAGGATGCTTGTTCTCCTTTGGAGGCCCCT\n+GAGTCTATCATGCTAAAGATTTTTGCCAACAGCAGCAGGCGAGCACGATGGGATGCTAAA\n+CTGGGATTTTATAGGGACCCACGGCCATTCCTGCTCCCTGTCTCTTCTTTGTACAACAGT\n+GGGGGACCTGTAGGATGTGTGGATATTATTATATTAAGAAGCTATCCCACATTATGGATG\n+GAGAGAAAACCAGAAGGAGGCACTGTGTTCCGGTCAGGCCGAGCAGAAGAAAAGGAGGCT\n+AGACGGTACAACGTCCACAAGGAAAAAGCTATGGAGATTCTGTTTGACAAGATTCAAGCG\n+GAATTTGAAAAGGAAGAGAGGGATAACAGGAAACCTCGGAGCAGAAGACGGACAATCGGT\n+GATCAAGATATCAAAAGTCTTCAAGATGGAGAGGAGCTGTACGAAGCAGTGGGCGATGAC\n+CCAGCTTACCTTGAGGCACATTTGACTGAGCAGCAGGCAGAGACTCTACAGAACTACAAA\n+CGTCTGCTGATAGAAAAGAAGCAAGCAGAGCTGCAGGATCGCTACCGGCGAGCTGTAGAA\n+ACTGCAGAGGATGGCACAGGCAGCTGTCCCAAGCGAGATGTAGCACCTGTATGGAGACTC\n+AGCATTGCTGACTTCATGGAAAAGCCAGGCAGTGTTTACCAGCTGAACATTTGGCGGCCT\n+CCCTCAGAGCTCCAGTCTTTACTAAAAGAAGGCTGTCGATATAAGGTGTATAATCTCACC\n+ACAACAGATTCAAAGAAACAAGGTGGAAACACAACCGTTCAGCTAAGTGGAACAAAAAAA\n+ACACAATTTGAGGACCTTCAGGCATCCGAGGAATTGTTGTCAACATATTTTCAGCCAAGG\n+GTCTCGGCCACATTCATCGATCTCCAAGATCCAGAATTCCATTCGTTGTGTGGTGAGGTT\n+GATCTCACAGGATACGTCATCAGTATAATAGATGGACAAGGTTTCTCACCTGCTTTTTAC\n+CTAACTGATGGGAAACAAAATTTTGTAAAAGTGCGTTGTTTCAGCAGCTTCGCTCAGTCA\n+GGCTTGGAAGATGTAATAAAGCCAAGTGTCCTTTTAGCTTTAAGCAACCTCCAACTGAGA\n+GGTCAGGCAACATCACCCACTCCAGTCTTGTACGCTGGAGATCTAACCGTCTTCTCCACA\n+AACCCCAAAGAAGTTCATCTGCAGGAATCCTTCAGCCAGCTCAAAACCCTGGTTCAG\n+>ENSTRUT00000015099_takifugurubripes\n+CAGCTGGCACGGGATATGCAGGATATGCGAATCAGAAAAAAGAAACGCCAGACCATTCGT\n+CCATTACCGGGAAGTTTGTTTCAGAAGAAGTCCTCTGGAGTCGCCAGGATTCCATTTAAA\n+GCTGCAGTAAACGGAAAGCCACCTGCACGCTACACTGCCAAACCGCTGTGTGGCCTCGGG\n+GTTCCTCTGAATGTGTTGGAGATCACCAGTGAGACTGCAGAATCTTTTCGCTTCAGCTTG\n+CAGCACTTTGTTAAGCTGGAGTCTCTCATAGATAAAGGTGGCATACAGCTCGCTGATGGA\n+GGATGGCTGATTCCCACGAATGACGGGACAGCGGGAAAAGAAGAGTTTTATCGAGCATTG\n+TGTGATACCCCGGGGGTTGATCCTAAACTAATGAGTGAGGAGTGGGTGTATAATCACTAC\n+CGATGGATTGTATGGAAACAAGCTTCCATGGAAAGGTCATTTCCAGAAGAGATGGGCAGC\n+CTCTGTCTCACCCCAGAGCAGGTTCTCCTACAACTTAAGTACAGATATGACATAGAGGTT\n+GACCACAGTCGCAGACCAGCTCTCAGAAAAATTATGGAAAAGGATGACACGGCAGCTAAA\n+ACCCTGGTCCTCTGTGTTTGTGGGGTTGTCTTCAGAGGCAGCTCCCCAAAAAACAAGAGT\n+TTTGGGGACATCAGTACTCCAGGAGCTGACCCAAAGGTTGAAAACCCCTGTGCTGTCGTT\n+TGGCTGACCGATGGATGGTATTCAATTAAAGCGCAACTGGATGGACCGTTGACCTCAATG\n+CTTCACAGAGGTCGACTACCAGTCGGCGGGAAGCTGATTATCCATGGTGCTCAGCTAGTC\n+GGATCAGAGAATGCTTGTTCCCCCCTGGAGGCCCCTGTGTCTTTAATGCTAAAGATTTGC\n+GCCAACAGCAGCAGACCAGCTCGATGGGATTCTAAACTAGGATTTCACAGGGACCCGCGG\n+CCATTCCTGCTTCCTGTCTCTTCTTTGTACAGCAGTGGAGGACCAGTAGGATGTGTGGAT\n+ATTATTATACTGAGAAGCTATCCCATATTGTGGATGGAGAGGAAACCAGAAGGAGGCACT\n+GTGTTCCGTTCAGGCAGAGCAGAAGAGAAGGAGGCGAGACGATACAACATTCACAAAGAA\n+AAAGCTATGGAAATCCTGTTTGACAAGATTAAAGCAGAATTTGAAAAGGAAGAAAAAGGT\n+AACAGGAAACCGCAGTGCAGAAGGACAATCAATGGTCAAAATATTACAAGTCTTCAAGAT\n+GGAGAGGAGCTGTACGAAGCAGTGGGCGATGACCCAGCTTTCCTTGAGGCGCATCTGACT\n+GAGAAGCAGGTGGAGGTTCTTCAGAACTACAAACGTCTGGTGATGGAGAAGCAGCAGGCA\n+GAGCTGCAGGATCGCTACCGGCGAGCTGTAGAAAGTGCAGAGGACGGCGTGGGGGGCTGC\n+CCCAAGCGAGATGTCGCACCTGTGTGGAGACTGTGCATTGCTGACTCCATGGGCCATTCT\n+GGCCGTGTTTACCAGCTGAGTCTTTGGCGGCCCCCCTCAGAGCTCCAGGCATTACTGAAG\n+GAAGGCTGTCGTTATAAAGTGTATAATCTCACCACTTTAGATTCAAAGAAACAGGGTGGA\n+AATGCAACGGTTCAGCTAACTGCAACAAAAAAAACACAGTTTGAGCACCTACAGGGATCT\n+GAGGAGTGGTTATCAAAACATTTTCAGCCGAGGGTTGCAACCAATTTTGTGAGACTCCAA\n+GATCCAGAATTCAACCCATTGTGTAGCGAGGTTGATCTCACAGGATATGTCATTACTATA\n+ATAGATGGGCAAGGTTTCTCTCCTGCATTTTACCTGGCTGATGGGAAACAGAATTTTGTA\n+AAAGTTCGGTGTTTCAGCAGCTTCGCCCAATCTGGCTTGGAAGATGTAATAAAGCCACGT\n+GTCCTTTTGGCCCTAAGCAACCTGCAGCTGAGGGGTCAGTCGACATCACCTACTCCAGTC\n+GTGTATGCTGGAGATTTAACCGTCTTCTCCACAAACCCCAAAGAGGTTCATCTGCAGGAA\n+TCCTTCAGCCAGCTCAAAACTCTGGTTCAGGGCCAGGAGAACTTTTTTGTGCACGCTGAA\n+GAGAAGCTTTCTCAGTTGATGTCTGATGGCCTGAGCGCTATCGCTTCTCCAGCTGGGCAA\n+ATACAAACCCCAGCTTCCACAGTAAAGAGAAGAGGAGACATGACGGATGTGAGCTCAAAT\n+ATAATGGTTATTAACAAGACTTCTAAGGTCACATGTCAGCAGCCAGGCAGAAGCCACAGA\n+TTCTCAACGCCTATAAACAGGAACTCTACTGCTCACAGTTCAGCAGAGAGAAACCCAAGC\n+ACTATTAAGAAGAGGAAAGCTCTCGACTATCTGTCCCACATCCCGTCTCCACCGCCTCTG\n+TCCTGTCTGAGTACACTATCTTCTCCCAGCGTAAAAAAGATATTTATTCCGCCTCGCCGA\n+ACTGAAATACCTGGTACTTTAAAAACTGTAAAGACTCCAAATCAAAAACCTTCCAATACA\n+CCTGTGGATGATCAGTGGGTGAATGATGAGGAACTGGCTATGATCGACACTCAGGCATTA\n' |
| b |
| diff -r 000000000000 -r 4f9e5110914b test-data/species.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/species.nhx Tue Dec 20 16:32:25 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(((((((((((((((((homosapiens*,gorillagorilla*,pantroglodytes*)207598,pongoabelii*)9604,nomascusleucogenys*)314295,(chlorocebussabaeus*,macacamulatta*,papioanubis*)9528)9526,callithrixjacchus*)314293,tarsiussyrichta*)376913,(microcebusmurinus*,otolemurgarnettii*)376911)9443,((oryctolaguscuniculus*,ochotonaprinceps*)9975,(((rattusnorvegicus*,musmusculus*)39107,dipodomysordii*,ictidomystridecemlineatus*)33553,caviaporcellus*)9989)314147,tupaiabelangeri*)314146,((myotislucifugus*,pteropusvampyrus*)9397,((ovisaries*,bostaurus*)9895,vicugnapacos*,susscrofa*,tursiopstruncatus*)91561,((ailuropodamelanoleuca*,canisfamiliaris*,mustelaputoriusfuro*)379584,feliscatus*)33554,(erinaceuseuropaeus*,sorexaraneus*)9362,equuscaballus*)314145)1437010,(dasypusnovemcinctus*,choloepushoffmanni*)9348,(echinopstelfairi*,loxodontaafricana*,procaviacapensis*)311790)9347,(macropuseugenii*,sarcophilusharrisii*,monodelphisdomestica*)9263)32525,ornithorhynchusanatinus*)40674,((pelodiscussinensis*,(((meleagrisgallopavo*,gallusgallus*)9005,anasplatyrhynchos*)1549675,(ficedulaalbicollis*,taeniopygiaguttata*)9126)8825)1329799,anoliscarolinensis*)32561)32524,xenopustropicalis*)32523,latimeriachalumnae*)8287,(((daniorerio*,astyanaxmexicanus*)186626,((((tetraodonnigroviridis*,takifugurubripes*)31031,gasterosteusaculeatus*)1489922,(((poeciliaformosa*,xiphophorusmaculatus*)586240,oryziaslatipes*)1489913,oreochromisniloticus*)1489908)1489872,gadusmorhua*)123368)186625,lepisosteusoculatus*)41665)117571,petromyzonmarinus*)root; |
| b |
| diff -r 000000000000 -r 4f9e5110914b test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fasta Tue Dec 20 16:32:25 2016 -0500 |
| b |
| b'@@ -0,0 +1,11171 @@\n+>ENSLACT00000008884\n+ATGGAATGGGAAGCAGTTGAAAGTGTCAAAGCTTTAATGCGAGATGATGAGCTTACAGAT\n+GCAGGACTAGATGCAAGCAAAGACAGTTTGAACCGTGCATGCAGGAGACAGTCAGGTGGA\n+AATTTCCGAGCTAGGAAGCGGATGAGACTTGAACAAGTGTCGGCTGATGAGCCACCAGTT\n+AAGAGGCAACTCTTGGCTGAATTTGACAGGACGGTTGAAAATGGCCATAAGTCACTTCAG\n+AAGCCTTTAATATGCACTCCAAATGGTACGCTGAAAGACAGAAGGAAGTTTATGTATAGT\n+GTTCCCCTTAAGCCTGTAGTGTGTGGTCCATGGAGCAACAACTCCAAAACTGGGCAACAG\n+GTCACAAAACCCAGCATTACTTTGCCTGGCAGAGGAGTAGAAACATTTCAACCCAAGAAC\n+CACATTGCTCCCAGTCCAGTTTATGATCCACCTTCAAATAGACGAGGCCCAGTCTTTGCT\n+CCACCATTTCATGGGGCCACGTTTCGGGGACTGCAGAAACCAAGTGCTTCACACACATCA\n+AGCAAAACTGCTAAAACTTTTGTTCCTCCATTTAAAATGAAAGCCAGTGCCTCCCACACA\n+GTACATTTCAGTAGCAAAGTTATCAACACTTGTGAAAAGATTTTAGAAAATCTAGTCTAC\n+TTGAAGCCTAGTTTAGCCTCTTGTAATATTTTTCAAAGTTTGGAAGAGATGACTGCTAAC\n+CTTCAGTGTGCCAGAGACCTACAGGAAATGAGGCTGAGAAAGAAGCAAAGGCAAAATATC\n+CGGCCGCAGCCAGGCAGCCTTTACCTTGCTAAAACATCTGGTGTTGCTAGGGTCTCCCTG\n+AAGGCAGCTACAGGAAATCAGTGCCCATCCTCCTACTCCACAGAGCAGTTATATGTTCAT\n+GGTGTAGGAAAAAGCACCTTGAAAGTACGCAGTGAGAATGCAGAATCTTTTCAGTTCAGT\n+TGCAGTGATTATTTTGGTAAAGATGTTCTCCTAGCTGGAAATGGCTTGAAGCTGGCAGAT\n+GGAGGGTGGCTTATACCCAGTGATAAAGGAATGGTAGGAAAAGAAGAATTTTACAGGGCA\n+CTGTGCGATACACCTGGTGTGGCCCCAAAGCTTATTAGTGAATCTTGGGTCTACAATCAT\n+TACAGATGGATTGTATGGAAGCTTGCAGCGATGGAGGCAGCTTTTCCAAAAGAATTTGGC\n+AACCGGTGTCTAACACCAGAGAGGGTGCTGCTACAGCTTAAATACAGGTATGACATTGAA\n+GTTGACAAGTGTCGAAGATCTACTGTAAAGAAGATAATGGAAAGAGATGACACTGCCGCC\n+AAGACACTTGTGCTGTGCATTTCGAAACTTATATCCGTGGAGGACCGTTTTAAACAAACC\n+AAAAATAAGAATGAAAAGGGTGCTGAAGAAGCTAGGAAAGAAGCAGTAGCTGGAGTCATT\n+GAAACTACGGATGGGTGGTATGGGATTAAGGTACTCTTGGATCCTCCCCTTACAGTGCTG\n+GTACAGAGAGGAAGGCTGTCAGTTGGCTGTAAAATTATAACACATGGAGCTGAAATAATT\n+GGCTCCCAGGATGCCTGTACACCACTGGAAGCTCCGGAGTGTCTCATGCTAAAGATTTCT\n+GCGAACAGTACTCGACCTGCTTGCTGGAGTGCTAAACTTGGGTTTCATCGAGATCCCCGA\n+CCTTTTCCTCTCCCATTAGCATCGCTTTTTAATGATGGTGGATTAGTTGGCTGTGTTGAT\n+GTTGTTGTAGTGCGACTGTACCCCATACAGTGGATGGAAAAGAAATCAGATGGGATTTTT\n+GTGTTTCGTAATGATCGAGCAGAAGAAAGAGAGGCTCAAAGGCAAGTTGAGAATCAGCAA\n+AGAAAAATGGAAAGTTTGTTTGCAAAGATTCAAACTGAATTTGAACAGAAATATGAAGCC\n+AAAAGCAAAAGGAGAGGCCAAAAGGCACAGAAATTCAGCAAGCAGGAAATCCAGGCTCTT\n+CAAGATGGTGCAGAACTGAATGAAGCAATTGAGAATTCAATGGATCCGGGTTACTTTGAG\n+GCTTGCTTAAGAGAGGAGCAGTTAAAAGTCCTGCATGGCCACAGACAAATGTTAAATGAA\n+AAGAAACAAGCAGAGTTCCAGGCAGAGTTCAAGAAGGCACTGGAGTCTGCTGAACAGGAG\n+GGGAAGAGCTGCTGCAAGCGAGGTGTAACCCCTGTTTGGAAACTACGCATTGTGGACTAT\n+AGAAAACCAAGTGCTGCAGAATATATATTAAATATTTGGCGACCATTGGCTGATCTGCAT\n+TCCCTGTTAAAGGAAGGTAACCGGTACAGAATTTACCAGTTACTTGCATCACAATCCAAA\n+GGAAGAACCACTACTGCTGACATACAGCTAACAGCTACAAAGAAAACCCAGTATCAGCAG\n+TTCCAGTCTTTCCCAGAATTGATATCAGAGCTGTACAGTCCAAGAAAAGCTGTTAAATTC\n+AACATGTTGATGGATCCAACTTTCCGACCAGCCTATGCAGAAGTAGACCTGGTAGGATAT\n+ACCATCTCTATAGAAGGAAAGCCAGGTGTTGCTCCAGTGGTGTACCTATCTGATGAAAGT\n+CATAACTTTGTGGCAATAAAAGTTTGGACTGCCCTAAATCAGCTTGCTGTTGAAGACATT\n+GTGAAGCCATTTTCACTGATTGCTGCAAGTAACTTACAGTGGAGATCAGACAGCAGATCA\n+ATAATTCCTATGTTGTATGCTGGGGACCTTTCAATATTTTCATCAAATCCAAAAGAAGGG\n+CATCTTCAAGAGGCTTTTAATCAAAGAAGGACTGCTATACAAGAGAACATTTCTGGTACA\n+TACCTCCCCCCAGAAAAAAAAAATCTGCATCAGGAGTCTTATAAATCATGTCAATACAAC\n+ACATTGAATGTTTTGATGAATGGAAACATACACACACAGAGCCCAGTGCTGTCCAGGGTT\n+CATATGGGTACATCCTGTGCTTTTCTCTTTCTACTGCCTTCACCCTACCCTGAAAGTAAA\n+CACACTAGTCCTTTGATAACTATGAAGGCAGGAGTCAAATCTATGACTTTCCCAGGCTCT\n+GCAAAACTAATGCCACAAGCAAGTGAAAATCAAGAACTGGATACTCCCAAGAATCGTAAA\n+AAGAAGGCAGCTTTAGACTATCTTTGCCGCATTCCTTCCCCACCTGCACTTACTCCTATT\n+CGCAGTTTTGTGTCTTCCTCCTTGCAAAAGGCTTTTCACCCACCAAGGAGCTGCGTCAAA\n+CTACAAAGCGGCGAAAACCCAGTCGTCCCCACAGTTGGCAATAACGCTGTCCTAGGGATT\n+CAGTCAAAAAAAGATGAAGGGCCTGCTGCTTTTAATGAAGAGGATTCAGTAGCAGACGAG\n+GAACTAGCAATGATCAATACACAGGCATTCTTAGTCGGCTTAAGAAGGGACAAAAGACCA\n+AGTTTACTGGACAAAACTGCCAGTTTAAAGGGGCATGTTCCCTCAGAAAGATTTCTTGAA\n+GAGAAGCTCTTGTCAGTACTAAAAGAGCAGGCAAGCTCTAATTCTGAGAGAAACGCCACA\n+TCATTGGAAAATAAGAGCTGTGATAAAAGCAGGACATGTGTGAAACCATGTGAACATTCT\n+AATGACAGCATTGCAGAGGAAACTTCAGAAATCATCCCAGGCTGTCATGGTGGAGAATCT\n+GCTGTGGAAAACCAAAGTAAAAATTCCTCATTGTGCCACAAAAAACTGCAACAGAAGAAA\n+AGACGGAAGTATTACTAA\n+>ENSXETT00000064180\n+ATGGCTGCACCGCAACTTGGAAAATCTGTCTTCTATGATCTGTTTAGCACGCATTGCTCT\n+CACTCAGATT'..b'GGCGGGAAGCTG\n+ATTATTCATGGTGCTCAGCTAGTCGGTTCACAGGATGCTTGTTCTCCTTTGGAGGCCCCT\n+GAGTCTATCATGCTAAAGATTTTTGCCAACAGCAGCAGGCGAGCACGATGGGATGCTAAA\n+CTGGGATTTTATAGGGACCCACGGCCATTCCTGCTCCCTGTCTCTTCTTTGTACAACAGT\n+GGGGGACCTGTAGGATGTGTGGATATTATTATATTAAGAAGCTATCCCACATTATGGATG\n+GAGAGAAAACCAGAAGGAGGCACTGTGTTCCGGTCAGGCCGAGCAGAAGAAAAGGAGGCT\n+AGACGGTACAACGTCCACAAGGAAAAAGCTATGGAGATTCTGTTTGACAAGATTCAAGCG\n+GAATTTGAAAAGGAAGAGAGGGATAACAGGAAACCTCGGAGCAGAAGACGGACAATCGGT\n+GATCAAGATATCAAAAGTCTTCAAGATGGAGAGGAGCTGTACGAAGCAGTGGGCGATGAC\n+CCAGCTTACCTTGAGGCACATTTGACTGAGCAGCAGGCAGAGACTCTACAGAACTACAAA\n+CGTCTGCTGATAGAAAAGAAGCAAGCAGAGCTGCAGGATCGCTACCGGCGAGCTGTAGAA\n+ACTGCAGAGGATGGCACAGGCAGCTGTCCCAAGCGAGATGTAGCACCTGTATGGAGACTC\n+AGCATTGCTGACTTCATGGAAAAGCCAGGCAGTGTTTACCAGCTGAACATTTGGCGGCCT\n+CCCTCAGAGCTCCAGTCTTTACTAAAAGAAGGCTGTCGATATAAGGTGTATAATCTCACC\n+ACAACAGATTCAAAGAAACAAGGTGGAAACACAACCGTTCAGCTAAGTGGAACAAAAAAA\n+ACACAATTTGAGGACCTTCAGGCATCCGAGGAATTGTTGTCAACATATTTTCAGCCAAGG\n+GTCTCGGCCACATTCATCGATCTCCAAGATCCAGAATTCCATTCGTTGTGTGGTGAGGTT\n+GATCTCACAGGATACGTCATCAGTATAATAGATGGACAAGGTTTCTCACCTGCTTTTTAC\n+CTAACTGATGGGAAACAAAATTTTGTAAAAGTGCGTTGTTTCAGCAGCTTCGCTCAGTCA\n+GGCTTGGAAGATGTAATAAAGCCAAGTGTCCTTTTAGCTTTAAGCAACCTCCAACTGAGA\n+GGTCAGGCAACATCACCCACTCCAGTCTTGTACGCTGGAGATCTAACCGTCTTCTCCACA\n+AACCCCAAAGAAGTTCATCTGCAGGAATCCTTCAGCCAGCTCAAAACCCTGGTTCAG\n+>ENSTRUT00000015099\n+CAGCTGGCACGGGATATGCAGGATATGCGAATCAGAAAAAAGAAACGCCAGACCATTCGT\n+CCATTACCGGGAAGTTTGTTTCAGAAGAAGTCCTCTGGAGTCGCCAGGATTCCATTTAAA\n+GCTGCAGTAAACGGAAAGCCACCTGCACGCTACACTGCCAAACCGCTGTGTGGCCTCGGG\n+GTTCCTCTGAATGTGTTGGAGATCACCAGTGAGACTGCAGAATCTTTTCGCTTCAGCTTG\n+CAGCACTTTGTTAAGCTGGAGTCTCTCATAGATAAAGGTGGCATACAGCTCGCTGATGGA\n+GGATGGCTGATTCCCACGAATGACGGGACAGCGGGAAAAGAAGAGTTTTATCGAGCATTG\n+TGTGATACCCCGGGGGTTGATCCTAAACTAATGAGTGAGGAGTGGGTGTATAATCACTAC\n+CGATGGATTGTATGGAAACAAGCTTCCATGGAAAGGTCATTTCCAGAAGAGATGGGCAGC\n+CTCTGTCTCACCCCAGAGCAGGTTCTCCTACAACTTAAGTACAGATATGACATAGAGGTT\n+GACCACAGTCGCAGACCAGCTCTCAGAAAAATTATGGAAAAGGATGACACGGCAGCTAAA\n+ACCCTGGTCCTCTGTGTTTGTGGGGTTGTCTTCAGAGGCAGCTCCCCAAAAAACAAGAGT\n+TTTGGGGACATCAGTACTCCAGGAGCTGACCCAAAGGTTGAAAACCCCTGTGCTGTCGTT\n+TGGCTGACCGATGGATGGTATTCAATTAAAGCGCAACTGGATGGACCGTTGACCTCAATG\n+CTTCACAGAGGTCGACTACCAGTCGGCGGGAAGCTGATTATCCATGGTGCTCAGCTAGTC\n+GGATCAGAGAATGCTTGTTCCCCCCTGGAGGCCCCTGTGTCTTTAATGCTAAAGATTTGC\n+GCCAACAGCAGCAGACCAGCTCGATGGGATTCTAAACTAGGATTTCACAGGGACCCGCGG\n+CCATTCCTGCTTCCTGTCTCTTCTTTGTACAGCAGTGGAGGACCAGTAGGATGTGTGGAT\n+ATTATTATACTGAGAAGCTATCCCATATTGTGGATGGAGAGGAAACCAGAAGGAGGCACT\n+GTGTTCCGTTCAGGCAGAGCAGAAGAGAAGGAGGCGAGACGATACAACATTCACAAAGAA\n+AAAGCTATGGAAATCCTGTTTGACAAGATTAAAGCAGAATTTGAAAAGGAAGAAAAAGGT\n+AACAGGAAACCGCAGTGCAGAAGGACAATCAATGGTCAAAATATTACAAGTCTTCAAGAT\n+GGAGAGGAGCTGTACGAAGCAGTGGGCGATGACCCAGCTTTCCTTGAGGCGCATCTGACT\n+GAGAAGCAGGTGGAGGTTCTTCAGAACTACAAACGTCTGGTGATGGAGAAGCAGCAGGCA\n+GAGCTGCAGGATCGCTACCGGCGAGCTGTAGAAAGTGCAGAGGACGGCGTGGGGGGCTGC\n+CCCAAGCGAGATGTCGCACCTGTGTGGAGACTGTGCATTGCTGACTCCATGGGCCATTCT\n+GGCCGTGTTTACCAGCTGAGTCTTTGGCGGCCCCCCTCAGAGCTCCAGGCATTACTGAAG\n+GAAGGCTGTCGTTATAAAGTGTATAATCTCACCACTTTAGATTCAAAGAAACAGGGTGGA\n+AATGCAACGGTTCAGCTAACTGCAACAAAAAAAACACAGTTTGAGCACCTACAGGGATCT\n+GAGGAGTGGTTATCAAAACATTTTCAGCCGAGGGTTGCAACCAATTTTGTGAGACTCCAA\n+GATCCAGAATTCAACCCATTGTGTAGCGAGGTTGATCTCACAGGATATGTCATTACTATA\n+ATAGATGGGCAAGGTTTCTCTCCTGCATTTTACCTGGCTGATGGGAAACAGAATTTTGTA\n+AAAGTTCGGTGTTTCAGCAGCTTCGCCCAATCTGGCTTGGAAGATGTAATAAAGCCACGT\n+GTCCTTTTGGCCCTAAGCAACCTGCAGCTGAGGGGTCAGTCGACATCACCTACTCCAGTC\n+GTGTATGCTGGAGATTTAACCGTCTTCTCCACAAACCCCAAAGAGGTTCATCTGCAGGAA\n+TCCTTCAGCCAGCTCAAAACTCTGGTTCAGGGCCAGGAGAACTTTTTTGTGCACGCTGAA\n+GAGAAGCTTTCTCAGTTGATGTCTGATGGCCTGAGCGCTATCGCTTCTCCAGCTGGGCAA\n+ATACAAACCCCAGCTTCCACAGTAAAGAGAAGAGGAGACATGACGGATGTGAGCTCAAAT\n+ATAATGGTTATTAACAAGACTTCTAAGGTCACATGTCAGCAGCCAGGCAGAAGCCACAGA\n+TTCTCAACGCCTATAAACAGGAACTCTACTGCTCACAGTTCAGCAGAGAGAAACCCAAGC\n+ACTATTAAGAAGAGGAAAGCTCTCGACTATCTGTCCCACATCCCGTCTCCACCGCCTCTG\n+TCCTGTCTGAGTACACTATCTTCTCCCAGCGTAAAAAAGATATTTATTCCGCCTCGCCGA\n+ACTGAAATACCTGGTACTTTAAAAACTGTAAAGACTCCAAATCAAAAACCTTCCAATACA\n+CCTGTGGATGATCAGTGGGTGAATGATGAGGAACTGGCTATGATCGACACTCAGGCATTA\n' |
| b |
| diff -r 000000000000 -r 4f9e5110914b test-data/test.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.json Tue Dec 20 16:32:25 2016 -0500 |
| [ |
| b'@@ -0,0 +1,31795 @@\n+{\n+ "ENSTNIG00000016261": {\n+ "source": "ensembl",\n+ "object_type": "Gene",\n+ "logic_name": "ensembl",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "description": "breast cancer 2, early onset [Source:ZFIN;Acc:ZDB-GENE-060510-3]",\n+ "display_name": "brca2",\n+ "assembly_name": "TETRAODON8",\n+ "biotype": "protein_coding",\n+ "end": 4705074,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIG00000016261",\n+ "Transcript": [\n+ {\n+ "source": "ensembl",\n+ "object_type": "Transcript",\n+ "logic_name": "ensembl",\n+ "Exon": [\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "assembly_name": "TETRAODON8",\n+ "end": 4700679,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIE00000057385",\n+ "start": 4700614\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "assembly_name": "TETRAODON8",\n+ "end": 4701157,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIE00000041338",\n+ "start": 4701103\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "assembly_name": "TETRAODON8",\n+ "end": 4701424,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIE00000031348",\n+ "start": 4701218\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "assembly_name": "TETRAODON8",\n+ "end": 4701571,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIE00000063263",\n+ "start": 4701502\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "assembly_name": "TETRAODON8",\n+ "end": 4701608,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIE00000054769",\n+ "start": 4701587\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "tetraodon_nigroviridis",\n+ "assembly_name": "TETRAODON8",\n+ "end": 4701940,\n+ "seq_region_name": "16",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSTNIE00000041082",\n+ "start": 4701626\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ '..b' "assembly_name": "cavPor3",\n+ "end": 33841095,\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSCPOE00000227172",\n+ "start": 33841075\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "cavia_porcellus",\n+ "assembly_name": "cavPor3",\n+ "end": 33841317,\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSCPOE00000067342",\n+ "start": 33841179\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "cavia_porcellus",\n+ "assembly_name": "cavPor3",\n+ "end": 33850200,\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSCPOE00000067343",\n+ "start": 33849956\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 1,\n+ "species": "cavia_porcellus",\n+ "assembly_name": "cavPor3",\n+ "end": 33851341,\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSCPOE00000067344",\n+ "start": 33851195\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 2,\n+ "species": "cavia_porcellus",\n+ "assembly_name": "cavPor3",\n+ "end": 33852801,\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSCPOE00000067345",\n+ "start": 33852516\n+ },\n+ {\n+ "object_type": "Exon",\n+ "version": 2,\n+ "species": "cavia_porcellus",\n+ "assembly_name": "cavPor3",\n+ "end": 33853154,\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "strand": 1,\n+ "id": "ENSCPOE00000067347",\n+ "start": 33852814\n+ }\n+ ],\n+ "Parent": "ENSCPOG00000005153",\n+ "seq_region_name": "scaffold_6",\n+ "db_type": "core",\n+ "is_canonical": 1,\n+ "strand": 1,\n+ "id": "ENSCPOT00000005208",\n+ "version": 2,\n+ "species": "cavia_porcellus",\n+ "assembly_name": "cavPor3",\n+ "display_name": "BRCA2-201",\n+ "end": 33853154,\n+ "biotype": "protein_coding",\n+ "Translation": {\n+ "object_type": "Translation",\n+ "species": "cavia_porcellus",\n+ "Parent": "ENSCPOT00000005208",\n+ "end": 33853154,\n+ "length": 3313,\n+ "db_type": "core",\n+ "id": "ENSCPOP00000004635",\n+ "start": 33778275\n+ },\n+ "start": 33778275\n+ }\n+ ],\n+ "start": 33778275\n+ }\n+}\n\\ No newline at end of file\n' |