| Next changeset 1:a3a5a1e44d18 (2015-11-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2 |
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added:
abundance-dist-single.xml filter-below-abund.py macros.xml test-data/normalize-by-median.c2.report.txt test-data/normalize-by-median.paired.report.txt test-data/normalize-by-median.report.txt test-data/random-20-a.fa test-data/random-20-a.fa.part test-data/random-20-a.part.extract.fa test-data/test-abund-read-2.fa test-data/test-abund-read-2.fa.below test-data/test-abund-read-2.large.oxlicg test-data/test-abund-read-2.large.oxlicg.info test-data/test-abund-read-2.oxlicg test-data/test-abund-read-2.oxlicg.info test-data/test-abund-read-paired.fa tool_dependencies.xml |
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| diff -r 000000000000 -r 47cea67b74ea abundance-dist-single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundance-dist-single.xml Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,91 @@ +<tool id="khmer_abundance_distribution_single" name="Abundance Distribution (all-in-one)" version="@WRAPPER_VERSION@.0"> + <description> + Calculate abundance distribution of the k-mers in a given sequence file + </description> + <macros> + <token name="@BINARY@">abundance-dist-single.py</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version" /> + <command><![CDATA[ +set -xu && +mkdir output && cd output && +@BINARY@ +@TABLEPARAMS@ +${zero} +${bigcount} +#if $save_countgraph + --savegraph=${optional_output_countgraph} +#end if +--squash +@THREADS@ +${input_sequence_filename} +${output_histogram_filename} + +]]> + </command> + <inputs> + <expand macro="input_sequence_filename" /> + <param name="save_countgraph" type="boolean" label="Save the k-mer countgraph to a file" + help="(--savegraph)" /> + <expand macro="input_zero" /> + <expand macro="input_bigcount" /> + <expand macro="tableinputs" /> + </inputs> + <outputs> + <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} k-mer countgraph"> + <filter>save_countgraph == True</filter> + </data> + <expand macro="abundance-histogram-output" /> + </outputs> + <tests> + <test> + <param name="input_sequence_filename" value="test-abund-read-2.fa" /> + <param name="type" value="specific" /> + <param name="tablesize_specific" value="1e7" /> + <param name="n_tables" value="2" /> + <param name="ksize" value="17" /> + <param name="no_zero" value="false" /> + <output name="output_histogram_filename" ftpye="txt"> + <assert_contents> + <has_text text="1,96,96,0.98" /> + <has_text text="1001,2,98,1.0" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_sequence_filename" value="test-abund-read-2.fa" /> + <param name="type" value="specific" /> + <param name="tablesize_specific" value="1e7" /> + <param name="n_tables" value="2" /> + <param name="ksize" value="17" /> + <param name="no_zero" value="false" /> + <param name="bigcount" value="false" /> + <output name="output_histogram_filename" ftype="txt"> + <assert_contents> + <has_text text="1,96,96,0.98" /> + <has_text text="255,2,98,1.0" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +Calculate the abundance distribution of k-mers from a single sequence file. + +Note that with `-b` this script is constant memory; in exchange, +k-mer counts will stop at 255. The memory usage of this script with +`-b` will be about 1.15x the product of the `-x` and +`-N` numbers. + + +@HELP_FOOTER@ +]]> + </help> + <citations> + <expand macro="software-citation" /> + <expand macro="counting-citation" /> + </citations> +</tool> |
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| diff -r 000000000000 -r 47cea67b74ea filter-below-abund.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter-below-abund.py Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,87 @@ +#! /usr/bin/env python +# This file is part of khmer, https://github.com/dib-lab/khmer/, and is +# Copyright (C) 2011-2015, Michigan State University. +# Copyright (C) 2015, The Regents of the University of California. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: +# +# * Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# * Redistributions in binary form must reproduce the above +# copyright notice, this list of conditions and the following +# disclaimer in the documentation and/or other materials provided +# with the distribution. +# +# * Neither the name of the Michigan State University nor the names +# of its contributors may be used to endorse or promote products +# derived from this software without specific prior written +# permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# Contact: khmer-project@idyll.org +from __future__ import print_function +import sys +import os +import khmer +from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter + +WORKER_THREADS = 8 +GROUPSIZE = 100 + +CUTOFF = 50 + +### + + +def main(): + counting_ht = sys.argv[1] + infiles = sys.argv[2:] + + print('file with ht: %s' % counting_ht) + print('-- settings:') + print('N THREADS', WORKER_THREADS) + print('--') + + print('making hashtable') + ht = khmer.load_countgraph(counting_ht) + K = ht.ksize() + + for infile in infiles: + print('filtering', infile) + outfile = os.path.basename(infile) + '.below' + + outfp = open(outfile, 'w') + + def process_fn(record, ht=ht): + name = record['name'] + seq = record['sequence'] + if 'N' in seq: + return None, None + + trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF) + + if trim_at >= K: + return name, trim_seq + + return None, None + + tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE) + + tsp.start(verbose_fasta_iter(infile), outfp) + +if __name__ == '__main__': + main() |
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| diff -r 000000000000 -r 47cea67b74ea macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,148 @@ +<macros> + <token name="@WRAPPER_VERSION@">2.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + </xml> + <token name="@TABLEPARAMS@"> +<![CDATA[ +#if $parameters.type == "simple" + --ksize=20 + --n_tables=4 + --max-tablesize=$parameters.tablesize +#else + --ksize=$parameters.ksize + --n_tables=$parameters.n_tables + --max-tablesize="$parameters.tablesize_specific" +#end if +]]> + </token> + <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token> + <xml name="tableinputs"> + <conditional name="parameters"> + <param name="type" type="select" label="Advanced Parameters" + help="ksize, n_tables, a specific tablesize" > + <option value="simple" selected="true">Hide</option> + <option value="specific">Show</option> + </param> + <when value="simple"> + <param name="tablesize" type="select" label="Sample Type" display="radio"> + <option value="1e9" selected="true">Microbial Genome</option> + <option value="2e9">Animal Transcriptome</option> + <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option> + <option value="16e9">Large Animal Genome</option> + </param> + </when> + <when value="specific"> + <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" /> + <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" /> + <param name="tablesize_specific" type="text" value="1000000.0" + label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" /> + </when> + </conditional> + </xml> + <xml name="input_sequences_filenames"> + <param name="inputs" multiple="true" type="data" format="fasta,fastq" + label="Sequences in FASTA or FASTQ format" + help="Put in order of precedence such as longest reads first." /> + </xml> + <xml name="input_sequence_filename"> + <param name="input_sequence_filename" type="data" format="fasta,fastq" + label="Sequence in FASTA or FASTQ format" /> + </xml> + <xml name="input_countgraph_filename"> + <param name="input_countgraph_filename" type="data" format="oxlicg" + label="the k-mer countgraph to query" + help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." /> + </xml> + <xml name="abundance-histogram-output"> + <data name="output_histogram_filename" format="txt" + label="${tool.name} k-mer abundance histogram. The + columns are: (1) k-mer abundance, (2) k-mer count, (3) + cumulative count, (4) fraction of total distinct k-mers." /> + </xml> + <xml name="output_sequences"> + <data name="output" format_source="inputs" + label="${tool.name} processed nucleotide sequence file"> + <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/> + </data> + </xml> + <xml name="output_sequences_single"> + <data name="output" format_source="input_sequence_filename" + label="${tool.name} processed nucleotide sequence file" /> + </xml> + <xml name="input_zero"> + <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true" + help="Output zero count bins (--no-zero)" /> + </xml> + <xml name="input_bigcount"> + <param name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount" + checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" /> + </xml> + <token name="@HELP_FOOTER@"><![CDATA[ +(from the khmer project: http://khmer.readthedocs.org/en/v@WRAPPER_VERSION@/ )]]></token> + <xml name="software-citation"> + <citation type="bibtex">@article{khmer2015, + author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine + and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau, + Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton, + Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and + Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah + and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and + Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David + and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric + and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy, + Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory, + Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and + Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and + Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan, + Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and + Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather + L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and + Brown, C. Titus" + title = "The khmer software package: enabling efficient nucleotide + sequence analysis", + year = "2015", + month = "08", + publisher = "F1000", + url = "http://dx.doi.org/10.12688/f1000research.6924.1" + }</citation> + </xml> + <xml name="diginorm-citation"> + <citation type="bibtex">@unpublished{diginorm, + author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz, +Alexis B and Brom, Timothy H", + title = "A Reference-Free Algorithm for Computational Normalization of +Shotgun Sequencing Data", + year = "2012", + eprint = "arXiv:1203.4802", + url = "http://arxiv.org/abs/1203.4802", +}</citation></xml> + <xml name="graph-citation"> + <citation type="bibtex">@article{Pell2012, + doi = {10.1073/pnas.1121464109}, + url = {http://dx.doi.org/10.1073/pnas.1121464109}, + year = {2012}, + month = {jul}, + publisher = {Proceedings of the National Academy of Sciences}, + volume = {109}, + number = {33}, + pages = {13272--13277}, + author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown}, + title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs}, + journal = {Proceedings of the National Academy of Sciences} + }</citation> + </xml> + <xml name="counting-citation"> + <citation type="doi">10.1371/journal.pone.0101271</citation> + </xml> +</macros> |
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| diff -r 000000000000 -r 47cea67b74ea test-data/normalize-by-median.c2.report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalize-by-median.c2.report.txt Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,2 @@ +total,kept,f_kept +1001,2,0.001998 |
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| diff -r 000000000000 -r 47cea67b74ea test-data/normalize-by-median.paired.report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalize-by-median.paired.report.txt Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,2 @@ +total,kept,f_kept +6,2,0.3333 |
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| diff -r 000000000000 -r 47cea67b74ea test-data/normalize-by-median.report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalize-by-median.report.txt Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,2 @@ +total,kept,f_kept +1001,1,0.000999 |
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| diff -r 000000000000 -r 47cea67b74ea test-data/random-20-a.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random-20-a.fa Wed Nov 11 09:47:17 2015 -0500 |
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| @@ -0,0 +1,198 @@ +>35 +CGCAGGCTGGATTCTAGAGGCAGAGGTGAGCTATAAGATATTGCATACGTTGAGCCAGC +>16 +CGGAAGCCCAATGAGTTGTCAGAGTCACCTCCACCCCGGGCCCTGTTAGCTACGTCCGT +>46 +GGTCGTGTTGGGTTAACAAAGGATCCCTGACTCGATCCAGCTGGGTAGGGTAACTATGT +>40 +GGCTGAAGGAGCGGGCGTACGTGTTTACGGCATGATGGCCGGTGATTATGGGGGACGGG +>33 +GCAGCGGCTTTGAATGCCGAATATATAACAGCGACGGGGTTCAATAAGCTGCACATGCG +>98 +ACCAGATGCATAGCCCAACAGCTGAGACATTCCCAGCTCGCGAACCAAGACGTGAGAGC +>17 +CCCTGTTAGCTACGTCCGTCTAAGGATATTAACATAGTTGCGACTGCGTCCTGTGCTCA +>89 +GCGAGATACTAGCAAAGGTTCATCAACAGCTACACCCGACGAACCCCGAGAAATTGGGA +>30 +GTTATGGTCCAGGATGAATGCGCGTACCGGGCGCCTATCACTCCTCTTGTCATTCAGAA +>82 +ATGCACTATATTTAAGAGGTCTAGAGTGTAAAAAGTGTACCCTTCGGGGTGGAGCTGTT +>60 +GTTTTTGTCATCGTGCATAAAGCGGGACAGAGTTCAACGGTATTCGAATGCACACCCTA +>83 +CCTTCGGGGTGGAGCTGTTAATGAACTCAAGTGGCGATGGAGGCTAAAACGATACGTTG +>12 +AGCCAATTGTAACCATATGGTATCCAGTTTCCGTAGCAGCAATGCGCGACGGGCAATCG +>85 +CGTGATATGATTACTAAAGGGGCCCGCAAAAACCCATTCACTGAGGGCTCTGTCCGTAC +>2 +CCCGTGGGGCGGGCTAATTTTAAAGGCAGGTTGCTACACGTCAACTCTACCCAAGCTCC +>45 +ATACGCCACTCGACTTGGCTCGCCCTCGATCTAAAATAGCGGTCGTGTTGGGTTAACAA +>11 +GCAGCAGACCAACATCCAACACTTTTCACAAGAGGCTGACAGCCAATTGTAACCATATG +>39 +CAATTGACTTCCATGTGGGTCGGCTGTCAAGTCTAAACCGGGCTGAAGGAGCGGGCGTA +>26 +AACATCTTAACCTCTGATCCCAACATGAGGGACATGAGTTTTCAAAGTAACGATGCGCA +>75 +GTCGGTGCCCGCGTGCGGAGCAGTCTTGATCCGGCGCGCTCTTACCTATGGTCGGCACG +>81 +GGCTACTGGTTGATAAGCGTACGTAAAAGGCGAGTCTTACATGCACTATATTTAAGAGG +>97 +ATTAGTGTGACTAGCCGAGTGCCCCAGCGTTTATCCAATGACCAGATGCATAGCCCAAC +>13 +AATGCGCGACGGGCAATCGCGTCTGCGTTGATCGTCGCCCCTATTGTCGCTCCCTTAGT +>92 +ATCAGGGCAAATTTGCTCGTGACTAAATGGTAATACTACCCGGGACAGTAAACTTTTGG +>56 +AGATCTGCTTGGGTGTATCCCCATTCAGAGATACCAGATCTAAGCGACCATCAGAAACA +>61 +TATTCGAATGCACACCCTAACATACTGGAAGATTCACTCTATATACCGGGAACTACTAA +>96 +ATTAGACCGCTATCAACTCTTGCGAGGAAGGTCTGGGCCTATTAGTGTGACTAGCCGAG +>31 +CTCCTCTTGTCATTCAGAAGGAATTTGATTAATTACCTGGGCTGACTCGCGCCCCCTGC +>29 +TGGAAGCGCCCTCCGCTCAGGCGTTTTAGTAGATCCCAGTGTTATGGTCCAGGATGAAT +>54 +TGGATGAGGTCCTTAAGGCCTAATTGACCAATCGCCCCAAGATTGGTGGTGAATGACTC +>0 +TAGTGATCAGCGGCTAGTGTCGCCCCTCTTAGCACCTTGCGATCATCGAATCGGGCTGT +>90 +GAACCCCGAGAAATTGGGAAGCCTGGAGGCAGTACAGTCATCCAGTCTGCTGCTCAAAG +>34 +TCAATAAGCTGCACATGCGTGGTTGTGGCACGATCAGTTCCGCAGGCTGGATTCTAGAG +>43 +AGGACTCGACGTCCGCCCCATGCTTGAGAGAAGGTTTCGGCCAACCATGGTAGGTTAGG +>8 +ACACACAAGGCCAGACACCAACTTGGCCGTGGAATTTATCAACACTTCTGAGACGAAGG +>37 +TGTGCGCTGTGAGATACAACTATAGGCACCGGGTTGCTGGCTAATAACCATTTAGAGTC +>51 +ACACAATGGACGCGTTAAGGAGAACCGGTCGCAACCAGGTTGAAAATGCCTGATATACG +>32 +GCTGACTCGCGCCCCCTGCAGGCTGCTATGATTGAGTGCGGCAGCGGCTTTGAATGCCG +>78 +TCTGGGGCGAGATCCCCTCTGCTCACTTTCTTGTAGTAAATACACCGAAGGGGCGAACC +>18 +CGACTGCGTCCTGTGCTCAGTTCGTGACGCCGAACTCAAGGACGCGGTACGAAGAACTG +>36 +TTGCATACGTTGAGCCAGCGCCGCCCGTATACACAGGGTCTGTGCGCTGTGAGATACAA +>53 +ATATAAGTTTTTTAGATGTAAAAAATTTTTTATGGCGGCCTGGATGAGGTCCTTAAGGC +>24 +AAGAAACAGGCTAGGTCTTCCATGCAATGGTTCTCACAGTGTAGTCGCGCATCAACTCC +>7 +AAACGTCTAAGTAATCATGCGACCGGCGCCTCGATTGGACACACACAAGGCCAGACACC +>9 +AACACTTCTGAGACGAAGGTCATTTACGATTGGGACACTTTCTCGAACTCCGGTTAATT +>47 +CTGGGTAGGGTAACTATGTAGCCATCGCTCAGTGGATTCTTCCGGGATAGGGTGTGCGA +>62 +ATATACCGGGAACTACTAAAATTTTGGGCTACTCTATGCTTACAGCCCAACATGCGCAA +>79 +TACACCGAAGGGGCGAACCCTGTCTACATTCGCAAATGCATCCTACCTGAGAGGCTTCG +>48 +TCCGGGATAGGGTGTGCGAATGTGCCGGGCATTCAGCTCCTTAGAGACGAGTTACGAGC +>66 +GGCGCGACCAATATTCATTTGATGAGAATTGAAATCGACTGAATCACGGGATTTATACA +>25 +GTAGTCGCGCATCAACTCCGCCAGTTTTATCGAAGCGCCCAACATCTTAACCTCTGATC +>5 +TCATTACGGGGTGTCCATCTAGAGAAAGTGGGTTTCCCTTATAGAAATGAGGAGGATTC +>72 +ATAAAAAACGACTTCTAAAGCGACACTGGTTTTATCCTTCCCTGTTTTCCTCGCCCCAT +>76 +CTTACCTATGGTCGGCACGATTCCATTGGCGGATATAGGATTGATTACGTGTGTTTACT +>69 +GCAGCGAGGTATTTAAACTGTTCAATCGGCGCAACCGAAAATCTGCTACCGTGGTTGCT +>87 +CAGTATACGCCCGTTGAGAAACAGGTGGTGGCGCAGTGTCGATTACTTCGTAATAATTT +>27 +TTCAAAGTAACGATGCGCAGATTGAATAATGCCATATCTGCGCGAGAGGTTTCAGGTAC +>77 +TTGATTACGTGTGTTTACTATACCGGTAGAAGCCTTCAGTTCTGGGGCGAGATCCCCTC +>95 +TACGTGTGGCATCGTTGCACCCTAATTCGCATTATTAAGTATTAGACCGCTATCAACTC +>63 +TACAGCCCAACATGCGCAACAACTATAAGCTGCTGCTGACAGATCCGTTTGTTCCGGAC +>38 +CTAATAACCATTTAGAGTCGCCCGCGGTGATGAGTAATCGCAATTGACTTCCATGTGGG +>20 +GTGCCTACCGTACCTGTCGAGCCAGTGCGATCAGTAAAACTACCGATTCGTGGCCTCCC +>88 +GATTACTTCGTAATAATTTGAGGGTGCTGCCGCGTGTTCCGCGAGATACTAGCAAAGGT +>49 +TTAGAGACGAGTTACGAGCCACTCTTGGATCGTCATGCATACCTCGCAGATCGGCAGAG +>91 +TCCAGTCTGCTGCTCAAAGTCCATCTACATGTAAAGAACCATCAGGGCAAATTTGCTCG +>86 +CTGAGGGCTCTGTCCGTACGTGTACTATAGATCCTTGCTCCAGTATACGCCCGTTGAGA +>42 +CATATTTCAGGCGTGCGCCAACTTACGATTCTTGAATCCAAGGACTCGACGTCCGCCCC +>70 +ATCTGCTACCGTGGTTGCTTCGACCATGGTAAACTGAGTAAGCCCTTATGAGTTGCGGG +>19 +GACGCGGTACGAAGAACTGCTCCAGCAACAGCATTCCTTGGTGCCTACCGTACCTGTCG +>84 +AGGCTAAAACGATACGTTGTATACTAAGAACTGTCTACATCGTGATATGATTACTAAAG +>52 +TGAAAATGCCTGATATACGAAGATTAAGCGGCTTTGGATCATATAAGTTTTTTAGATGT +>71 +AGCCCTTATGAGTTGCGGGTCGTGCTGTTAGACTGAACACATAAAAAACGACTTCTAAA +>93 +CGGGACAGTAAACTTTTGGTGATGCCAGCACGACCAGCGCAGGGTCAAGAAAACTATTA +>58 +TCGTGGTACACCCGGAGTCTCGAAAGGAGCTTGCAAAGCTTTTCAGCATGGGTCGCATT +>22 +TTCATTCCCCTGTAACGTTTCGAACTCAACTTGCTTGCCCGACATATGGCGGTACGCGG +>50 +ACCTCGCAGATCGGCAGAGAACGGTTTGGTCTGTTTGCGTACACAATGGACGCGTTAAG +>21 +TACCGATTCGTGGCCTCCCGTTCGTCGCAATGAACGGCTTTTCATTCCCCTGTAACGTT +>73 +CCTGTTTTCCTCGCCCCATGCAATGGTAACTAATATACCGCCCCATAGTCTTAATAACC +>68 +CTGTCCCAACGGTAACAATGGAGGCACTATACCGACGCTCGCAGCGAGGTATTTAAACT +>23 +GACATATGGCGGTACGCGGGCTCAGCGCTCCGCCAGTAAGAAGAAACAGGCTAGGTCTT +>94 +AGGGTCAAGAAAACTATTAATTTAAGCGCTGTTTAGTAACTACGTGTGGCATCGTTGCA +>10 +TCTCGAACTCCGGTTAATTTGCAATCCGGGGGTTTGCTCAGCAGCAGACCAACATCCAA +>41 +GGTGATTATGGGGGACGGGTATAGTACTAATAGTTTTGGGCATATTTCAGGCGTGCGCC +>80 +TCCTACCTGAGAGGCTTCGACTAAAGAATGCGGGTATACTGGCTACTGGTTGATAAGCG +>64 +AGATCCGTTTGTTCCGGACGGTCGTCGTACCCACCCCTTGTCGATAGGTAAAGGAGTAA +>57 +TAAGCGACCATCAGAAACACAGCATCAGCTTACCAGCCTTTCGTGGTACACCCGGAGTC +>1 +GATCATCGAATCGGGCTGTCGCCAAAGGCCGACCAAGGTTCCCGTGGGGCGGGCTAATT +>55 +GATTGGTGGTGAATGACTCACAAAATGCTCATAGAATATTAGATCTGCTTGGGTGTATC +>67 +GAATCACGGGATTTATACATCATTTATAGCTAAATTACACCTGTCCCAACGGTAACAAT +>14 +CTATTGTCGCTCCCTTAGTTGTTGGGCGTAGTCCGCACCTAGAGTCCAACCAGGCCTCG +>15 +AGAGTCCAACCAGGCCTCGACAATCCTTTGTCCTGTCCCCCGGAAGCCCAATGAGTTGT +>59 +TTTCAGCATGGGTCGCATTCCTACCTAAGGCTAGGGGCATGTTTTTGTCATCGTGCATA +>28 +CGCGAGAGGTTTCAGGTACCTATCGGGACAGACTTGTTTCTGGAAGCGCCCTCCGCTCA +>74 +CCCCATAGTCTTAATAACCGACACCGAGACGCTACATGGCGTCGGTGCCCGCGTGCGGA +>4 +TGTAACCTGTGTGGGGTCGGTCCTGGGGAAACTTTGGGTTTCATTACGGGGTGTCCATC +>65 +TCGATAGGTAAAGGAGTAAGCGTCCGACTCCCTCTTACTTGGCGCGACCAATATTCATT +>6 +ATAGAAATGAGGAGGATTCACAGACACGTCAGTCACCATCAAACGTCTAAGTAATCATG +>44 +CCAACCATGGTAGGTTAGGAAAGCCGCCAAATAAGTTCTTATACGCCACTCGACTTGGC +>3 +TCAACTCTACCCAAGCTCCTTGCATCTCGGTACCCCCCCTTGTAACCTGTGTGGGGTCG |
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| diff -r 000000000000 -r 47cea67b74ea test-data/random-20-a.fa.part --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random-20-a.fa.part Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,198 @@ +>35 2 +CGCAGGCTGGATTCTAGAGGCAGAGGTGAGCTATAAGATATTGCATACGTTGAGCCAGC +>16 2 +CGGAAGCCCAATGAGTTGTCAGAGTCACCTCCACCCCGGGCCCTGTTAGCTACGTCCGT +>46 2 +GGTCGTGTTGGGTTAACAAAGGATCCCTGACTCGATCCAGCTGGGTAGGGTAACTATGT +>40 2 +GGCTGAAGGAGCGGGCGTACGTGTTTACGGCATGATGGCCGGTGATTATGGGGGACGGG +>33 2 +GCAGCGGCTTTGAATGCCGAATATATAACAGCGACGGGGTTCAATAAGCTGCACATGCG +>98 2 +ACCAGATGCATAGCCCAACAGCTGAGACATTCCCAGCTCGCGAACCAAGACGTGAGAGC +>17 2 +CCCTGTTAGCTACGTCCGTCTAAGGATATTAACATAGTTGCGACTGCGTCCTGTGCTCA +>89 2 +GCGAGATACTAGCAAAGGTTCATCAACAGCTACACCCGACGAACCCCGAGAAATTGGGA +>30 2 +GTTATGGTCCAGGATGAATGCGCGTACCGGGCGCCTATCACTCCTCTTGTCATTCAGAA +>82 2 +ATGCACTATATTTAAGAGGTCTAGAGTGTAAAAAGTGTACCCTTCGGGGTGGAGCTGTT +>60 2 +GTTTTTGTCATCGTGCATAAAGCGGGACAGAGTTCAACGGTATTCGAATGCACACCCTA +>83 2 +CCTTCGGGGTGGAGCTGTTAATGAACTCAAGTGGCGATGGAGGCTAAAACGATACGTTG +>12 2 +AGCCAATTGTAACCATATGGTATCCAGTTTCCGTAGCAGCAATGCGCGACGGGCAATCG +>85 2 +CGTGATATGATTACTAAAGGGGCCCGCAAAAACCCATTCACTGAGGGCTCTGTCCGTAC +>2 2 +CCCGTGGGGCGGGCTAATTTTAAAGGCAGGTTGCTACACGTCAACTCTACCCAAGCTCC +>45 2 +ATACGCCACTCGACTTGGCTCGCCCTCGATCTAAAATAGCGGTCGTGTTGGGTTAACAA +>11 2 +GCAGCAGACCAACATCCAACACTTTTCACAAGAGGCTGACAGCCAATTGTAACCATATG +>39 2 +CAATTGACTTCCATGTGGGTCGGCTGTCAAGTCTAAACCGGGCTGAAGGAGCGGGCGTA +>26 2 +AACATCTTAACCTCTGATCCCAACATGAGGGACATGAGTTTTCAAAGTAACGATGCGCA +>75 2 +GTCGGTGCCCGCGTGCGGAGCAGTCTTGATCCGGCGCGCTCTTACCTATGGTCGGCACG +>81 2 +GGCTACTGGTTGATAAGCGTACGTAAAAGGCGAGTCTTACATGCACTATATTTAAGAGG +>97 2 +ATTAGTGTGACTAGCCGAGTGCCCCAGCGTTTATCCAATGACCAGATGCATAGCCCAAC +>13 2 +AATGCGCGACGGGCAATCGCGTCTGCGTTGATCGTCGCCCCTATTGTCGCTCCCTTAGT +>92 2 +ATCAGGGCAAATTTGCTCGTGACTAAATGGTAATACTACCCGGGACAGTAAACTTTTGG +>56 2 +AGATCTGCTTGGGTGTATCCCCATTCAGAGATACCAGATCTAAGCGACCATCAGAAACA +>61 2 +TATTCGAATGCACACCCTAACATACTGGAAGATTCACTCTATATACCGGGAACTACTAA +>96 2 +ATTAGACCGCTATCAACTCTTGCGAGGAAGGTCTGGGCCTATTAGTGTGACTAGCCGAG +>31 2 +CTCCTCTTGTCATTCAGAAGGAATTTGATTAATTACCTGGGCTGACTCGCGCCCCCTGC +>29 2 +TGGAAGCGCCCTCCGCTCAGGCGTTTTAGTAGATCCCAGTGTTATGGTCCAGGATGAAT +>54 2 +TGGATGAGGTCCTTAAGGCCTAATTGACCAATCGCCCCAAGATTGGTGGTGAATGACTC +>0 2 +TAGTGATCAGCGGCTAGTGTCGCCCCTCTTAGCACCTTGCGATCATCGAATCGGGCTGT +>90 2 +GAACCCCGAGAAATTGGGAAGCCTGGAGGCAGTACAGTCATCCAGTCTGCTGCTCAAAG +>34 2 +TCAATAAGCTGCACATGCGTGGTTGTGGCACGATCAGTTCCGCAGGCTGGATTCTAGAG +>43 2 +AGGACTCGACGTCCGCCCCATGCTTGAGAGAAGGTTTCGGCCAACCATGGTAGGTTAGG +>8 2 +ACACACAAGGCCAGACACCAACTTGGCCGTGGAATTTATCAACACTTCTGAGACGAAGG +>37 2 +TGTGCGCTGTGAGATACAACTATAGGCACCGGGTTGCTGGCTAATAACCATTTAGAGTC +>51 2 +ACACAATGGACGCGTTAAGGAGAACCGGTCGCAACCAGGTTGAAAATGCCTGATATACG +>32 2 +GCTGACTCGCGCCCCCTGCAGGCTGCTATGATTGAGTGCGGCAGCGGCTTTGAATGCCG +>78 2 +TCTGGGGCGAGATCCCCTCTGCTCACTTTCTTGTAGTAAATACACCGAAGGGGCGAACC +>18 2 +CGACTGCGTCCTGTGCTCAGTTCGTGACGCCGAACTCAAGGACGCGGTACGAAGAACTG +>36 2 +TTGCATACGTTGAGCCAGCGCCGCCCGTATACACAGGGTCTGTGCGCTGTGAGATACAA +>53 2 +ATATAAGTTTTTTAGATGTAAAAAATTTTTTATGGCGGCCTGGATGAGGTCCTTAAGGC +>24 2 +AAGAAACAGGCTAGGTCTTCCATGCAATGGTTCTCACAGTGTAGTCGCGCATCAACTCC +>7 2 +AAACGTCTAAGTAATCATGCGACCGGCGCCTCGATTGGACACACACAAGGCCAGACACC +>9 2 +AACACTTCTGAGACGAAGGTCATTTACGATTGGGACACTTTCTCGAACTCCGGTTAATT +>47 2 +CTGGGTAGGGTAACTATGTAGCCATCGCTCAGTGGATTCTTCCGGGATAGGGTGTGCGA +>62 2 +ATATACCGGGAACTACTAAAATTTTGGGCTACTCTATGCTTACAGCCCAACATGCGCAA +>79 2 +TACACCGAAGGGGCGAACCCTGTCTACATTCGCAAATGCATCCTACCTGAGAGGCTTCG +>48 2 +TCCGGGATAGGGTGTGCGAATGTGCCGGGCATTCAGCTCCTTAGAGACGAGTTACGAGC +>66 2 +GGCGCGACCAATATTCATTTGATGAGAATTGAAATCGACTGAATCACGGGATTTATACA +>25 2 +GTAGTCGCGCATCAACTCCGCCAGTTTTATCGAAGCGCCCAACATCTTAACCTCTGATC +>5 2 +TCATTACGGGGTGTCCATCTAGAGAAAGTGGGTTTCCCTTATAGAAATGAGGAGGATTC +>72 2 +ATAAAAAACGACTTCTAAAGCGACACTGGTTTTATCCTTCCCTGTTTTCCTCGCCCCAT +>76 2 +CTTACCTATGGTCGGCACGATTCCATTGGCGGATATAGGATTGATTACGTGTGTTTACT +>69 2 +GCAGCGAGGTATTTAAACTGTTCAATCGGCGCAACCGAAAATCTGCTACCGTGGTTGCT +>87 2 +CAGTATACGCCCGTTGAGAAACAGGTGGTGGCGCAGTGTCGATTACTTCGTAATAATTT +>27 2 +TTCAAAGTAACGATGCGCAGATTGAATAATGCCATATCTGCGCGAGAGGTTTCAGGTAC +>77 2 +TTGATTACGTGTGTTTACTATACCGGTAGAAGCCTTCAGTTCTGGGGCGAGATCCCCTC +>95 2 +TACGTGTGGCATCGTTGCACCCTAATTCGCATTATTAAGTATTAGACCGCTATCAACTC +>63 2 +TACAGCCCAACATGCGCAACAACTATAAGCTGCTGCTGACAGATCCGTTTGTTCCGGAC +>38 2 +CTAATAACCATTTAGAGTCGCCCGCGGTGATGAGTAATCGCAATTGACTTCCATGTGGG +>20 2 +GTGCCTACCGTACCTGTCGAGCCAGTGCGATCAGTAAAACTACCGATTCGTGGCCTCCC +>88 2 +GATTACTTCGTAATAATTTGAGGGTGCTGCCGCGTGTTCCGCGAGATACTAGCAAAGGT +>49 2 +TTAGAGACGAGTTACGAGCCACTCTTGGATCGTCATGCATACCTCGCAGATCGGCAGAG +>91 2 +TCCAGTCTGCTGCTCAAAGTCCATCTACATGTAAAGAACCATCAGGGCAAATTTGCTCG +>86 2 +CTGAGGGCTCTGTCCGTACGTGTACTATAGATCCTTGCTCCAGTATACGCCCGTTGAGA +>42 2 +CATATTTCAGGCGTGCGCCAACTTACGATTCTTGAATCCAAGGACTCGACGTCCGCCCC +>70 2 +ATCTGCTACCGTGGTTGCTTCGACCATGGTAAACTGAGTAAGCCCTTATGAGTTGCGGG +>19 2 +GACGCGGTACGAAGAACTGCTCCAGCAACAGCATTCCTTGGTGCCTACCGTACCTGTCG +>84 2 +AGGCTAAAACGATACGTTGTATACTAAGAACTGTCTACATCGTGATATGATTACTAAAG +>52 2 +TGAAAATGCCTGATATACGAAGATTAAGCGGCTTTGGATCATATAAGTTTTTTAGATGT +>71 2 +AGCCCTTATGAGTTGCGGGTCGTGCTGTTAGACTGAACACATAAAAAACGACTTCTAAA +>93 2 +CGGGACAGTAAACTTTTGGTGATGCCAGCACGACCAGCGCAGGGTCAAGAAAACTATTA +>58 2 +TCGTGGTACACCCGGAGTCTCGAAAGGAGCTTGCAAAGCTTTTCAGCATGGGTCGCATT +>22 2 +TTCATTCCCCTGTAACGTTTCGAACTCAACTTGCTTGCCCGACATATGGCGGTACGCGG +>50 2 +ACCTCGCAGATCGGCAGAGAACGGTTTGGTCTGTTTGCGTACACAATGGACGCGTTAAG +>21 2 +TACCGATTCGTGGCCTCCCGTTCGTCGCAATGAACGGCTTTTCATTCCCCTGTAACGTT +>73 2 +CCTGTTTTCCTCGCCCCATGCAATGGTAACTAATATACCGCCCCATAGTCTTAATAACC +>68 2 +CTGTCCCAACGGTAACAATGGAGGCACTATACCGACGCTCGCAGCGAGGTATTTAAACT +>23 2 +GACATATGGCGGTACGCGGGCTCAGCGCTCCGCCAGTAAGAAGAAACAGGCTAGGTCTT +>94 2 +AGGGTCAAGAAAACTATTAATTTAAGCGCTGTTTAGTAACTACGTGTGGCATCGTTGCA +>10 2 +TCTCGAACTCCGGTTAATTTGCAATCCGGGGGTTTGCTCAGCAGCAGACCAACATCCAA +>41 2 +GGTGATTATGGGGGACGGGTATAGTACTAATAGTTTTGGGCATATTTCAGGCGTGCGCC +>80 2 +TCCTACCTGAGAGGCTTCGACTAAAGAATGCGGGTATACTGGCTACTGGTTGATAAGCG +>64 2 +AGATCCGTTTGTTCCGGACGGTCGTCGTACCCACCCCTTGTCGATAGGTAAAGGAGTAA +>57 2 +TAAGCGACCATCAGAAACACAGCATCAGCTTACCAGCCTTTCGTGGTACACCCGGAGTC +>1 2 +GATCATCGAATCGGGCTGTCGCCAAAGGCCGACCAAGGTTCCCGTGGGGCGGGCTAATT +>55 2 +GATTGGTGGTGAATGACTCACAAAATGCTCATAGAATATTAGATCTGCTTGGGTGTATC +>67 2 +GAATCACGGGATTTATACATCATTTATAGCTAAATTACACCTGTCCCAACGGTAACAAT +>14 2 +CTATTGTCGCTCCCTTAGTTGTTGGGCGTAGTCCGCACCTAGAGTCCAACCAGGCCTCG +>15 2 +AGAGTCCAACCAGGCCTCGACAATCCTTTGTCCTGTCCCCCGGAAGCCCAATGAGTTGT +>59 2 +TTTCAGCATGGGTCGCATTCCTACCTAAGGCTAGGGGCATGTTTTTGTCATCGTGCATA +>28 2 +CGCGAGAGGTTTCAGGTACCTATCGGGACAGACTTGTTTCTGGAAGCGCCCTCCGCTCA +>74 2 +CCCCATAGTCTTAATAACCGACACCGAGACGCTACATGGCGTCGGTGCCCGCGTGCGGA +>4 2 +TGTAACCTGTGTGGGGTCGGTCCTGGGGAAACTTTGGGTTTCATTACGGGGTGTCCATC +>65 2 +TCGATAGGTAAAGGAGTAAGCGTCCGACTCCCTCTTACTTGGCGCGACCAATATTCATT +>6 2 +ATAGAAATGAGGAGGATTCACAGACACGTCAGTCACCATCAAACGTCTAAGTAATCATG +>44 2 +CCAACCATGGTAGGTTAGGAAAGCCGCCAAATAAGTTCTTATACGCCACTCGACTTGGC +>3 2 +TCAACTCTACCCAAGCTCCTTGCATCTCGGTACCCCCCCTTGTAACCTGTGTGGGGTCG |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/random-20-a.part.extract.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random-20-a.part.extract.fa Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,198 @@ +>35 2 +CGCAGGCTGGATTCTAGAGGCAGAGGTGAGCTATAAGATATTGCATACGTTGAGCCAGC +>16 2 +CGGAAGCCCAATGAGTTGTCAGAGTCACCTCCACCCCGGGCCCTGTTAGCTACGTCCGT +>46 2 +GGTCGTGTTGGGTTAACAAAGGATCCCTGACTCGATCCAGCTGGGTAGGGTAACTATGT +>40 2 +GGCTGAAGGAGCGGGCGTACGTGTTTACGGCATGATGGCCGGTGATTATGGGGGACGGG +>33 2 +GCAGCGGCTTTGAATGCCGAATATATAACAGCGACGGGGTTCAATAAGCTGCACATGCG +>98 2 +ACCAGATGCATAGCCCAACAGCTGAGACATTCCCAGCTCGCGAACCAAGACGTGAGAGC +>17 2 +CCCTGTTAGCTACGTCCGTCTAAGGATATTAACATAGTTGCGACTGCGTCCTGTGCTCA +>89 2 +GCGAGATACTAGCAAAGGTTCATCAACAGCTACACCCGACGAACCCCGAGAAATTGGGA +>30 2 +GTTATGGTCCAGGATGAATGCGCGTACCGGGCGCCTATCACTCCTCTTGTCATTCAGAA +>82 2 +ATGCACTATATTTAAGAGGTCTAGAGTGTAAAAAGTGTACCCTTCGGGGTGGAGCTGTT +>60 2 +GTTTTTGTCATCGTGCATAAAGCGGGACAGAGTTCAACGGTATTCGAATGCACACCCTA +>83 2 +CCTTCGGGGTGGAGCTGTTAATGAACTCAAGTGGCGATGGAGGCTAAAACGATACGTTG +>12 2 +AGCCAATTGTAACCATATGGTATCCAGTTTCCGTAGCAGCAATGCGCGACGGGCAATCG +>85 2 +CGTGATATGATTACTAAAGGGGCCCGCAAAAACCCATTCACTGAGGGCTCTGTCCGTAC +>2 2 +CCCGTGGGGCGGGCTAATTTTAAAGGCAGGTTGCTACACGTCAACTCTACCCAAGCTCC +>45 2 +ATACGCCACTCGACTTGGCTCGCCCTCGATCTAAAATAGCGGTCGTGTTGGGTTAACAA +>11 2 +GCAGCAGACCAACATCCAACACTTTTCACAAGAGGCTGACAGCCAATTGTAACCATATG +>39 2 +CAATTGACTTCCATGTGGGTCGGCTGTCAAGTCTAAACCGGGCTGAAGGAGCGGGCGTA +>26 2 +AACATCTTAACCTCTGATCCCAACATGAGGGACATGAGTTTTCAAAGTAACGATGCGCA +>75 2 +GTCGGTGCCCGCGTGCGGAGCAGTCTTGATCCGGCGCGCTCTTACCTATGGTCGGCACG +>81 2 +GGCTACTGGTTGATAAGCGTACGTAAAAGGCGAGTCTTACATGCACTATATTTAAGAGG +>97 2 +ATTAGTGTGACTAGCCGAGTGCCCCAGCGTTTATCCAATGACCAGATGCATAGCCCAAC +>13 2 +AATGCGCGACGGGCAATCGCGTCTGCGTTGATCGTCGCCCCTATTGTCGCTCCCTTAGT +>92 2 +ATCAGGGCAAATTTGCTCGTGACTAAATGGTAATACTACCCGGGACAGTAAACTTTTGG +>56 2 +AGATCTGCTTGGGTGTATCCCCATTCAGAGATACCAGATCTAAGCGACCATCAGAAACA +>61 2 +TATTCGAATGCACACCCTAACATACTGGAAGATTCACTCTATATACCGGGAACTACTAA +>96 2 +ATTAGACCGCTATCAACTCTTGCGAGGAAGGTCTGGGCCTATTAGTGTGACTAGCCGAG +>31 2 +CTCCTCTTGTCATTCAGAAGGAATTTGATTAATTACCTGGGCTGACTCGCGCCCCCTGC +>29 2 +TGGAAGCGCCCTCCGCTCAGGCGTTTTAGTAGATCCCAGTGTTATGGTCCAGGATGAAT +>54 2 +TGGATGAGGTCCTTAAGGCCTAATTGACCAATCGCCCCAAGATTGGTGGTGAATGACTC +>0 2 +TAGTGATCAGCGGCTAGTGTCGCCCCTCTTAGCACCTTGCGATCATCGAATCGGGCTGT +>90 2 +GAACCCCGAGAAATTGGGAAGCCTGGAGGCAGTACAGTCATCCAGTCTGCTGCTCAAAG +>34 2 +TCAATAAGCTGCACATGCGTGGTTGTGGCACGATCAGTTCCGCAGGCTGGATTCTAGAG +>43 2 +AGGACTCGACGTCCGCCCCATGCTTGAGAGAAGGTTTCGGCCAACCATGGTAGGTTAGG +>8 2 +ACACACAAGGCCAGACACCAACTTGGCCGTGGAATTTATCAACACTTCTGAGACGAAGG +>37 2 +TGTGCGCTGTGAGATACAACTATAGGCACCGGGTTGCTGGCTAATAACCATTTAGAGTC +>51 2 +ACACAATGGACGCGTTAAGGAGAACCGGTCGCAACCAGGTTGAAAATGCCTGATATACG +>32 2 +GCTGACTCGCGCCCCCTGCAGGCTGCTATGATTGAGTGCGGCAGCGGCTTTGAATGCCG +>78 2 +TCTGGGGCGAGATCCCCTCTGCTCACTTTCTTGTAGTAAATACACCGAAGGGGCGAACC +>18 2 +CGACTGCGTCCTGTGCTCAGTTCGTGACGCCGAACTCAAGGACGCGGTACGAAGAACTG +>36 2 +TTGCATACGTTGAGCCAGCGCCGCCCGTATACACAGGGTCTGTGCGCTGTGAGATACAA +>53 2 +ATATAAGTTTTTTAGATGTAAAAAATTTTTTATGGCGGCCTGGATGAGGTCCTTAAGGC +>24 2 +AAGAAACAGGCTAGGTCTTCCATGCAATGGTTCTCACAGTGTAGTCGCGCATCAACTCC +>7 2 +AAACGTCTAAGTAATCATGCGACCGGCGCCTCGATTGGACACACACAAGGCCAGACACC +>9 2 +AACACTTCTGAGACGAAGGTCATTTACGATTGGGACACTTTCTCGAACTCCGGTTAATT +>47 2 +CTGGGTAGGGTAACTATGTAGCCATCGCTCAGTGGATTCTTCCGGGATAGGGTGTGCGA +>62 2 +ATATACCGGGAACTACTAAAATTTTGGGCTACTCTATGCTTACAGCCCAACATGCGCAA +>79 2 +TACACCGAAGGGGCGAACCCTGTCTACATTCGCAAATGCATCCTACCTGAGAGGCTTCG +>48 2 +TCCGGGATAGGGTGTGCGAATGTGCCGGGCATTCAGCTCCTTAGAGACGAGTTACGAGC +>66 2 +GGCGCGACCAATATTCATTTGATGAGAATTGAAATCGACTGAATCACGGGATTTATACA +>25 2 +GTAGTCGCGCATCAACTCCGCCAGTTTTATCGAAGCGCCCAACATCTTAACCTCTGATC +>5 2 +TCATTACGGGGTGTCCATCTAGAGAAAGTGGGTTTCCCTTATAGAAATGAGGAGGATTC +>72 2 +ATAAAAAACGACTTCTAAAGCGACACTGGTTTTATCCTTCCCTGTTTTCCTCGCCCCAT +>76 2 +CTTACCTATGGTCGGCACGATTCCATTGGCGGATATAGGATTGATTACGTGTGTTTACT +>69 2 +GCAGCGAGGTATTTAAACTGTTCAATCGGCGCAACCGAAAATCTGCTACCGTGGTTGCT +>87 2 +CAGTATACGCCCGTTGAGAAACAGGTGGTGGCGCAGTGTCGATTACTTCGTAATAATTT +>27 2 +TTCAAAGTAACGATGCGCAGATTGAATAATGCCATATCTGCGCGAGAGGTTTCAGGTAC +>77 2 +TTGATTACGTGTGTTTACTATACCGGTAGAAGCCTTCAGTTCTGGGGCGAGATCCCCTC +>95 2 +TACGTGTGGCATCGTTGCACCCTAATTCGCATTATTAAGTATTAGACCGCTATCAACTC +>63 2 +TACAGCCCAACATGCGCAACAACTATAAGCTGCTGCTGACAGATCCGTTTGTTCCGGAC +>38 2 +CTAATAACCATTTAGAGTCGCCCGCGGTGATGAGTAATCGCAATTGACTTCCATGTGGG +>20 2 +GTGCCTACCGTACCTGTCGAGCCAGTGCGATCAGTAAAACTACCGATTCGTGGCCTCCC +>88 2 +GATTACTTCGTAATAATTTGAGGGTGCTGCCGCGTGTTCCGCGAGATACTAGCAAAGGT +>49 2 +TTAGAGACGAGTTACGAGCCACTCTTGGATCGTCATGCATACCTCGCAGATCGGCAGAG +>91 2 +TCCAGTCTGCTGCTCAAAGTCCATCTACATGTAAAGAACCATCAGGGCAAATTTGCTCG +>86 2 +CTGAGGGCTCTGTCCGTACGTGTACTATAGATCCTTGCTCCAGTATACGCCCGTTGAGA +>42 2 +CATATTTCAGGCGTGCGCCAACTTACGATTCTTGAATCCAAGGACTCGACGTCCGCCCC +>70 2 +ATCTGCTACCGTGGTTGCTTCGACCATGGTAAACTGAGTAAGCCCTTATGAGTTGCGGG +>19 2 +GACGCGGTACGAAGAACTGCTCCAGCAACAGCATTCCTTGGTGCCTACCGTACCTGTCG +>84 2 +AGGCTAAAACGATACGTTGTATACTAAGAACTGTCTACATCGTGATATGATTACTAAAG +>52 2 +TGAAAATGCCTGATATACGAAGATTAAGCGGCTTTGGATCATATAAGTTTTTTAGATGT +>71 2 +AGCCCTTATGAGTTGCGGGTCGTGCTGTTAGACTGAACACATAAAAAACGACTTCTAAA +>93 2 +CGGGACAGTAAACTTTTGGTGATGCCAGCACGACCAGCGCAGGGTCAAGAAAACTATTA +>58 2 +TCGTGGTACACCCGGAGTCTCGAAAGGAGCTTGCAAAGCTTTTCAGCATGGGTCGCATT +>22 2 +TTCATTCCCCTGTAACGTTTCGAACTCAACTTGCTTGCCCGACATATGGCGGTACGCGG +>50 2 +ACCTCGCAGATCGGCAGAGAACGGTTTGGTCTGTTTGCGTACACAATGGACGCGTTAAG +>21 2 +TACCGATTCGTGGCCTCCCGTTCGTCGCAATGAACGGCTTTTCATTCCCCTGTAACGTT +>73 2 +CCTGTTTTCCTCGCCCCATGCAATGGTAACTAATATACCGCCCCATAGTCTTAATAACC +>68 2 +CTGTCCCAACGGTAACAATGGAGGCACTATACCGACGCTCGCAGCGAGGTATTTAAACT +>23 2 +GACATATGGCGGTACGCGGGCTCAGCGCTCCGCCAGTAAGAAGAAACAGGCTAGGTCTT +>94 2 +AGGGTCAAGAAAACTATTAATTTAAGCGCTGTTTAGTAACTACGTGTGGCATCGTTGCA +>10 2 +TCTCGAACTCCGGTTAATTTGCAATCCGGGGGTTTGCTCAGCAGCAGACCAACATCCAA +>41 2 +GGTGATTATGGGGGACGGGTATAGTACTAATAGTTTTGGGCATATTTCAGGCGTGCGCC +>80 2 +TCCTACCTGAGAGGCTTCGACTAAAGAATGCGGGTATACTGGCTACTGGTTGATAAGCG +>64 2 +AGATCCGTTTGTTCCGGACGGTCGTCGTACCCACCCCTTGTCGATAGGTAAAGGAGTAA +>57 2 +TAAGCGACCATCAGAAACACAGCATCAGCTTACCAGCCTTTCGTGGTACACCCGGAGTC +>1 2 +GATCATCGAATCGGGCTGTCGCCAAAGGCCGACCAAGGTTCCCGTGGGGCGGGCTAATT +>55 2 +GATTGGTGGTGAATGACTCACAAAATGCTCATAGAATATTAGATCTGCTTGGGTGTATC +>67 2 +GAATCACGGGATTTATACATCATTTATAGCTAAATTACACCTGTCCCAACGGTAACAAT +>14 2 +CTATTGTCGCTCCCTTAGTTGTTGGGCGTAGTCCGCACCTAGAGTCCAACCAGGCCTCG +>15 2 +AGAGTCCAACCAGGCCTCGACAATCCTTTGTCCTGTCCCCCGGAAGCCCAATGAGTTGT +>59 2 +TTTCAGCATGGGTCGCATTCCTACCTAAGGCTAGGGGCATGTTTTTGTCATCGTGCATA +>28 2 +CGCGAGAGGTTTCAGGTACCTATCGGGACAGACTTGTTTCTGGAAGCGCCCTCCGCTCA +>74 2 +CCCCATAGTCTTAATAACCGACACCGAGACGCTACATGGCGTCGGTGCCCGCGTGCGGA +>4 2 +TGTAACCTGTGTGGGGTCGGTCCTGGGGAAACTTTGGGTTTCATTACGGGGTGTCCATC +>65 2 +TCGATAGGTAAAGGAGTAAGCGTCCGACTCCCTCTTACTTGGCGCGACCAATATTCATT +>6 2 +ATAGAAATGAGGAGGATTCACAGACACGTCAGTCACCATCAAACGTCTAAGTAATCATG +>44 2 +CCAACCATGGTAGGTTAGGAAAGCCGCCAAATAAGTTCTTATACGCCACTCGACTTGGC +>3 2 +TCAACTCTACCCAAGCTCCTTGCATCTCGGTACCCCCCCTTGTAACCTGTGTGGGGTCG |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-abund-read-2.fa Wed Nov 11 09:47:17 2015 -0500 |
| b |
| b'@@ -0,0 +1,2002 @@\n+>895:1:37:17593:9954/1\n+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGG'..b'\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n+>seq\n+GGTTGACGGGGCTCAGGG\n' |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-2.fa.below --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-abund-read-2.fa.below Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>895:1:37:17593:9954/1 +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-2.large.oxlicg |
| b |
| Binary file test-data/test-abund-read-2.large.oxlicg has changed |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-2.large.oxlicg.info --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-abund-read-2.large.oxlicg.info Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +through test-abund-read-2.fa +Total number of unique k-mers: 83 +fp rate estimated to be 0.000 + |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-2.oxlicg |
| b |
| Binary file test-data/test-abund-read-2.oxlicg has changed |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-2.oxlicg.info --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-abund-read-2.oxlicg.info Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +through /home/mcrusoe/khmer/tests/test-data/test-abund-read-2.fa +Total number of unique k-mers: 98 +fp rate estimated to be 0.000 + |
| b |
| diff -r 000000000000 -r 47cea67b74ea test-data/test-abund-read-paired.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-abund-read-paired.fa Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,12 @@ +>895:1:37:17593:9954/1 +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG +>895:1:37:17593:9954/2 +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG +>895:1:37:17593:9954 1::FOO +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG +>895:1:37:17593:9954 2::FOO +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG +>895:1:37:17593:9954/1 +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG +>895:1:37:17593:9954/2 +GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG |
| b |
| diff -r 000000000000 -r 47cea67b74ea tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Nov 11 09:47:17 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="khmer" version="2.0"> + <repository changeset_revision="f257b2dba774" name="package_khmer_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |