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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty |
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modified:
ete_species_tree_generator.py ete_species_tree_generator.xml |
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added:
ete_init_taxdb.py ete_init_taxdb.xml ete_lineage_generator.py ete_lineage_generator.xml ete_macros.xml ete_mod.xml test-data/lineage-compress-lower.txt test-data/lineage-compress.txt test-data/lineage-full.txt test-data/lineage.txt test-data/taxdump.sqlite test-data/taxdump.tar.gz test-data/tree1.nhx test-data/tree1_ladder.nhx test-data/tree1_ogA.nhx test-data/tree1_pruneAC.nhx test-data/tree1_pruneACpreserve.nhx test-data/tree1_unroot.nhx test-data/tree1_unroot_resolve.nhx test-data/tree2.nhx test-data/tree2_sort.nhx test-data/tree3.nhx test-data/tree3_stand.nhx |
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removed:
test-data/out.nhx |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_init_taxdb.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_init_taxdb.py Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -0,0 +1,24 @@ +import optparse + +import ete3.ncbi_taxonomy +from six.moves.urllib.request import urlretrieve + +parser = optparse.OptionParser() +parser.add_option('-t', '--taxdump', dest='taxdump', default=None, + help='NCBI taxdump (tar.gz) will be downloaded if not given') +parser.add_option('-d', '--database', dest="database", default=None, + help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)') +options, args = parser.parse_args() +if options.database is None: + parser.error("-d option must be specified") +if options.taxdump is not None: + taxdump = options.taxdump +else: + urlretrieve("http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz") + taxdump = "taxdump.tar.gz" + +# will remove a taxdump.tar.gz file at the end +# which will lead to an errmessage if not present +# if the tool is run on a taxdump in the current dir it will be +# deleted in the end +ete3.ncbi_taxonomy.ncbiquery.update_db(dbfile=options.database, targz_file=taxdump) |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_init_taxdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_init_taxdb.xml Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -0,0 +1,48 @@ +<tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@VERSION@"> + <description>generates the ETE sqlite DB from the NCBI taxdump.tar.gz</description> + <macros> + <import>ete_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/ete_init_taxdb.py' +#if $latestcond.latest == "local" + -t '$latestcond.taxdump' +#end if +-d '$database' + ]]></command> + <inputs> + <conditional name="latestcond"> + <param name="latest" type="select" label="Get latest version" help="Get the latest version of the taxdump from the NCBI website"> + <option value="local" selected="true">Use a local taxdump</option> + <option value="latest">Get latest taxdump online</option> + </param> + <when value="local"> + <param name="taxdump" type="data" format="tar" label="NCBI taxdump" help="NCBI taxonomy database dump in tar.gz format" /> + </when> + <when value="latest" /> + </conditional> + </inputs> + <outputs> + <data name="database" format="sqlite" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="latest" value="local" /> + <param name="taxdump" ftype="tar" value="taxdump.tar.gz" /> + <output name="database" file="taxdump.sqlite" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the .. _ETE Toolkit: http://etetoolkit.org/ + +**Input** + +- NCBI taxdump: NCBI taxdump in tar.gz format. If not given the latest is downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz + +**Output** + +- *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_lineage_generator.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_lineage_generator.py Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -0,0 +1,128 @@ +import optparse +import sys + +from ete3 import NCBITaxa + +# - compared to gi2taxonomy the root is excluded, since +# the value is always "root", i.e. useless information +# - additional levels that appear in the ncbi taxdb have +# been added +# (order from https://en.wikipedia.org/wiki/Taxonomic_rank#All_ranks) +# TODO the full list of ranks could be derived from the input DB +LONG_RANKS = [u"superkingdom", u"kingdom", u"subkingdom", + u"superphylum", u"phylum", u"subphylum", + u"superclass", u"class", u"subclass", "infraclass", + u"cohort", + u"superorder", u"order", u"suborder", u"infraorder", u"parvorder", + u"superfamily", u"family", u"subfamily", + u"tribe", u"subtribe", + u"genus", u"subgenus", + u"species group", u"species subgroup", u"species", u"subspecies", + u"varietas", "forma"] + +SHORT_RANKS = [u"kingdom", + u"phylum", + u"class", + u"order", + u"family", + u"genus", + u"species"] + + +def process_taxid(ncbi, taxid, ranks, RANK_IDX, lower=False): + """ + process one taxid: + - get lineage (as list of taxids, ranks, and names) + - reverse the lineage if lower ranks are to be used for filling + - fill the ranks with the data from the lineage + ncbi: ete NCBITaxa object + taxid: a taxid (int) + ranks: list of ranks (should be initialized with "NA" x number of levels of interest) + RANK_IDX: mapping from rank names to indices (distance to root/leaf?) + lower: use lower taxa for filling "NA"s + """ + lineage = ncbi.get_lineage(taxid) + lineage_ranks = ncbi.get_rank(lineage) + lineage_names = ncbi.get_taxid_translator(lineage, try_synonyms=True) + if lower: + lineage.reverse() + for l in lineage: + if not lineage_ranks[l] in RANK_IDX: + continue + if ranks[RANK_IDX[lineage_ranks[l]]] != "NA": + continue + ranks[RANK_IDX[lineage_ranks[l]]] = lineage_names[l] + + +# get command line options +parser = optparse.OptionParser() +parser.add_option('-s', '--species', dest="input_species_filename", + help='Species/taxid list in text format one species in each line') +parser.add_option('-d', '--database', dest="database", default=None, + help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)') +parser.add_option('-o', '--output', dest="output", help='output file name (default: stdout)') +parser.add_option('-f', dest="full", action="store_true", default=False, + help='Show all available (named) taxonomic ranks (default: only primary levels)') +parser.add_option('-c', dest="compress", action="store_true", default=False, + help='Fill unnamed ranks with super/sub ranks (see -l)') +parser.add_option('-l', dest="lower", action="store_true", default=False, + help='Prefer lower levels when compressed') +parser.add_option('-r', '--rank', dest='ranks', action="append", + help='include rank - multiple ones can be specified') + +options, args = parser.parse_args() +# check command line options +if options.input_species_filename is None: + parser.error("-s option must be specified, Species list in text format one species in each line") +if options.full and options.ranks: + parser.error("-f and -r can not be used at the same time") +if options.ranks: + for r in options.ranks: + if r not in LONG_RANKS: + parser.error("unknown rank %s" % r) +# setup output +if not options.output: # if filename is not given + of = sys.stdout +else: + of = open(options.output, "w") +# load NCBI taxonomy DB +ncbi = NCBITaxa(dbfile=options.database) +# get list of ranks that are of interest +if options.ranks: + RANKS = [] + for r in LONG_RANKS: + if r in options.ranks: + RANKS.append(r) +else: + if options.full: + RANKS = LONG_RANKS + else: + RANKS = SHORT_RANKS +RANK_IDX = {item: index for index, item in enumerate(RANKS)} +COMP_RANK_IDX = RANK_IDX +if options.compress: + for ir in range(len(RANKS)): + for ilr in range(len(LONG_RANKS)): + if RANKS[ir] in LONG_RANKS[ilr]: + COMP_RANK_IDX[LONG_RANKS[ilr]] = ir +with open(options.input_species_filename) as f: + for line in f.readlines(): + line = line.strip().replace('_', ' ') + try: + taxid = int(line) + except ValueError: + # TODO: one could use fuzzy name lookup (i.e. accept typos in the species names), + # but then a pysqlite version that supports this is needed (needs to be enabled + # during compilation) + name2tax = ncbi.get_name_translator([line]) + if line in name2tax: + taxid = name2tax[line][0] + else: + sys.stderr.write("[%s] could not be translated into a taxid!\n" % line) + continue + ranks = ["NA"] * len(RANKS) + process_taxid(ncbi, taxid, ranks, RANK_IDX) + if options.compress: + process_taxid(ncbi, taxid, ranks, COMP_RANK_IDX, options.lower) + of.write("%s\t%s\n" % (line, "\t".join(ranks))) +of.close() |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_lineage_generator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_lineage_generator.xml Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -0,0 +1,145 @@ +<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@"> + <description>from a list of species/taxids using the ETE Toolkit</description> + <macros> + <import>ete_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/ete_lineage_generator.py' +-s '$speciesFile' +-d '$database' +-o '$outputFile' +#if $ranks.levels == "full" + -f +#elif $ranks.levels == "manual" + #for $rank in $ranks.manualranks: + -r $rank + #end for +#end if +#if $compresscond.compress == "-c" + $compresscond.compress + $compresscond.lower +#end if + ]]></command> + <inputs> + <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species/taxid per line" /> + <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" /> + <conditional name="ranks"> + <param name="levels" type="select" label="Taxonomic levels" help="Taxonomic levels to include in the output"> + <option value="primary" selected="true">Primary</option> + <option value="full">Full</option> + <option value="manual">Manual</option> + </param> + <when value="manual"> + <param name="manualranks" type="select" multiple="true" label="Manual selection of ranks"> + <option value="superkingdom">superkingdom</option> + <option value="kingdom" selected="true">kingdom</option> + <option value="subkingdom">subkingdom</option> + <option value="superphylum">superphylum</option> + <option value="phylum" selected="true">phylum</option> + <option value="subphylum">subphylum</option> + <option value="superclass">superclass</option> + <option value="class" selected="true">class</option> + <option value="subclass">subclass</option> + <option value="infraclass">infraclass</option> + <option value="cohort">cohort</option> + <option value="superorder">superorder</option> + <option value="order" selected="true">order</option> + <option value="suborder">suborder</option> + <option value="infraorder">infraorder</option> + <option value="parvorder">parvorder</option> + <option value="superfamily">superfamily</option> + <option value="family" selected="true">family</option> + <option value="subfamily">subfamily</option> + <option value="tribe">tribe</option> + <option value="subtribe">subtribe</option> + <option value="genus" selected="true">genus</option> + <option value="subgenus">subgenus</option> + <option value="species group">species group</option> + <option value="species subgroup">species subgroup</option> + <option value="species" selected="true">species</option> + <option value="subspecies">subspecies</option> + <option value="varietas">varietas</option> + <option value="forma">forma</option> + </param> + </when> + <when value="primary" /> + <when value="full" /> + </conditional> + <conditional name="compresscond"> + <param name="compress" type="select" label="Fill unnamed ranks" help="Fill unnamed ranks with super/sub ranks (see -l)"> + <option value="-c">Yes</option> + <option value="">No</option> + </param> + <when value="-c"> + <param name="lower" type="select" label="Prefer lower ranks for filling" help="Prefer lower levels for filling"> + <option value="-l">Yes</option> + <option value="">No</option> + </param> + </when> + <when value="" /> + </conditional> + </inputs> + <outputs> + <data name="outputFile" format="tsv" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> + <param name="compress" value="" /> + <param name="levels" value="primary" /> + <output name="outputFile" file="lineage.txt" /> + </test> + <test> + <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> + <param name="compress" value="-c" /> + <param name="levels" value="primary" /> + <output name="outputFile" file="lineage-compress.txt" /> + </test> + <test> + <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> + <param name="compress" value="-c" /> + <param name="levels" value="primary" /> + <param name="lower" value="-l" /> + <output name="outputFile" file="lineage-compress-lower.txt" /> + </test> + <test> + <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> + <param name="compress" value="" /> + <param name="levels" value="full" /> + <output name="outputFile" file="lineage-full.txt" /> + </test> + </tests> + <help><![CDATA[ +Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the .. _ETE Toolkit: http://etetoolkit.org/ + +**Input** + +- *Species file* a single column tabular file +- *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump + +**Options** + +- *Taxonomic levels* the columns to be incuded in the output table. There are two presets (full and primary) + + - *Full* contains all 29 ranks included in the NCBI taxonomy + - *Primary* contains the primary ranks (kingdom, phylum, class, order, family, genus, species) + - *Manual* the ranks of interest can be chosen by the user. The primary levels are chosen by default. + +- *Fill unnamed ranks* Get missing data from "nearby" levels: + + - Some nodes in the NCBI taxonomy tree have no name (no rank) these are shown by default as "NA" in the output. If the *compress* option is selected then the rank is accepted if the level name is included (e.g. superorder is accepted as order if the order is unnamed but the name of the superorder is given) + +- *Prefer lower ranks for filling* for compressing lower levels are prefered over higher ones + +**Output** + +Table (tab separated). The first column contains the species names. The following columns contain the +rank names of the levels of interest. + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_macros.xml Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">3.0.0b35</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">ete3</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/molbev/msw046</citation> + </citations> + </xml> +</macros> + |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_mod.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ete_mod.xml Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -0,0 +1,108 @@ +<tool id="ete3_mod" name="ETE mod" version="@VERSION@"> + <description>manipulates tree topology by rooting, pruning or sorting branches</description> + <macros> + <import>ete_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +ete3 mod -t +#for $input_tree in $input_trees: + '$input_tree' +#end for +-v '$verbosity' +#if $outgroup: + --outgroup '$outgroup' +#end if +## #if float($ultrametric) > 0.0: +## --ultrametric $ultrametric +## #end if +#if $prune: + #set node_list = "'" + "' '".join($prune.split(',')) + "'" + --prune $node_list +#end if +$prune_preserve_lengths +$unroot +$sort_branches +$ladderize +$resolve_polytomies +$standardize +> '$output_tree' + ]]></command> + <inputs> + <param name="input_trees" argument="-t" type="data" format="nhx" multiple="true" label="Newick trees" /> + <param name="verbosity" argument="-v" type="integer" value="0" min="0" max="4" label="Verbosity level" + help="0=totally quite, 1=errors only, 2=warning+errors, 3=info+warnings+errors 4=debug (-v)" /> + <param argument="--outgroup" type="text" value="" label="Reroot tree with outgroup (space separated list of leaf names)" + help="Root the tree using the provided outgroup. If several + names are provided, the first common ancestor grouping + all of them will be selected as outgroup" /> + <!-- parameter does not work in the current version + <param argument="- -ultrametric" type="float" value="0" min="0" label="Convert tree into ultrametric" + help="Convert tree into ultrametric (all leaves have the + same distance to root). If an argument (!=0) is provided, it + will be used as the expected tree length" />--> + <param argument="--prune" type="text" value="" label="Prune nodes from the tree (comma-separated list of leaf names)" + help="Remove all nodes in the tree except the ones provided (empty does not prune)" /> + <param argument="--prune_preserve_lengths" type="boolean" truevalue="--prune_preserve_lengths" falsevalue="" label="Prune: preserve length" + help="Branch lengths of the removed nodes are added to the kept branches, thus preserving original tree length" /> + <param argument="--unroot" type="boolean" truevalue="--unroot" falsevalue="" label="Unroots the tree" /> + <param argument="--sort_branches" type="boolean" truevalue="--sort_branches" falsevalue="" label="Sort branches" + help="Sort branches according to node names" /> + <param argument="--ladderize" type="boolean" truevalue="--ladderize" falsevalue="" label="Ladderize" + help="Sort branches by partition size" /> + <param argument="--resolve_polytomies" type="boolean" truevalue="--resolve_polytomies" falsevalue="" label="Resolve polytomies" + help="Converts polytomies into bifurcations" /> + <param argument="--standardize" type="boolean" truevalue="--standardize" falsevalue="" label="Standardize tree" + help="Standardize tree topology by expanding polytomies and single child nodes" /> + </inputs> + <outputs> + <data name="output_tree" format="nhx" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input_trees" ftype="nhx" value="tree1.nhx" /> + <param name="outgroup" value="A" /> + <output name="output_tree" file="tree1_ogA.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree1.nhx" /> + <param name="prune" value="A,C" /> + <output name="output_tree" file="tree1_pruneAC.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree1.nhx" /> + <param name="prune" value="A,C" /> + <param name="prune_preserve_lengths" value="--prune_preserve_lengths" /> + <output name="output_tree" file="tree1_pruneACpreserve.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree1.nhx" /> + <param name="unroot" value="--unroot" /> + <output name="output_tree" file="tree1_unroot.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree2.nhx" /> + <param name="sort_branches" value="--sort_branches" /> + <output name="output_tree" file="tree2_sort.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree1.nhx" /> + <param name="ladderize" value="--ladderize" /> + <output name="output_tree" file="tree1_ladder.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree1_unroot.nhx" /> + <param name="resolve_polytomies" value="--resolve_polytomies" /> + <output name="output_tree" file="tree1_unroot_resolve.nhx" /> + </test> + <test> + <param name="input_trees" ftype="nhx" value="tree3.nhx" /> + <param name="standardize" value="--standardize" /> + <output name="output_tree" file="tree3_stand.nhx" /> + </test> + </tests> + <help><![CDATA[ +Modify a given input tree using the etetoolkit: http://etetoolkit.org/ + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_species_tree_generator.py --- a/ete_species_tree_generator.py Fri Mar 17 16:23:39 2017 -0400 +++ b/ete_species_tree_generator.py Tue Nov 07 11:45:13 2017 -0500 |
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| @@ -1,33 +1,24 @@ import optparse +import sys from ete3 import NCBITaxa -ncbi = NCBITaxa() parser = optparse.OptionParser() parser.add_option('-s', '--species', dest="input_species_filename", help='Species list in text format one species in each line') - +parser.add_option('-d', '--database', dest="database", default=None, + help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)') +parser.add_option('-o', '--output', dest="output", help='output file name (default: stdout)') parser.add_option('-f', '--format', type='choice', choices=['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '100'], dest="format", default='8', help='outpur format for tree') - parser.add_option('-t', '--treebest', type='choice', choices=['yes', 'no'], dest="treebest", default='no', help='To be used in TreeBest') - -parser.add_option('-d', '--database', type='choice', choices=['yes', 'no'], dest="database", - default='no', help='Update database') - options, args = parser.parse_args() +if options.input_species_filename is None: + parser.error("-s option must be specified, Species list in text format one species in each line") -if options.database == "yes": - try: - ncbi.update_taxonomy_database() - except: - pass - -if options.input_species_filename is None: - raise Exception('-s option must be specified, Species list in text format one species in each line') - +ncbi = NCBITaxa(dbfile=options.database) with open(options.input_species_filename) as f: species_name = [_.strip().replace('_', ' ') for _ in f.readlines()] @@ -51,6 +42,10 @@ if options.treebest == "yes": newickTree = newickTree.rstrip(';') newickTree = newickTree + "root;" - -with open('newickTree.nhx', 'w') as newickFile: - newickFile.write(newickTree) +# setup output +if not options.output: # if filename is not given + of = sys.stdout +else: + of = open(options.output, "w") +of.write(newickTree) +of.close() |
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| diff -r a4ba317fc713 -r 03c10736e497 ete_species_tree_generator.xml --- a/ete_species_tree_generator.xml Fri Mar 17 16:23:39 2017 -0400 +++ b/ete_species_tree_generator.xml Tue Nov 07 11:45:13 2017 -0500 |
| [ |
| @@ -1,27 +1,30 @@ -<tool id="ete_species_tree_generator" name="ETE species tree generator" version="3.0.0b35"> +<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@.1"> <description>from a list of species using the ETE Toolkit</description> - <requirements> - <requirement type="package" version="3.0.0b35">ete3</requirement> - </requirements> + <macros> + <import>ete_macros.xml</import> + </macros> + <expand macro="requirements" /> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> </stdio> <command> <![CDATA[ -python $__tool_directory__/ete_species_tree_generator.py +python '$__tool_directory__/ete_species_tree_generator.py' -s '$speciesFile' +-d $database +-o '$outputFile' #if $output_format.treebest == 'yes' -f 8 #else -f ${output_format.format_selector} #end if -t $output_format.treebest --d $database ]]> </command> <inputs> - <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" /> + <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" /> + <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" /> <conditional name="output_format"> <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest"> <option value="yes">Yes</option> @@ -44,19 +47,21 @@ </param> </when> </conditional> - <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> </inputs> <outputs> - <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/> + <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test> <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> <param name="treebest" value="yes" /> - <output name="outputFile" file="out.nhx" /> + <output name="outputFile"> + <assert_contents> + <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" /> + <has_text text=")root;" /> + </assert_contents> + </output> </test> </tests> <help> @@ -84,7 +89,5 @@ ======= ============================================= ======================================================================================== ]]> </help> - <citations> - <citation type="doi">10.1093/molbev/msw046</citation> - </citations> + <expand macro="citations" /> </tool> |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/lineage-compress-lower.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage-compress-lower.txt Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,62 @@ +Latimeria chalumnae Eukaryota Chordata NA Coelacanthiformes Coelacanthidae Latimeria Latimeria chalumnae +Xenopus tropicalis Eukaryota Chordata Amphibia Batrachia Pipoidea Xenopus Xenopus tropicalis +Ornithorhynchus anatinus Eukaryota Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus Ornithorhynchus anatinus +Macropus eugenii Eukaryota Chordata Mammalia Diprotodontia Macropodidae Notamacropus Notamacropus eugenii +Sarcophilus harrisii Eukaryota Chordata Mammalia Dasyuromorphia Dasyuridae Sarcophilus Sarcophilus harrisii +Monodelphis domestica Eukaryota Chordata Mammalia Didelphimorphia Didelphidae Monodelphis Monodelphis domestica +Echinops telfairi Eukaryota Chordata Mammalia Afrotheria Tenrecidae Echinops Echinops telfairi +Procavia capensis Eukaryota Chordata Mammalia Afrotheria Procaviidae Procavia Procavia capensis +Loxodonta africana Eukaryota Chordata Mammalia Afrotheria Elephantidae Loxodonta Loxodonta africana +Dasypus novemcinctus Eukaryota Chordata Mammalia Xenarthra Dasypodidae Dasypus Dasypus novemcinctus +Choloepus hoffmanni Eukaryota Chordata Mammalia Xenarthra Megalonychidae Choloepus Choloepus hoffmanni +Ochotona princeps Eukaryota Chordata Mammalia Euarchontoglires Ochotonidae Ochotona Ochotona princeps +Oryctolagus cuniculus Eukaryota Chordata Mammalia Euarchontoglires Leporidae Oryctolagus Oryctolagus cuniculus +Cavia porcellus Eukaryota Chordata Mammalia Euarchontoglires Caviidae Cavia Cavia porcellus +Ictidomys tridecemlineatus Eukaryota Chordata Mammalia Euarchontoglires Sciuridae Ictidomys Ictidomys tridecemlineatus +Dipodomys ordii Eukaryota Chordata Mammalia Euarchontoglires Heteromyidae Dipodomys Dipodomys ordii +Rattus norvegicus Eukaryota Chordata Mammalia Euarchontoglires Muridae Rattus Rattus norvegicus +Mus musculus Eukaryota Chordata Mammalia Euarchontoglires Muridae Mus Mus musculus +Tupaia belangeri Eukaryota Chordata Mammalia Euarchontoglires Tupaiidae Tupaia Tupaia belangeri +Otolemur garnettii Eukaryota Chordata Mammalia Euarchontoglires Galagidae Otolemur Otolemur garnettii +Microcebus murinus Eukaryota Chordata Mammalia Euarchontoglires Cheirogaleidae Microcebus Microcebus murinus +Tarsius syrichta Eukaryota Chordata Mammalia Euarchontoglires Tarsiidae Carlito Carlito syrichta +Callithrix jacchus Eukaryota Chordata Mammalia Euarchontoglires Cebidae Callithrix Callithrix jacchus +Chlorocebus sabaeus Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Chlorocebus Chlorocebus sabaeus +Papio anubis Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Papio Papio anubis +Macaca mulatta Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Macaca Macaca mulatta +Nomascus leucogenys Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Nomascus Nomascus leucogenys +Pongo abelii Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pongo Pongo abelii +Gorilla gorilla gorilla Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Gorilla Gorilla gorilla +Pan troglodytes Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pan Pan troglodytes +Homo sapiens Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Homo Homo sapiens +Sorex araneus Eukaryota Chordata Mammalia Laurasiatheria Soricidae Sorex Sorex araneus +Erinaceus europaeus Eukaryota Chordata Mammalia Laurasiatheria Erinaceidae Erinaceus Erinaceus europaeus +Pteropus vampyrus Eukaryota Chordata Mammalia Laurasiatheria Pteropodidae Pteropus Pteropus vampyrus +Myotis lucifugus Eukaryota Chordata Mammalia Laurasiatheria Vespertilionidae Myotis Myotis lucifugus +Felis catus Eukaryota Chordata Mammalia Laurasiatheria Felidae Felis Felis catus +Canis lupus familiaris Eukaryota Chordata Mammalia Laurasiatheria Canidae Canis Canis lupus +Mustela putorius furo Eukaryota Chordata Mammalia Laurasiatheria Mustelidae Mustela Mustela putorius +Ailuropoda melanoleuca Eukaryota Chordata Mammalia Laurasiatheria Ursidae Ailuropoda Ailuropoda melanoleuca +Equus caballus Eukaryota Chordata Mammalia Laurasiatheria Equidae Equus Equus caballus +Vicugna pacos Eukaryota Chordata Mammalia Laurasiatheria Camelidae Vicugna Vicugna pacos +Sus scrofa Eukaryota Chordata Mammalia Laurasiatheria Suidae Sus Sus scrofa +Tursiops truncatus Eukaryota Chordata Mammalia Laurasiatheria Delphinidae Tursiops Tursiops truncatus +Ovis aries Eukaryota Chordata Mammalia Laurasiatheria Bovidae Ovis Ovis aries +Bos taurus Eukaryota Chordata Mammalia Laurasiatheria Bovidae Bos Bos taurus +Anolis carolinensis Eukaryota Chordata NA Lepidosauria Dactyloidae Anolis Anolis carolinensis +Pelodiscus sinensis Eukaryota Chordata NA Testudines Trionychidae Pelodiscus Pelodiscus sinensis +Taeniopygia guttata Eukaryota Chordata Aves Neognathae Passeroidea Taeniopygia Taeniopygia guttata +Ficedula albicollis Eukaryota Chordata Aves Neognathae Muscicapidae Ficedula Ficedula albicollis +Anas platyrhynchos Eukaryota Chordata Aves Neognathae Anatidae Anas Anas platyrhynchos +Meleagris gallopavo Eukaryota Chordata Aves Neognathae Phasianidae Meleagris Meleagris gallopavo +Gallus gallus Eukaryota Chordata Aves Neognathae Phasianidae Gallus Gallus gallus +Lepisosteus oculatus Eukaryota Chordata Actinopterygii Semionotiformes Lepisosteidae Lepisosteus Lepisosteus oculatus +Danio rerio Eukaryota Chordata Actinopterygii Cypriniphysae Cyprinoidea Danio Danio rerio +Astyanax mexicanus Eukaryota Chordata Actinopterygii Characiphysae Characidae Astyanax Astyanax mexicanus +Gadus morhua Eukaryota Chordata Actinopterygii Gadiformes Gadidae Gadus Gadus morhua +Oreochromis niloticus Eukaryota Chordata Actinopterygii Cichlomorphae Cichlidae Oreochromis Oreochromis niloticus +Poecilia formosa Eukaryota Chordata Actinopterygii Atherinomorphae Poeciliidae Poecilia Poecilia formosa +Xiphophorus maculatus Eukaryota Chordata Actinopterygii Atherinomorphae Poeciliidae Xiphophorus Xiphophorus maculatus +Gasterosteus aculeatus Eukaryota Chordata Actinopterygii Perciformes Gasterosteidae Gasterosteus Gasterosteus aculeatus +Tetraodon nigroviridis Eukaryota Chordata Actinopterygii Tetraodontiformes Tetradontoidea Tetraodon Tetraodon nigroviridis +Takifugu rubripes Eukaryota Chordata Actinopterygii Tetraodontiformes Tetradontoidea Takifugu Takifugu rubripes |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/lineage-compress.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage-compress.txt Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,62 @@ +Latimeria chalumnae Eukaryota Chordata NA Coelacanthiformes Coelacanthidae Latimeria Latimeria chalumnae +Xenopus tropicalis Eukaryota Chordata Amphibia Batrachia Pipoidea Xenopus Xenopus tropicalis +Ornithorhynchus anatinus Eukaryota Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus Ornithorhynchus anatinus +Macropus eugenii Eukaryota Chordata Mammalia Diprotodontia Macropodidae Notamacropus Notamacropus eugenii +Sarcophilus harrisii Eukaryota Chordata Mammalia Dasyuromorphia Dasyuridae Sarcophilus Sarcophilus harrisii +Monodelphis domestica Eukaryota Chordata Mammalia Didelphimorphia Didelphidae Monodelphis Monodelphis domestica +Echinops telfairi Eukaryota Chordata Mammalia Afrotheria Tenrecidae Echinops Echinops telfairi +Procavia capensis Eukaryota Chordata Mammalia Afrotheria Procaviidae Procavia Procavia capensis +Loxodonta africana Eukaryota Chordata Mammalia Afrotheria Elephantidae Loxodonta Loxodonta africana +Dasypus novemcinctus Eukaryota Chordata Mammalia Xenarthra Dasypodidae Dasypus Dasypus novemcinctus +Choloepus hoffmanni Eukaryota Chordata Mammalia Xenarthra Megalonychidae Choloepus Choloepus hoffmanni +Ochotona princeps Eukaryota Chordata Mammalia Euarchontoglires Ochotonidae Ochotona Ochotona princeps +Oryctolagus cuniculus Eukaryota Chordata Mammalia Euarchontoglires Leporidae Oryctolagus Oryctolagus cuniculus +Cavia porcellus Eukaryota Chordata Mammalia Euarchontoglires Caviidae Cavia Cavia porcellus +Ictidomys tridecemlineatus Eukaryota Chordata Mammalia Euarchontoglires Sciuridae Ictidomys Ictidomys tridecemlineatus +Dipodomys ordii Eukaryota Chordata Mammalia Euarchontoglires Heteromyidae Dipodomys Dipodomys ordii +Rattus norvegicus Eukaryota Chordata Mammalia Euarchontoglires Muridae Rattus Rattus norvegicus +Mus musculus Eukaryota Chordata Mammalia Euarchontoglires Muridae Mus Mus musculus +Tupaia belangeri Eukaryota Chordata Mammalia Euarchontoglires Tupaiidae Tupaia Tupaia belangeri +Otolemur garnettii Eukaryota Chordata Mammalia Euarchontoglires Galagidae Otolemur Otolemur garnettii +Microcebus murinus Eukaryota Chordata Mammalia Euarchontoglires Cheirogaleidae Microcebus Microcebus murinus +Tarsius syrichta Eukaryota Chordata Mammalia Euarchontoglires Tarsiidae Carlito Carlito syrichta +Callithrix jacchus Eukaryota Chordata Mammalia Euarchontoglires Cebidae Callithrix Callithrix jacchus +Chlorocebus sabaeus Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Chlorocebus Chlorocebus sabaeus +Papio anubis Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Papio Papio anubis +Macaca mulatta Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Macaca Macaca mulatta +Nomascus leucogenys Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Nomascus Nomascus leucogenys +Pongo abelii Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pongo Pongo abelii +Gorilla gorilla gorilla Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Gorilla Gorilla gorilla +Pan troglodytes Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pan Pan troglodytes +Homo sapiens Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Homo Homo sapiens +Sorex araneus Eukaryota Chordata Mammalia Laurasiatheria Soricidae Sorex Sorex araneus +Erinaceus europaeus Eukaryota Chordata Mammalia Laurasiatheria Erinaceidae Erinaceus Erinaceus europaeus +Pteropus vampyrus Eukaryota Chordata Mammalia Laurasiatheria Pteropodidae Pteropus Pteropus vampyrus +Myotis lucifugus Eukaryota Chordata Mammalia Laurasiatheria Vespertilionidae Myotis Myotis lucifugus +Felis catus Eukaryota Chordata Mammalia Laurasiatheria Felidae Felis Felis catus +Canis lupus familiaris Eukaryota Chordata Mammalia Laurasiatheria Canidae Canis Canis lupus +Mustela putorius furo Eukaryota Chordata Mammalia Laurasiatheria Mustelidae Mustela Mustela putorius +Ailuropoda melanoleuca Eukaryota Chordata Mammalia Laurasiatheria Ursidae Ailuropoda Ailuropoda melanoleuca +Equus caballus Eukaryota Chordata Mammalia Laurasiatheria Equidae Equus Equus caballus +Vicugna pacos Eukaryota Chordata Mammalia Laurasiatheria Camelidae Vicugna Vicugna pacos +Sus scrofa Eukaryota Chordata Mammalia Laurasiatheria Suidae Sus Sus scrofa +Tursiops truncatus Eukaryota Chordata Mammalia Laurasiatheria Delphinidae Tursiops Tursiops truncatus +Ovis aries Eukaryota Chordata Mammalia Laurasiatheria Bovidae Ovis Ovis aries +Bos taurus Eukaryota Chordata Mammalia Laurasiatheria Bovidae Bos Bos taurus +Anolis carolinensis Eukaryota Chordata NA Lepidosauria Dactyloidae Anolis Anolis carolinensis +Pelodiscus sinensis Eukaryota Chordata NA Testudines Trionychidae Pelodiscus Pelodiscus sinensis +Taeniopygia guttata Eukaryota Chordata Aves Neognathae Passeroidea Taeniopygia Taeniopygia guttata +Ficedula albicollis Eukaryota Chordata Aves Neognathae Muscicapidae Ficedula Ficedula albicollis +Anas platyrhynchos Eukaryota Chordata Aves Neognathae Anatidae Anas Anas platyrhynchos +Meleagris gallopavo Eukaryota Chordata Aves Neognathae Phasianidae Meleagris Meleagris gallopavo +Gallus gallus Eukaryota Chordata Aves Neognathae Phasianidae Gallus Gallus gallus +Lepisosteus oculatus Eukaryota Chordata Actinopterygii Semionotiformes Lepisosteidae Lepisosteus Lepisosteus oculatus +Danio rerio Eukaryota Chordata Actinopterygii Cypriniphysae Cyprinoidea Danio Danio rerio +Astyanax mexicanus Eukaryota Chordata Actinopterygii Characiphysae Characidae Astyanax Astyanax mexicanus +Gadus morhua Eukaryota Chordata Actinopterygii Gadiformes Gadidae Gadus Gadus morhua +Oreochromis niloticus Eukaryota Chordata Actinopterygii Cichlomorphae Cichlidae Oreochromis Oreochromis niloticus +Poecilia formosa Eukaryota Chordata Actinopterygii Atherinomorphae Poeciliidae Poecilia Poecilia formosa +Xiphophorus maculatus Eukaryota Chordata Actinopterygii Atherinomorphae Poeciliidae Xiphophorus Xiphophorus maculatus +Gasterosteus aculeatus Eukaryota Chordata Actinopterygii Perciformes Gasterosteidae Gasterosteus Gasterosteus aculeatus +Tetraodon nigroviridis Eukaryota Chordata Actinopterygii Tetraodontiformes Tetradontoidea Tetraodon Tetraodon nigroviridis +Takifugu rubripes Eukaryota Chordata Actinopterygii Tetraodontiformes Tetradontoidea Takifugu Takifugu rubripes |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/lineage-full.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage-full.txt Tue Nov 07 11:45:13 2017 -0500 |
| b |
| b'@@ -0,0 +1,62 @@\n+Latimeria chalumnae\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tNA\tNA\tNA\tNA\tNA\tCoelacanthiformes\tNA\tNA\tNA\tNA\tCoelacanthidae\tNA\tNA\tNA\tLatimeria\tNA\tNA\tNA\tLatimeria chalumnae\tNA\tNA\tNA\n+Xenopus tropicalis\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tAmphibia\tNA\tNA\tNA\tBatrachia\tAnura\tNA\tNA\tNA\tPipoidea\tPipidae\tXenopodinae\tNA\tNA\tXenopus\tSilurana\tNA\tNA\tXenopus tropicalis\tNA\tNA\tNA\n+Ornithorhynchus anatinus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tNA\tMonotremata\tNA\tNA\tNA\tNA\tOrnithorhynchidae\tNA\tNA\tNA\tOrnithorhynchus\tNA\tNA\tNA\tOrnithorhynchus anatinus\tNA\tNA\tNA\n+Macropus eugenii\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tNA\tDiprotodontia\tNA\tNA\tNA\tNA\tMacropodidae\tNA\tNA\tNA\tNotamacropus\tNA\tNA\tNA\tNotamacropus eugenii\tNA\tNA\tNA\n+Sarcophilus harrisii\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tNA\tDasyuromorphia\tNA\tNA\tNA\tNA\tDasyuridae\tNA\tNA\tNA\tSarcophilus\tNA\tNA\tNA\tSarcophilus harrisii\tNA\tNA\tNA\n+Monodelphis domestica\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tNA\tDidelphimorphia\tNA\tNA\tNA\tNA\tDidelphidae\tDidelphinae\tNA\tNA\tMonodelphis\tNA\tNA\tNA\tMonodelphis domestica\tNA\tNA\tNA\n+Echinops telfairi\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tAfrotheria\tNA\tNA\tNA\tNA\tNA\tTenrecidae\tTenrecinae\tNA\tNA\tEchinops\tNA\tNA\tNA\tEchinops telfairi\tNA\tNA\tNA\n+Procavia capensis\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tAfrotheria\tHyracoidea\tNA\tNA\tNA\tNA\tProcaviidae\tNA\tNA\tNA\tProcavia\tNA\tNA\tNA\tProcavia capensis\tNA\tNA\tNA\n+Loxodonta africana\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tAfrotheria\tProboscidea\tNA\tNA\tNA\tNA\tElephantidae\tNA\tNA\tNA\tLoxodonta\tNA\tNA\tNA\tLoxodonta africana\tNA\tNA\tNA\n+Dasypus novemcinctus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tXenarthra\tCingulata\tNA\tNA\tNA\tNA\tDasypodidae\tNA\tNA\tNA\tDasypus\tNA\tNA\tNA\tDasypus novemcinctus\tNA\tNA\tNA\n+Choloepus hoffmanni\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tXenarthra\tPilosa\tFolivora\tNA\tNA\tNA\tMegalonychidae\tNA\tNA\tNA\tCholoepus\tNA\tNA\tNA\tCholoepus hoffmanni\tNA\tNA\tNA\n+Ochotona princeps\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tLagomorpha\tNA\tNA\tNA\tNA\tOchotonidae\tNA\tNA\tNA\tOchotona\tNA\tNA\tNA\tOchotona princeps\tNA\tNA\tNA\n+Oryctolagus cuniculus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tLagomorpha\tNA\tNA\tNA\tNA\tLeporidae\tNA\tNA\tNA\tOryctolagus\tNA\tNA\tNA\tOryctolagus cuniculus\tNA\tNA\tNA\n+Cavia porcellus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tRodentia\tHystricomorpha\tNA\tNA\tNA\tCaviidae\tNA\tNA\tNA\tCavia\tNA\tNA\tNA\tCavia porcellus\tNA\tNA\tNA\n+Ictidomys tridecemlineatus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tRodentia\tSciuromorpha\tNA\tNA\tNA\tSciuridae\tXerinae\tMarmotini\tNA\tIctidomys\tNA\tNA\tNA\tIctidomys tridecemlineatus\tNA\tNA\tNA\n+Dipodomys ordii\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tRodentia\tCastorimorpha\tNA\tNA\tNA\tHeteromyidae\tDipodomyinae\tNA\tNA\tDipodomys\tNA\tNA\tNA\tDipodomys ordii\tNA\tNA\tNA\n+Rattus norvegicus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tRodentia\tMyomorpha\tNA\tNA\tNA\tMuridae\tMurinae\tNA\tNA\tRattus\tNA\tNA\tNA\tRattus norvegicus\tNA\tNA\tNA\n+Mus musculus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tRodentia\tMyomorpha\tNA\tNA\tNA\tMuridae\tMurinae\tNA\tNA\tMus\tMus\tNA\tNA\tMus musculus\tNA\tNA\tNA\n+Tupaia belangeri\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tScandentia\tNA\tNA\tNA\tNA\tTupaiidae\tNA\tNA\tNA\tTupaia\tNA\tNA\tNA\tTupaia belangeri\tNA\tNA\tNA\n+Otolemur garnettii\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tPrimates\tStrepsirrhini\tLorisiformes\tNA\tNA\tGalagidae\tNA\tNA\tNA\tOtolemur\tNA\tNA\tNA\tOtolemur garnettii\tNA\tNA\tNA\n+Microcebus murinus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tEuarchontoglires\tPrimates\tStrepsirrhini\tLemuriformes\tNA\tNA\tCh'..b'is aries\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tLaurasiatheria\tNA\tRuminantia\tPecora\tNA\tNA\tBovidae\tCaprinae\tNA\tNA\tOvis\tNA\tNA\tNA\tOvis aries\tNA\tNA\tNA\n+Bos taurus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tMammalia\tNA\tNA\tNA\tLaurasiatheria\tNA\tRuminantia\tPecora\tNA\tNA\tBovidae\tBovinae\tNA\tNA\tBos\tNA\tNA\tNA\tBos taurus\tNA\tNA\tNA\n+Anolis carolinensis\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tNA\tNA\tNA\tNA\tLepidosauria\tSquamata\tIguania\tNA\tNA\tNA\tDactyloidae\tNA\tNA\tNA\tAnolis\tNA\tNA\tNA\tAnolis carolinensis\tNA\tNA\tNA\n+Pelodiscus sinensis\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tNA\tNA\tNA\tNA\tNA\tTestudines\tCryptodira\tNA\tNA\tNA\tTrionychidae\tNA\tNA\tNA\tPelodiscus\tNA\tNA\tNA\tPelodiscus sinensis\tNA\tNA\tNA\n+Taeniopygia guttata\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tAves\tNA\tNA\tNA\tNeognathae\tPasseriformes\tNA\tNA\tNA\tPasseroidea\tEstrildidae\tEstrildinae\tNA\tNA\tTaeniopygia\tNA\tNA\tNA\tTaeniopygia guttata\tNA\tNA\tNA\n+Ficedula albicollis\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tAves\tNA\tNA\tNA\tNeognathae\tPasseriformes\tNA\tNA\tNA\tNA\tMuscicapidae\tNA\tNA\tNA\tFicedula\tNA\tNA\tNA\tFicedula albicollis\tNA\tNA\tNA\n+Anas platyrhynchos\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tAves\tNA\tNA\tNA\tNeognathae\tAnseriformes\tNA\tNA\tNA\tNA\tAnatidae\tNA\tNA\tNA\tAnas\tNA\tNA\tNA\tAnas platyrhynchos\tNA\tNA\tNA\n+Meleagris gallopavo\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tAves\tNA\tNA\tNA\tNeognathae\tGalliformes\tNA\tNA\tNA\tNA\tPhasianidae\tMeleagridinae\tNA\tNA\tMeleagris\tNA\tNA\tNA\tMeleagris gallopavo\tNA\tNA\tNA\n+Gallus gallus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tNA\tAves\tNA\tNA\tNA\tNeognathae\tGalliformes\tNA\tNA\tNA\tNA\tPhasianidae\tPhasianinae\tNA\tNA\tGallus\tNA\tNA\tNA\tGallus gallus\tNA\tNA\tNA\n+Lepisosteus oculatus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tHolostei\tNA\tNA\tSemionotiformes\tNA\tNA\tNA\tNA\tLepisosteidae\tNA\tNA\tNA\tLepisosteus\tNA\tNA\tNA\tLepisosteus oculatus\tNA\tNA\tNA\n+Danio rerio\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tCypriniphysae\tCypriniformes\tNA\tNA\tNA\tCyprinoidea\tCyprinidae\tNA\tNA\tNA\tDanio\tNA\tNA\tNA\tDanio rerio\tNA\tNA\tNA\n+Astyanax mexicanus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tCharaciphysae\tCharaciformes\tCharacoidei\tNA\tNA\tNA\tCharacidae\tNA\tNA\tNA\tAstyanax\tNA\tNA\tNA\tAstyanax mexicanus\tNA\tNA\tNA\n+Gadus morhua\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tNA\tGadiformes\tGadoidei\tNA\tNA\tNA\tGadidae\tNA\tNA\tNA\tGadus\tNA\tNA\tNA\tGadus morhua\tNA\tNA\tNA\n+Oreochromis niloticus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tCichlomorphae\tCichliformes\tNA\tNA\tNA\tNA\tCichlidae\tPseudocrenilabrinae\tOreochromini\tNA\tOreochromis\tNA\tNA\tNA\tOreochromis niloticus\tNA\tNA\tNA\n+Poecilia formosa\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tAtherinomorphae\tCyprinodontiformes\tCyprinodontoidei\tNA\tNA\tNA\tPoeciliidae\tPoeciliinae\tNA\tNA\tPoecilia\tNA\tNA\tNA\tPoecilia formosa\tNA\tNA\tNA\n+Xiphophorus maculatus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tAtherinomorphae\tCyprinodontiformes\tCyprinodontoidei\tNA\tNA\tNA\tPoeciliidae\tPoeciliinae\tNA\tNA\tXiphophorus\tNA\tNA\tNA\tXiphophorus maculatus\tNA\tNA\tNA\n+Gasterosteus aculeatus\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tNA\tPerciformes\tCottioidei\tGasterosteales\tNA\tNA\tGasterosteidae\tNA\tNA\tNA\tGasterosteus\tNA\tNA\tNA\tGasterosteus aculeatus\tNA\tNA\tNA\n+Tetraodon nigroviridis\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tNA\tTetraodontiformes\tTetraodontoidei\tNA\tNA\tTetradontoidea\tTetraodontidae\tNA\tNA\tNA\tTetraodon\tNA\tNA\tNA\tTetraodon nigroviridis\tNA\tNA\tNA\n+Takifugu rubripes\tEukaryota\tMetazoa\tNA\tNA\tChordata\tCraniata\tActinopterygii\tActinopteri\tNeopterygii\tTeleostei\tNA\tNA\tTetraodontiformes\tTetraodontoidei\tNA\tNA\tTetradontoidea\tTetraodontidae\tNA\tNA\tNA\tTakifugu\tNA\tNA\tNA\tTakifugu rubripes\tNA\tNA\tNA\n' |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/lineage.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage.txt Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,62 @@ +Latimeria chalumnae Metazoa Chordata NA Coelacanthiformes Coelacanthidae Latimeria Latimeria chalumnae +Xenopus tropicalis Metazoa Chordata Amphibia Anura Pipidae Xenopus Xenopus tropicalis +Ornithorhynchus anatinus Metazoa Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus Ornithorhynchus anatinus +Macropus eugenii Metazoa Chordata Mammalia Diprotodontia Macropodidae Notamacropus Notamacropus eugenii +Sarcophilus harrisii Metazoa Chordata Mammalia Dasyuromorphia Dasyuridae Sarcophilus Sarcophilus harrisii +Monodelphis domestica Metazoa Chordata Mammalia Didelphimorphia Didelphidae Monodelphis Monodelphis domestica +Echinops telfairi Metazoa Chordata Mammalia NA Tenrecidae Echinops Echinops telfairi +Procavia capensis Metazoa Chordata Mammalia Hyracoidea Procaviidae Procavia Procavia capensis +Loxodonta africana Metazoa Chordata Mammalia Proboscidea Elephantidae Loxodonta Loxodonta africana +Dasypus novemcinctus Metazoa Chordata Mammalia Cingulata Dasypodidae Dasypus Dasypus novemcinctus +Choloepus hoffmanni Metazoa Chordata Mammalia Pilosa Megalonychidae Choloepus Choloepus hoffmanni +Ochotona princeps Metazoa Chordata Mammalia Lagomorpha Ochotonidae Ochotona Ochotona princeps +Oryctolagus cuniculus Metazoa Chordata Mammalia Lagomorpha Leporidae Oryctolagus Oryctolagus cuniculus +Cavia porcellus Metazoa Chordata Mammalia Rodentia Caviidae Cavia Cavia porcellus +Ictidomys tridecemlineatus Metazoa Chordata Mammalia Rodentia Sciuridae Ictidomys Ictidomys tridecemlineatus +Dipodomys ordii Metazoa Chordata Mammalia Rodentia Heteromyidae Dipodomys Dipodomys ordii +Rattus norvegicus Metazoa Chordata Mammalia Rodentia Muridae Rattus Rattus norvegicus +Mus musculus Metazoa Chordata Mammalia Rodentia Muridae Mus Mus musculus +Tupaia belangeri Metazoa Chordata Mammalia Scandentia Tupaiidae Tupaia Tupaia belangeri +Otolemur garnettii Metazoa Chordata Mammalia Primates Galagidae Otolemur Otolemur garnettii +Microcebus murinus Metazoa Chordata Mammalia Primates Cheirogaleidae Microcebus Microcebus murinus +Tarsius syrichta Metazoa Chordata Mammalia Primates Tarsiidae Carlito Carlito syrichta +Callithrix jacchus Metazoa Chordata Mammalia Primates Cebidae Callithrix Callithrix jacchus +Chlorocebus sabaeus Metazoa Chordata Mammalia Primates Cercopithecidae Chlorocebus Chlorocebus sabaeus +Papio anubis Metazoa Chordata Mammalia Primates Cercopithecidae Papio Papio anubis +Macaca mulatta Metazoa Chordata Mammalia Primates Cercopithecidae Macaca Macaca mulatta +Nomascus leucogenys Metazoa Chordata Mammalia Primates Hylobatidae Nomascus Nomascus leucogenys +Pongo abelii Metazoa Chordata Mammalia Primates Hominidae Pongo Pongo abelii +Gorilla gorilla gorilla Metazoa Chordata Mammalia Primates Hominidae Gorilla Gorilla gorilla +Pan troglodytes Metazoa Chordata Mammalia Primates Hominidae Pan Pan troglodytes +Homo sapiens Metazoa Chordata Mammalia Primates Hominidae Homo Homo sapiens +Sorex araneus Metazoa Chordata Mammalia Insectivora Soricidae Sorex Sorex araneus +Erinaceus europaeus Metazoa Chordata Mammalia Insectivora Erinaceidae Erinaceus Erinaceus europaeus +Pteropus vampyrus Metazoa Chordata Mammalia Chiroptera Pteropodidae Pteropus Pteropus vampyrus +Myotis lucifugus Metazoa Chordata Mammalia Chiroptera Vespertilionidae Myotis Myotis lucifugus +Felis catus Metazoa Chordata Mammalia Carnivora Felidae Felis Felis catus +Canis lupus familiaris Metazoa Chordata Mammalia Carnivora Canidae Canis Canis lupus +Mustela putorius furo Metazoa Chordata Mammalia Carnivora Mustelidae Mustela Mustela putorius +Ailuropoda melanoleuca Metazoa Chordata Mammalia Carnivora Ursidae Ailuropoda Ailuropoda melanoleuca +Equus caballus Metazoa Chordata Mammalia Perissodactyla Equidae Equus Equus caballus +Vicugna pacos Metazoa Chordata Mammalia NA Camelidae Vicugna Vicugna pacos +Sus scrofa Metazoa Chordata Mammalia NA Suidae Sus Sus scrofa +Tursiops truncatus Metazoa Chordata Mammalia Cetacea Delphinidae Tursiops Tursiops truncatus +Ovis aries Metazoa Chordata Mammalia NA Bovidae Ovis Ovis aries +Bos taurus Metazoa Chordata Mammalia NA Bovidae Bos Bos taurus +Anolis carolinensis Metazoa Chordata NA Squamata Dactyloidae Anolis Anolis carolinensis +Pelodiscus sinensis Metazoa Chordata NA Testudines Trionychidae Pelodiscus Pelodiscus sinensis +Taeniopygia guttata Metazoa Chordata Aves Passeriformes Estrildidae Taeniopygia Taeniopygia guttata +Ficedula albicollis Metazoa Chordata Aves Passeriformes Muscicapidae Ficedula Ficedula albicollis +Anas platyrhynchos Metazoa Chordata Aves Anseriformes Anatidae Anas Anas platyrhynchos +Meleagris gallopavo Metazoa Chordata Aves Galliformes Phasianidae Meleagris Meleagris gallopavo +Gallus gallus Metazoa Chordata Aves Galliformes Phasianidae Gallus Gallus gallus +Lepisosteus oculatus Metazoa Chordata Actinopteri Semionotiformes Lepisosteidae Lepisosteus Lepisosteus oculatus +Danio rerio Metazoa Chordata Actinopteri Cypriniformes Cyprinidae Danio Danio rerio +Astyanax mexicanus Metazoa Chordata Actinopteri Characiformes Characidae Astyanax Astyanax mexicanus +Gadus morhua Metazoa Chordata Actinopteri Gadiformes Gadidae Gadus Gadus morhua +Oreochromis niloticus Metazoa Chordata Actinopteri Cichliformes Cichlidae Oreochromis Oreochromis niloticus +Poecilia formosa Metazoa Chordata Actinopteri Cyprinodontiformes Poeciliidae Poecilia Poecilia formosa +Xiphophorus maculatus Metazoa Chordata Actinopteri Cyprinodontiformes Poeciliidae Xiphophorus Xiphophorus maculatus +Gasterosteus aculeatus Metazoa Chordata Actinopteri Perciformes Gasterosteidae Gasterosteus Gasterosteus aculeatus +Tetraodon nigroviridis Metazoa Chordata Actinopteri Tetraodontiformes Tetraodontidae Tetraodon Tetraodon nigroviridis +Takifugu rubripes Metazoa Chordata Actinopteri Tetraodontiformes Tetraodontidae Takifugu Takifugu rubripes |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/out.nhx --- a/test-data/out.nhx Fri Mar 17 16:23:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -((((((((((((((((Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)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,(((Ailuropodamelanoleuca*,Canislupusfamiliaris*,Mustelaputoriusfuro*)379584,Feliscatus*)33554,(Erinaceuseuropaeus*,Sorexaraneus*)9362,(Myotislucifugus*,Pteropusvampyrus*)9397,((Ovisaries*,Bostaurus*)9895,Vicugnapacos*,Susscrofa*,Tursiopstruncatus*)91561,Equuscaballus*)314145)1437010,(Dasypusnovemcinctus*,Choloepushoffmanni*)9348,(Echinopstelfairi*,Loxodontaafricana*,Procaviacapensis*)311790)9347,(Sarcophilusharrisii*,Macropuseugenii*,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,Oreochromisniloticus*)1489908)1489872,Gadusmorhua*)123368)186625,Lepisosteusoculatus*)41665)root; \ No newline at end of file |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/taxdump.sqlite |
| b |
| Binary file test-data/taxdump.sqlite has changed |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/taxdump.tar.gz |
| b |
| Binary file test-data/taxdump.tar.gz has changed |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +((A,B),C); + |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1_ladder.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1_ladder.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(C:2,(A:1,B:1)1:1); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1_ogA.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1_ogA.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(A:2.5,(B:1.25,C:1.25)1:1.25); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1_pruneAC.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1_pruneAC.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(C:1,A:1); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1_pruneACpreserve.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1_pruneACpreserve.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(C:2,A:2); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1_unroot.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1_unroot.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(C:1,A:1,B:1); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree1_unroot_resolve.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree1_unroot_resolve.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((A:0.5,B:0.5)0:0.5,C:1); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree2.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +((C,A),B); + |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree2_sort.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree2_sort.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((A:1,C:1)1:1,B:2); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree3.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree3.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(C:1,(A:1):1,B:1); |
| b |
| diff -r a4ba317fc713 -r 03c10736e497 test-data/tree3_stand.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree3_stand.nhx Tue Nov 07 11:45:13 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((B:1,A:1)0:1,C:2); |