Mercurial > repos > yating-l > bigbed_to_fa_340
changeset 0:512ed6da2367 draft default tip
planemo upload
author | yating-l |
---|---|
date | Wed, 17 May 2017 16:49:32 -0400 |
parents | |
children | |
files | bigbed_to_fa.xml bigbed_to_standard_bed.pl test-data/contigs.models_12_2.bb test-data/contigs.models_12_2.fa test-data/contigs.models_6_2.bb test-data/contigs.models_6_2.fa test-data/contigs.out.2bit test-data/contigs.trf_4.bb test-data/contigs.trf_4.hard.fa test-data/contigs.trf_4.nomask.fa test-data/contigs.trf_4.soft.fa test-data/contigs.trf_4_12.bb test-data/contigs.trf_4_12.fa tool_dependencies.xml ucsc_macros.xml |
diffstat | 15 files changed, 1419 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigbed_to_fa.xml Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,110 @@ +<?xml version="1.0"?> +<tool id="bigbed_to_fa" name="bigBedToFa" version="1.0"> + <description>Retrieve sequences associated with bigBed features</description> + + <macros> + <import>ucsc_macros.xml</import> + </macros> + + <expand macro="requirements_twobit"> + <requirement type="package" version="340">ucsc_bigbed</requirement> + </expand> + + <command detect_errors="exit_code"> +<![CDATA[ + #set no_mask = "" + #if str($masking_option) == "upper": + #set no_mask = "-noMask" + #end if + + ${__tool_directory__}/bigbed_to_standard_bed.pl -i "${bigbed_input}" | + twoBitToFa ${no_mask} -bed=stdin "${twobit_input}" stdout + + ## Add extra option to change soft masked bases to N's + #if str($masking_option) == "hard": + | awk '{ if (/^>/) { print } else { gsub(/[acgt]/, "N"); print } }' + #end if + + > "${fasta_output}" +]]> + </command> + <inputs> + <param name="twobit_input" type="data" format="twobit" label="twoBit input file" /> + + <param name="bigbed_input" type="data" format="bigbed" label="bigBed input file" /> + + <param name="masking_option" type="select" + label="Repeat masking option" + help="Specify how repeats within the twoBit file should be represented"> + + <option value="upper">Show repeats in uppercase (no masking)</option> + + <option value="lower" selected="true">Show repeats in lowercase (soft masking)</option> + + <option value="hard">Show repeats as N's (hard masking)</option> + </param> + + </inputs> + <outputs> + <data name="fasta_output" format="fasta" /> + </outputs> + <tests> + <test> + <!-- Test bigBedToFa with bed4 and default (soft) masking --> + <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" /> + <param name="bigbed_input" value="contigs.trf_4.bb" ftype="bigbed" /> + <output name="fasta_output" file="contigs.trf_4.soft.fa" /> + </test> + <test> + <!-- Test bigBedToFa with bed4 and no masking --> + <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" /> + <param name="bigbed_input" value="contigs.trf_4.bb" ftype="bigbed" /> + <param name="masking_option" value="upper" /> + <output name="fasta_output" file="contigs.trf_4.nomask.fa" /> + </test> + <test> + <!-- Test bigBedToFa with bed4 and hard masking --> + <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" /> + <param name="bigbed_input" value="contigs.trf_4.bb" ftype="bigbed" /> + <param name="masking_option" value="hard" /> + <output name="fasta_output" file="contigs.trf_4.hard.fa" /> + </test> + <test> + <!-- Test bigBedToFa with bed4+12 with default masking --> + <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" /> + <param name="bigbed_input" value="contigs.trf_4_12.bb" ftype="bigbed" /> + <output name="fasta_output" file="contigs.trf_4_12.fa" /> + </test> + <test> + <!-- Test bigBedToFa with bed6+2 with default masking --> + <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" /> + <param name="bigbed_input" value="contigs.models_6_2.bb" ftype="bigbed" /> + <output name="fasta_output" file="contigs.models_6_2.fa" /> + </test> + <test> + <!-- Test bigBedToFa with bed12+2 with default masking --> + <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" /> + <param name="bigbed_input" value="contigs.models_12_2.bb" ftype="bigbed" /> + <output name="fasta_output" file="contigs.models_12_2.fa" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +bigBedToFa retrieves sequences associated with the features in a +`bigBed <https://genome.ucsc.edu/goldenpath/help/bigBed.html>`_ file +from a `twoBit Sequence Archive <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_. + +.. class:: infomark + +**Extracted sequences:** + +For files with `12 standard BED columns <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_, +this program will concatenate the sequences associated with each block (e.g., exons), and +exclude the sequences between adjacent blocks (e.g., introns). + + ]]></help> + + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigbed_to_standard_bed.pl Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,140 @@ +#!/usr/bin/perl +use warnings; +use strict; + +=head1 NAME + +bigbed_to_standard_bed.pl - Convert bigBed file to standard BED file + +=head1 SYNOPSIS + +bigbed_to_standard_bed.pl -i ${input}.bb > ${out.bed} + +=head1 DESCRIPTION + +This script converts a bigBed file to a BED file that contains only +the standard BED fields. This BED output file can then be used with +tools that do not support the bedPlus format. + +=head1 OPTIONS + +=over 4 + +=item -i,--infile <in.bb> + +=back + +=head1 VERSION + +Last update: 2017-05-08 + +=cut + + +#==================== +# Libraries +#==================== +use Getopt::Long; +use Pod::Usage; +use Carp; + +## no critic (ProhibitConstantPragma) +# Use constant instead of Readonly to avoid dependence on CPAN modules +use constant BIGBED_SUMMARY => "bigBedSummary"; +use constant BIGBED_TO_BED => "bigBedToBed"; +## use critic + +#==================== +# Main Program +#==================== +sub main { + my %params = parse_arguments(); + + my $field_count = get_num_defined_fields($params{infile}); + + bigbed_to_bed($params{infile}, $field_count); + + return; +} + +main(); + + +#==================== +# Subroutines +#==================== +sub bigbed_to_bed { + my ($infile, $field_count) = @_; + + my @cmd_args = (BIGBED_TO_BED, $infile, "stdout"); + + open(my $cmd_ph, "-|", @cmd_args) or + croak("Cannot run bigBedToBed: $!"); + + while (defined(my $line = <$cmd_ph>)) { + chomp($line); + + my @fields = (split(/\t/x, $line)); + + my $last_idx = $field_count - 1; + + print join("\t", @fields[0..$last_idx]), "\n"; + } + + close($cmd_ph) or croak("Cannot close input stream: $!"); + + return; +} + +sub get_num_defined_fields { + my ($infile) = @_; + + my $num_fields = 3; + + my @cmd_args = (BIGBED_SUMMARY, "-fields", $infile); + + open(my $cmd_ph, "-|", @cmd_args) or + croak("Cannot run bigBedSummary: $!"); + + while (defined(my $line = <$cmd_ph>)) { + chomp($line); + + if ($line =~ /(\d+)\s+bed\s+definition\s+fields/x) { + $num_fields = $1; + last; + } + } + + close($cmd_ph) or croak("Cannot close input stream: $!"); + + return $num_fields; +} + +#==================== +# Parse command-line arguments +#==================== +sub parse_arguments { + my $infile = undef; + my $help = 0; + + GetOptions( + 'help|?' => \$help, + 'infile|i=s' => \$infile + ) or usage(); + + pod2usage( { verbose => 2 } ) if ($help); + + # check required arguments + usage("Missing bigBed file") unless ( defined($infile) ); + + return ( + infile => $infile, + ); +} + +sub usage { + my $msg = shift; + + pod2usage({ verbose => 1, message => $msg || "" }); + exit 1; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.models_12_2.fa Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,194 @@ +>CG33978-RD +AAAACAGTGGAAGACATGTTTCTTGCTTCCAAGCAGTTAACAGGTCGGGA +AGAATTAATACGAGGTATGTACAGGTGTCGGAGAACACAATGGAAGAAGC +AAGGTATAATCTTGCCACTCACGTTATGTCAAATGGAGTAGAACTAATTA +TTGCCTGTGAAAGGGAAAAACCTATGGAAAAGATCGTGGCAACTACCCAA +AAACTTACAAATGTTATTAGTCGACTGATAATACAACAATTCGACAAGCC +CTCGACTCTGGCTCCAAGTACATTAAAAAATCAGATGATTTTAACATTGC +CTTCAATTAAACAGGAAACCATTTTACTTCCTCATAATTCTTTTATTACA +AACATTTTTCTAACCACGTGCACCTATATCACAACATATGTGGAAAATGG +AAGCTCGAATGTAGTAAAAGAAAAAATGGTTATATCAAACACCATTACGC +AAGATCGAAAGTATTTGCATGCAAGTAATCCTATGATAATAGACATCACT +TTTTCAAGGACTCCAGAACTAGTGGTTGGAATGTTCCCAACAAGATATCA +TTATTTTAACACAATACGTAGAGACCAACCGGATTCAACTCTAATGGTAG +TCACTTCAAAATATACTGTTATAAATACAATCACGAGACCTGCACATTCT +TTGACTTTTATAAATTCAGGCGACAATCTTTCGCCCACCACAAATACCTA +CATCAGTCAAATATTTTTTACTAAAACTGTCTACGGCAAAAACCAAACAC +CAACATATGGCACAAGTATAAGTAATCTTACACAAGTCGTTATTACAGAA +TCCCTTTCAGAAACCGGTCCAGCTTATATAAGTTCAATAGGACCTGAGTA +TTTTTCAATTTCGGACAAAAAAAAAAATTATTTACTTCGGTAATAGAAAT +ATCTGACTATCTAATGATATACTCAACCAAGTCCTTATTAGAAACGAATA +CTCTATGTTCAGCAAAATTTAATAATAGTTTGACTATGGTAGCTTCATAT +GTTTCTTTGACAAAGACAGTCTGCGAAAGTGATCCAAAAGTATCTAACAA +TAACTTAAAGCTTCACACTAACACTATAAATAATATTGCTACCAATACAG +TGGGTAGTTCGCTGATAAACTCAGATCTTTTATTTTCTATCAAATCCGCA +CTTATGCTTAAAAAGAGAAACAACCAACGCCAAACTATTGTAACAATGGC +CACATTGGGGGCAGGTGAAACTATTAAAGTAACTGCCGTGAATATAATCA +AAAAACCAAATTGGAAATATATTTCCACTTTGGCAAAGGCAAAGGAATAT +TGTAATTCTGAAATGAGTGATACATGTACATCTAATGACACAAAATCAAC +TTTTAGTTCAAAACTACCCCACTTTTCTGAAAATACTATAAATATATCAG +AAAAAAGCAGCGTCATCAAGAACATTTATAGGAACAATATTACACAATTT +TTATTAGAGGAAACTGAAAATAATGAAATGTTGATAAAAAATAAAAAACT +AATAAAGCCTTCAATGTTCAGTTCATTAGTGTCTTCACAGGGCACAAGCT +CTGAAAACTGGAATTTAGAGCGTTTTCGCCCAATGCTGAATGTCGTAGCA +AACTTAATTAAAAACCAACTAACTAATACACAATATACGCAACTTCATAC +ACATTCATTTATAAAAGGCAAATCAGGAACAACAACGAAAAATCCTATTT +ATATACCTTTAAAGCGAAATGTGAAAGGCAAACCCTTAAACATGACGAAT +GCAAAACCAAATACGGCTGATTTACTCGGAAAATTAAAAATTATGGCATT +ACATATACATCCCCCAATGACGTATGTACTAAATAAGTGTCTAAAACATA +ATCTAAAAAAACTTTCATCTTCCGTCGGATATAAAGGAACATCTATGGTG +TATAGGAACGCGTTCATTAATCCAGGTATTCCCATTAGACCCGGAGAGGT +TATAACAGCCAGCGCTAATGTTATATTTGGAAAGCCAAGTATTGAGCAAA +ACATTAGAACTACGATAACGAATCGTCCCTTAACTTCGATAAATTCGATT +TACCCCAGTGATGAAAGGATCCATTCCACTATGGTACACAGTTCCTTTTC +GTATGAAAATGAAATTATGACAGAGTACGCCACTTTATTAAAGCCTCCAC +CACTGCCTGCAAATCGACTACTACAGTACACATCAACATTCCAGTCTCAA +ATGGGAAGAACGAGGAATGCTGCAAAAAATTGGTTTTCACCAATTACAGT +TTTACAAAACAATCCGATTTATGATTACTATTCATCTGAGACACAAATAA +ACTTAAATACTGACTTTTTTGTATTTCGAATACCACAAATTGTTGGTGAA +AGTCGGCCAGCTACTGCAAGTTATACTGTGTCAAACACGCTTGACTATTC +TTTAATTCATGATTGTTCTTTCGACTCTTTAAAACCAACTTTGTCTTACA +TGACGCCTATTTCTACATTTTCTACCCTTCACCAAATTAACCTTAAAAAT +GACGTCATTAGCCATACAATTAATATGCAAGCTCGCCCTCTAACGTTTAA +AAGGGAATCCGATAATATTCCGCACGCAACAACCGTAAGAGGTCATATGG +ATAGTTTTTTAATTTCACAAATTAAAATACCTTTTAATGACAAAAATGTT +GAAGTCCAGTTGACGGCCAACCGGAAAAGAGTTTTTCCCGTTCAATATAA +GGACTTAACGTCAGATGAGACTAATATTAAATTGGAACAACGAACTAATA +TATTAAGCAACTATGAGAATGCTCAGCATTTATTTTCCTTTAAGGATATT +AAAACCCATAGCGGATTAAACAATTATACTTCTATATACAAAAATGAATA +TTTTTCTCAAACTACTTCTAACCTCAATCATTCAGATAATATGAATGGTA +AACCAATAAGACATGATAATGGAATTCCTAAAGAAAATATAGAACAATTT +ACAGAGCTAGATCAAAAAGCAGAAAACTCAAACAAATCATTGTACTTTTT +AAGGTTTAATTCTACTAAAAAACGCGATCTTAACAGTACAACTACATTAA +ATATCTGGTCTTCAATGATTAAATATTTAAGTATAGCCATGCCTAAGAGT +GTACACACAAATACAAAATCGTTGATGTCTACAAAAAGACGTATTGAGAC +TGGCAATACAAACATGGTGTTTCTGACAACAGGTGACCATTTGCGTGTCG +AACCCTTAACAGAAAATACAATTAATTCAGTAAATTCTGAATTTATCTCG +AGCACAAACATCTTTAACACAAATTACTCAGTTATCGCTACTGAACCCTC +TCAACTAAGATCAAGAATATATAAAGAATCAAATATGTTTGGCCTTACGT +CAAACAACAACCTCCAGGTAAAACCATCTTTTGTAAAACCCCTGCGCAGT +TCAGCAATGCCAGTTATAAATGCAATTACATTTTCACACGTTTTAGTAAG +AGCACCGCATTCTGACTTTGGTCCAAACTGGCAAGATTCGACATTAGGCA +TAATATGCCACACTGAAAGTTGCAAAAAAAAATTATTAAAAGAATTTAAG +CACGATATCAAAATGCTTGAACCATCTGAAATGTTGCAGGATGAAATACC +TTCAGTTTCAAAAAAAACATCTGAATGGGATAAGATTTCAGTGCTAGCAG +AAAATTCGAACGCCATAATCCCTATGCATTCTACACCTTCGCATACTAAC +AAAACAATTAAATATTTTAAAATAGTAACCCCCACTAAAACAAACCGGGT +TAGTATAAAAAACGTATCTACAATCAAAACAAATTTTGATGCAAATAAAT +ACATATTTATGAATCACTCTATCGCTAACCTATCGAAATACTATATGAAG +GAACCAATTTCGATTGGTTCAGACAAATTATTTACATCCTCAAGGATAAG +CAACCAGTCACAAGTAATTGACAAAAGTAATGTTACAACTTTAAGTGACG +TGCCTCAAAGATTAAAGACTTCAGACTATCTAGCGAACGAATCTTTTACA +GAAAACATTTTAGGGTTTTCCAAGCACTCAGGGCTCAGAAGCAAATCAAG +CTTAGGTTCTAATCGAGATGAGCATGTGTATGCTTCCAGCGACATAGATA +GTATGCTCTTTGGTGCTATTGTTGCTGATTCATTTTTAAAGACAAATTAT +GCAAAAAAAAACAAATCTTTTAATGGTTGCCATCCGCCGTGCAGATTGAA +CAAAAATGAATTATGCGTTACTTATGCTAATAATACCGAGTCCTCGAGTC +TTTGTGAATGCCGACCAAGTTTTGGACGCATGTTTCCCGACCGACCTTGC +AGACCTACTTATACTTACGAAATGAAGATTCAAGTCAACTGGGCGGGCAA +CCACTCTATAAAGCTTGGCGATATCATGAAAAGTAATTTGAAAAATGAAA +CTTCTTATATAAATACAATTTTATTAGAAGCAGCTGATCGCATGGTTATG +CAATCTGATTATAGAGATATTTTTCATGGTGTTCAGTTACGAAAAGTTTT +TGTAGAAGAAAAAGATAAGTTAACGGTTACGTTCCTGCTACAGTTGTCAG +AGAATAGTGATGAGGATCAACTTAATTCCGTCTTTCAAAAGTATTTACGG +CAAAGCAACTTCAGTATTGGAGGCACTGGATTTTACACTTCAAAAAACAG +TCTACACTTACTAGAATTTAAAGATTTTGACGAATGTCGTTACGAAAACT +TTAACGACTGTTCTACTGATGCCAACTGTTTTAATTTGGTTGGCAGCTAC +ACTTGCAGTTGCAAAGAGGGTTACACAGATTCATCTAATAATTATTTATA +CCCAGGTCGACATTGCTCAAATAATATAATCGGCTGCGATGATTGTAACT +ATAATGGCAAATGTATGAATAAGTCGGATGACCACGGGCATCAGGGGATA +ACCTTATGTAAATGCTTTTCTTGGTACGCTGGAACAAAGTGTCAAGTTAA +CATGAAGGTCATAATAGTCTTTCTTTTTATGAGTGGAACCTTTTTGTCCT +TTTTTCTTCTTTTATTCTTCCTTAAAACAAACACCAAGCTTAAAAGGCTA +GACAACGGAAAAGCAAGCAAATTATGCACTGCGCCTTCCAATATAAATCC +TAGTTTATTAACATCAACCGAAATAATTCGACCAACTTACAGTAAAAAAG +AATCTATCAGTAAATTAGGTCAATGCATGACTTCCAATTCTAAAGAGAAA +TATATTGGTGTGCATAATACTTATTTTAAACCTGCAGAACTTAAAGAAAG +GTTGACACATAGTTACAAGGCTTCTTCATCCTCTTACTTGAGCAATGATT +TTAATATCAAGAGTACAACTAAAGAACACGGTTTTTTGCATAGTAGTGAA +GACCATAGCCCAGAAGAAGACCAAACAGAGCGATCTCTTACCCTTATGAT +TCCAAGGGCAAAATATTGTTTACCCTACATTGCTCAAAACTCTCATTTAC +CTCATCACGCTAATAAATCATTTATGGATAATACAGAGCAAAGGGCAGTA +CATACAGATGATGGTAATACAAACATATGCCGAACTTTTGCTTTTAATTG +TCTTAACAATTTTACATTGCCAGAAAATATATTCTACAGAGGCACCAACA +GACCCAGAACTGATCTTGTATCTGCTGGCTTCCAGGTATCTGTCCTTGTT +AGTGAGAAAAATGTATTGGAAATTCCCATATTAGATGAGATAACATTTAA +TGAGTACGCCCATAAACGAAGCCCATTAAATAAGGATGATAATACAAAGA +TGAGTGAAAGAGATATGGATTCAACTTTCTTGTTGCCACATACACATCTT +TATAAGCCTGACGAGGTAATAACACTCTTATAA +>CG31997-RB +ATGGGTTTCCATTTTCATTTTGATATTTTGCTCCTCATTTTACTCTTAAC +TCTAATAGCTCCTTTTTGTATTGCGGCTGAACAAAAAGTGTTGAAAGATG +AAACTGCCAATGTTGGTGAAATACGAATTTTTAAACGCCTTATTCCTGCT +GATGTTCTGAGAGATTTTCCGGCGATGTGCTTTGCTTCCACTCGATGCGC +TACTGTTGAACCAGGGAAGACTTGGGACTTAACTCCGTTCTGCGGTCGTT +CTACTTGCGTGCAAAATGAGGAAAATGAAACAAAGCTTTTGGAACTAGTA +GAAGACTGTGGCCCATTGCCACTGGCAAACGACAAATGTAAGTTGGACAC +TGAGAAGACAAATAAAACGGCTTCGTTTCCTTACTGCTGCCCCATCTTCA +CATGTGAGCCTGGCGTTGCATTGGAATATCCTGAGGTTGGAAAGGAAAAT +GACAAAAAGAATGTTGAGTGA +>Arl4-RA +ATGGGGGCAACCATGGTAAAACCTCTGGTAAAAAACGGAAATTTTTTAGA +CGCATTGCCTTCTCAGGCAACCCTCCATGTAGTAATGTTAGGCTTGGACT +CTGCGGGGAAAACCACTGCATTATACAGACTTAAGTTCGATCAGTATTTA +AACACGGTGCCGACTATTGGTTTTAATTGCGAAAAAGTTCAAGGTACTAT +TGGTAAGGCTAAAGGAGTTCATTTTCTTGTTTGGGATGTTGGAGGTCAAG +AAAAACTAAGACCTCTTTGGAGAAGCTATACACGCTGCACCGATGGAATT +TTGTTTGTTATCGATTCGGTCGATACGGAACGAATGGAAGAAGCAAAAAT +GGAGTTGATGCGTACCGCTAAATGTCCTGATAATCAGGGTGTTCCAGTGC +TGATATTAGCAAATAAGCAAGATCTTCCAAACGCGTGTGGTGCAATGGAG +CTGGAAAAACTTTTAGGACTGAACGAGCTTTATAACCCAGTGCCGAACAT +ATCGATGCTAACTTGTTCCGACTCTTCTTCCACCATCAATTTAATCGGAT +GTAGCAAGTCAAACCAAAGTATTACAGAAACCTCGTTAACAGAGCAAAGA +TCAAATCACCTGCATTCATCAATGATTCACATTAAACCTGCTCCTGAAAG +TGACGAACAAAGGACTACGTTAAGTGGAGAGGCGTTGTCTACATTCATAT +ATCCGCATTCTGGCAAAGGTTCTGATGTGAAGGACCAAAAAAATTCGCGT +GATGGTAAAAACTGTTTTCATAACAAAAAACATAACAGGACCTTTTCCAA +CTCGATGCACTTTAGGGGGTGGTATATACAACCGACCTGTGCGATAACTG +GCGAGGGACTTCAAGAAGGCCTAGAAGCTCTTTATGATATGATATTGAAA +CGCCGGAAACTTAATAAATCTCATAAGAAAAAACTGTAG +>CG2316-RA +ATGAGTGTCCTATCCAAATATGTTGACTGTTTTGCAGAAAAATGTGAACA +TAATGGGCTAACAAAACACGTTTTCAGCTATGCTCTTGTGACTAGTGCTA +TATTGGCACTTACTATCAAGGTGACTATCCCCTACGCGAAGAAAGGAATA +ACTCAAAATGGAAAACCCAAAGTCCACAATGGGACACTTACACCATTGGA +AGCAGATATTTCAGAGGAGGATTTAAAGCTAGCGGAGGCCGAAAAGTTGT +TAGTTGCTCAGCAGCAAAAAAAAAAATCAAATGATTTTGTTGAGCCAGGA +CTAAACCAAGAATTTTTGAAACAACTGAAAATGCTTTCAAAAATAATGAT +CCCACAGACCTTATGTTACGAAACTGGATTGCTGGCTGTTCATACATTTT +GCCTAATTTCTCGCACATTTCTTAGTATTTATGTGGCTGCTTTGGAGGGA +GCCCTTGTAAAATTCATAGTACGAAAAGACGTTAAACAATTTGCTCTTGT +ATTACTGAAATGGTTCGGGATTGCTATCCCTGCTACGTTTGTTAATTCCA +TGATACGGTTTCTTGAAAGTAAACTTGCTCTGGCTTTTCGAACTCGACTG +GTACGTCACTCATATCGTCTTTACTTTAAAAACCAAAATTATTATAGAGT +ATCGAATTTGGATGGACGCATTGAAAATGCGGATCACAGACTTACCGAAG +ATATTTCCGTGTTCGCTAGCTCTGTAGCTCATTTGTATAGTAGCCTGACA +AAACCATGTTTCGATCTAATGCTTATTGGCTTGGCATTGATGAGATCCTC +TAGAAAAATGAAAGCTAACATTATAACCGGACCGGCTTTATCTGTTGGTG +TTATTGCTCTAACAGCCCATATATTACGAATCGTGTCACCGAAGTTTGGA +CAGTTGGTATCGGAAGAAGCCAATAGGTATGGCTACTTGAGGCACATTCA +CTCCCGCATAATAACTAATGCAGAAGAAATCGCCTTTTACGGTGGTCACA +AAGTGGAGATGCAGCAGCTACGGCAGGCATACAACCGTCTAGTAAATCAA +ATGACTACAATTTTTAACCAAAAACTTTGGTTTATTATGCTTGAACAATT +TTTTATGAAATATGTTTGGTCCGGTACTGGAATGATTATGGTGTCACTTC +CTATTCTGACAGGCAGTGACGTAGGATCTGCATCAAAGCCCGACTCGGCC +ATTACGGAGTCGCGTGTTAGCGAACGTACGCAGTATTTAACAACAGCTAG +AAATTTACTAATTTCTGCAGCAGACGCTATTGAGCGATTGATGTCTTCTT +ACAAAGAAATTGTGTCGCTTGCTGGATACACTTATCGCGTGGCTGGCATG +ATGGATGTGTTCGAGGAAACTGCACAGGGACTCTACTGCAAGGCGAGTGT +AATAGATAACAATCAGTCAAAAGGAATTATAGAGCACCGTAACGGAAAGC +CAATAGCAAAGGGTCGCATTATTTACTCAGATGATCCGGAAAATATGTCA +ATAAACTTACGTGCAGTGCCAGTAGTGACACCAAACTGTGATATAGTTGT +ACCGAAACTTACATTGTGCATCGAGCCTGGGGTGCATTTGTTAATAACTG +GGCCGAACGGTTGTGGTAAATCCAGCTTGTTTAGAATACTAAGTGGTCTT +TGGCCCATATACGCTGGAGAATTGCAAATACCGCGGCCCGTAAAAGATAT +TCCTTGTATGTTTTACATTCCACAACGTCCATACATGTCAATTGGTAGTC +TTTGCGACCAAATTATATACCCCGACACACGGGATGATATGAAACGCAAA +GAAATATCTGAAAATGAGTTAAGATGCATTTTGAAGTTGGTCAGCCTTGA +ACACATCGCCCAACGTGATAGTTTTGACGTTGTTCGTGATTGGAAGGATA +TATTATCTGGAGGTGAAAAACAACGTATGGCGATAGCTCGCTTGTTTTAC +CACAAGCCACGTTATGCCCTACTTGATGAATGTACGAGCGCAGTGTCTAT +AGACGTTGAAAGCTCAATATATGAAATTGCTAAAGGCATGGGAATTACGC +TGTTGACTATAACACACAGGCCTACCTTATGGAAATACCACACACATATA +TTGGAGTTCGACGGCCTTGGCAACTGGCAGTTTAGAAAAATGAATGAAGA +TGAGCAACAAAAGGAACTATTCCTTTCTTAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.models_6_2.fa Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,586 @@ +>CG33978-RD +AAAACAGTGGAAGACATGTTTCTTGCTTCCAAGCAGTTAACAGGTCGGGA +AGAATTAATACGAGGTATGTACAGGTGTCGGAGAACACAATGGAAGAAGC +AAGGTATAATCTTGCCACTCACGTTATGTCAAATGGAGTAGAACTAATTA +TTGCCTGTGAAAGGGAAAAACCTATGGAAAAGATCGTGGCAACTACCCAA +AAACTTACAAATGTTATTAGTCGACTGATAATACAACAATTCGACAAGCC +CTCGACTCTGGCTCCAAGTACATTAAAAAATCAGATGATTTTAACATTGC +CTTCAATTAAACAGGTAAGATTTATTACAAAATATTGAATAATTTACAAA +TCGCGTTAATTCATTCTGCAGGAAACCATTTTACTTCCTCATAATTCTTT +TATTACAAACATTTTTCTAACCACGTGCACCTATATCACAACATATGTGG +AAAATGGAAGCTCGAATGTAGTAAAAGAAAAAATGGTTATATCAAACACC +ATTACGCAAGATCGAAAGTATTTGCATGCAAGTAATCCTATGATAATAGA +CATCACTTTTTCAAGGGTAAGCATCAAATCAATTGTAAAATTGCACGTCT +TAAAACTTGTTTGTTATTTTTAATGTTCAGACTCCAGAACTAGTGGTTGG +AATGTTCCCAACAAGATATCATTATTTTAACACAATACGTAGAGACCAAC +CGGATTCAACTCTAATGGTAGTCACTTCAAAATATACTGTTATAAATACA +ATCACGAGACCTGCACATTCTTTGACTTTTATAAATTCAGGCGACAATCT +TTCGCCCACCACAAATACCTACATCAGTCAAATATTTTTTACTAAAACTG +TCTACGGCAAAAACCAAACACCAACATATGGCACAAGTATAAGTAATCTT +ACACAAGTCGTTATTACAGAATCCCTTTCAGAAACCGGTCCAGCTTATAT +AAGTTCAATAGGACCTGAGTATTTTTCAATTTCGGACAAAAAAAAAAATT +ATTTACTTCGGTAATAGAAATATCTGACTATCTAATGATATACTCAACCA +AGTCCTTATTAGAAACGAATACTCTATGTTCAGCAAAATTTAATAATAGT +TTGACTATGGTAGCTTCATATGTTTCTTTGACAAAGACAGTCTGCGAAAG +TGATCCAAAAGTATCTAACAATAACTTAAAGCTTCACACTAACACTATAA +ATAATATTGCTACCAATACAGTGGGTAGTTCGCTGATAAACTCAGATCTT +TTATTTTCTATCAAATCCGCACTTATGCTTAAAAAGAGAAACAACCAACG +CCAAACTATTGTAACAATGGCCACATTGGGGGCAGGTGAAACTATTAAAG +TAACTGCCGTGAATATAATCAAAAAACCAAATTGGAAATATATTTCCACT +TTGGCAAAGGCAAAGGAATATTGTAATTCTGAAATGAGTGATACATGTAC +ATCTAATGACACAAAATCAACTTTTAGTTCAAAACTACCCCACTTTTCTG +AAAATACTATAAATATATCAGAAAAAAGCAGCGTCATCAAGAACATTTAT +AGGAACAATATTACACAATTTTTATTAGAGGAAACTGAAAATAATGAAAT +GTTGATAAAAAATAAAAAACTAATAAAGCCTTCAATGTTCAGTTCATTAG +TGTCTTCACAGGGCACAAGCTCTGAAAACTGGAATTTAGAGCGTTTTCGC +CCAATGCTGAATGTCGTAGCAAACTTAATTAAAAACCAACTAACTAATAC +ACAATATACGCAACTTCATACACATTCATTTATAAAAGGCAAATCAGGAA +CAACAACGAAAAATCCTATTTATATACCTTTAAAGCGAAATGTGAAAGGC +AAACCCTTAAACATGACGAATGCAAAACCAAATACGGCTGATTTACTCGG +AAAATTAAAAATTATGGCATTACATATACATCCCCCAATGACGTATGTAC +TAAATAAGTGTCTAAAACATAATCTAAAAAAACTTTCATCTTCCGTCGGA +TATAAAGGAACATCTATGGTGTATAGGAACGCGTTCATTAATCCAGGTAT +TCCCATTAGACCCGGAGAGGTTATAACAGCCAGCGCTAATGTTATATTTG +GAAAGCCAAGTATTGAGCAAAACATTAGAACTACGATAACGAATCGTCCC +TTAACTTCGATAAATTCGATTTACCCCAGTGATGAAAGGATCCATTCCAC +TATGGTACACAGTTCCTTTTCGTATGAAAATGAAATTATGACAGAGTACG +CCACTTTATTAAAGCCTCCACCACTGCCTGCAAATCGACTACTACAGTAC +ACATCAACATTCCAGTCTCAAATGGGAAGAACGAGGAATGCTGCAAAAAA +TTGGTTTTCACCAATTACAGTTTTACAAAACAATCCGATTTATGATTACT +ATTCATCTGAGACACAAATAAACTTAAATACTGACTTTTTTGTATTTCGA +ATACCACAAATTGTTGGTGAAAGTCGGCCAGCTACTGCAAGTTATACTGT +GTCAAACACGCTTGACTATTCTTTAATTCATGATTGTTCTTTCGACTCTT +TAAAACCAACTTTGTCTTACATGACGCCTATTTCTACATTTTCTACCCTT +CACCAAATTAACCTTAAAAATGACGTCATTAGCCATACAATTAATATGCA +AGCTCGCCCTCTAACGTTTAAAAGGGAATCCGATAATATTCCGCACGCAA +CAACCGTAAGAGGTCATATGGATAGTTTTTTAATTTCACAAATTAAAATA +CCTTTTAATGACAAAAATGTTGAAGTCCAGTTGACGGCCAACCGGAAAAG +AGTTTTTCCCGTTCAATATAAGGACTTAACGTCAGATGAGACTAATATTA +AATTGGAACAACGAACTAATATATTAAGCAACTATGAGAATGCTCAGCAT +TTATTTTCCTTTAAGGATATTAAAACCCATAGCGGATTAAACAATTATAC +TTCTATATACAAAAATGAATATTTTTCTCAAACTACTTCTAACCTCAATC +ATTCAGATAATATGAATGGTAAACCAATAAGACATGATAATGGAATTCCT +AAAGAAAATATAGAACAATTTACAGAGCTAGATCAAAAAGCAGAAAACTC +AAACAAATCATTGTACTTTTTAAGGTTTAATTCTACTAAAAAACGCGATC +TTAACAGTACAACTACATTAAATATCTGGTCTTCAATGATTAAATATTTA +AGTATAGCCATGCCTAAGAGTGTACACACAAATACAAAATCGTTGATGTC +TACAAAAAGACGTATTGAGACTGGCAATACAAACATGGTGTTTCTGACAA +CAGGTGACCATTTGCGTGTCGAACCCTTAACAGAAAATACAATTAATTCA +GTAAATTCTGAATTTATCTCGAGCACAAACATCTTTAACACAAATTACTC +AGTTATCGCTACTGAACCCTCTCAACTAAGATCAAGAATATATAAAGAAT +CAAATATGTTTGGCCTTACGTCAAACAACAACCTCCAGGTAAAACCATCT +TTTGTAAAACCCCTGCGCAGTTCAGCAATGCCAGTTATAAATGCAATTAC +ATTTTCACACGTTTTAGTAAGAGCACCGCATTCTGACTTTGGTCCAAACT +GGCAAGATTCGACATTAGGCATAATATGCCACACTGAAAGTTGCAAAAAA +AAATTATTAAAAGAATTTAAGCACGATATCAAAATGCTTGAACCATCTGA +AATGTTGCAGGATGAAATACCTTCAGTTTCAAAAAAAACATCTGAATGGG +ATAAGATTTCAGTGCTAGCAGAAAATTCGAACGCCATAATCCCTATGCAT +TCTACACCTTCGCATACTAACAAAACAATTAAATATTTTAAAATAGTAAC +CCCCACTAAAACAAACCGGGTTAGTATAAAAAACGTATCTACAATCAAAA +CAAATTTTGATGCAAATAAATACATATTTATGAATCACTCTATCGCTAAC +CTATCGAAATACTATATGAAGGAACCAATTTCGATTGGTTCAGACAAATT +ATTTACATCCTCAAGGATAAGCAACCAGTCACAAGTAATTGACAAAAGTA +ATGTTACAACTTTAAGTGACGTGCCTCAAAGATTAAAGACTTCAGACTAT +CTAGCGAACGAATCTTTTACAGAAAACATTTTAGGGTTTTCCAAGCACTC +AGGGCTCAGAAGCAAATCAAGCTTAGGTTCTAATCGAGATGAGCATGTGT +ATGCTTCCAGCGACATAGATAGTATGCTCTTTGGTGCTATTGTTGCTGAT +TCATTTTTAAAGACAAATTATGCAAAAAAAAACAAATCTTTTAATGGTTG +CCATCCGCCGTGCAGATTGAACAAAAATGAATTATGCGTTACTTATGCTA +ATAATACCGAGTCCTCGAGTCTTTGTGAATGCCGACCAAGTTTTGGACGC +ATGTTTCCCGACCGACCTTGCAGACGTACGTATTACTGTTATATTTTTCT +TACAAACTACATCCCTTTATGTTTATTTTAGCTACTTATACTTACGAAAT +GAAGATTCAAGTCAACTGGGCGGGCAACCACTCTATAAAGCTTGGCGATA +TCATGAAAAGTAATTTGAAAAATGAAACTTCTTATATAAATACAATTTTA +TTAGAAGCAGCTGATCGCATGGTTATGCAATCTGATTATAGAGATATTTT +TCATGGTGTTCAGTTACGAAAAGTTTTTGTAGAAGAAAAAGATAAGTTAA +CGGTTACGTTCCTGCTACAGGTAAGCATTCAATGAAAGCTAATATTAAAT +TAAAAATTCTGGAAAAAAATAATATATATATACGCAGTTGTCAGAGAATA +GTGATGAGGATCAACTTAATTCCGTCTTTCAAAAGTATTTACGGCAAAGC +AACTTCAGTATTGGAGGCACTGGATTTTACACTTCAAAAAACAGTCTACA +CTTACTAGAATTTAAAGGTTTTTATTTTAAATGCTTAAGGTTATTCTCTT +AAAATGTTATCATTTTAATCGTTTTAGATTTTGACGAATGTCGTTACGAA +AACTTTAACGACTGTTCTACTGATGCCAACTGTTTTAATTTGGTTGGCAG +CTACACTTGCAGTTGCAAAGAGGGTTACACAGATTCATCTAATAATTATT +TATACCCAGGTCGACATTGCTCAAATAATATAATCGGCTGCGATGATTGT +AACTATAATGGCAAATGTATGAATAAGTCGGATGACCACGGGCATCAGGG +GATAACCTTATGTAAATGCTTTTCTTGGTACGCTGGAACAAAGTGTCAAG +TTAACATGAAGGTCATAATAGTCTTTCTTTTTATGAGTGGAACCTTTTTG +TCCTTTTTTCTTCTTTTATTCTTCCTTAAAACAAACACCAAGCTTAAAAG +GCTAGACAACGGAAAAGCAAGCAAATTATGCACTGCGCCTTCCAATATAA +ATCCTAGTTTATTAACATCAACCGAAATAATTCGACCAACTTACAGTAAA +AAAGAATCTATCAGTAAATTAGGTCAATGCATGACTTCCAATTCTAAAGA +GGCAAGTAAGAGAAGAAAATTGGGATTAATAATAAATATTTATATTTTCT +TTTATAGAAATATATTGGTGTGCATAATACTTATTTTAAACCTGCAGAAC +TTAAAGAAAGGTTGACACATAGTTACAAGGCTTCTTCATCCTCTTACTTG +AGCAATGATTTTAATATCAAGAGTACAACTAAAGAACACGGTTTTTTGCA +TAGTAGTGAAGACCATAGCCCAGAAGAAGACCAAACAGAGCGATCTCTTA +CCCTTATGATTCCAAGGGCAAAATATTGTTTACCCTACATTGCTCAAAAC +TCTCATTTACCTCATCACGCTAATAAATCATTTATGGATAATACAGAGCA +AAGGGCAGTACATACAGATGATGGTAATACAAACATATGCCGAACTTTTG +CTTTTAATTGTCTTAACAATTTTACATTGCCAGAAAATATATTCTACAGA +GGCACCAACAGACCCAGAACTGATCTTGTATCTGCTGGCTTCCAGGTATC +TGTCCTTGTTAGTGAGAAAAATGTATTGGAAATTCCCATGTAAGTAACAT +ACTTATTATTTTCAGCATATAGTAGGAGAGGGATGGAGATATGATTCCTT +GCGGCACCAAGCGCCGCATAAAGCACAAACTGGTAGCGCCCTTAGCGGCT +AGtgcgcagaaatttctgttttttcgacacatcatttttaccatgaaata +atgtcagattggtacccaaaaatgtaattttctcgaattctctctttgcg +aatatttcttgacatcgaaaatgagaggacatattattacatgagtggaa +gcgcaatTCGAaaggtcccaggttcaagtacgcttcaaggcagagtatgc +tttaagtatttaagaataatatctaacatgtccttataatggtaataaca +atgatgcatttaaatgctgcatttaaatgtcagatttcaataaaaacaag +aaaggacaagacgaagtttgtatatccttgcagttataagaaacatcatg +tgaaatttttaaggattgttgctgacttcagtgataataaaaaaaataat +tatttaatgtttttttcgaccattttttgagatctaagtctagactagtc +cgatttttattaaattgaattcgaaattcagaaccaattaaaaaatgtta +tttccaaacttagaaggttatatgttaaaaaacacagtcgatatgatata +gtctttttaataaaatttaattcgaaattcagaactaattacaaaatatt +atttataagaaggttatatgttaaaaaacattgaagataaaagtttttcc +tattatattatcactaatttttcgatagttactatggcagctatatgata +tagtcgtccgattttaataaaatttaattcgaagtttagaactaattaaa +aaatgttgtttctaagcttagaaggttatatgtttaaaaacaccaaagat +ataaatttttcatattatttcacgactaattttccgatcgttcctatgac +agctatatgataagtagtccgattttgataaaatttagttcgaaattcag +cactaattaaaaaatgttatttctgagaaggttatatgttaaaaaacacc +aaagataaaattttgttttcattttgtccccgatagttcctatgggagct +ataagatatagttgtccaattcggttgcttccgacttatatactaccagc +aatagaaagaagtcttttgggaaagtttcagcccgatagtcttagaactg +agagactagtttgcgtagaaacggacagacagacggacgaacagacggac +ggacggacatggctagatcgactcgtctagtgacgctgatcaagaataga +gttaccttatggggtcagaaacgcttccttctacctgttacatacatact +ttccaaagaatttagtatacccttttactctacgagtaacgggtataAAT +ACAAATTACGTTAAAAATTGGACATGCAGGTTCTAAATAAAAAATTaacg +gtatagtcgagttccccgactgtcagatatcctttactcagcataaggaa +gcaaaagggaaatgtagatatataagcagcaaggcgatattgtaaagtca +cctactagctatttcagtatatgttatgtgtgcggcaaacatattacaag +tttttgacttttgtggaagtggcacattttttttaggtcaatcaataggt +attaatgagacaaatacacttcagttatttttttctagcactaaaactgt +agacgccatagtctttcgcgAGACCTGGTACCCTGCTAAAACAAACTTGC +GGTGCGTTCATacggtcagaagaacatagctagatcgactcggcagtgat +cctgattaagaatatatacactttatggggtcggaaaacgcttttttcta +ccttctacatactttcggacgaatatagtatatccttttattctacgagt +aacgggtTAACAAGAGAGagacgagtgtctcgactattaaaaaccagttt +ctcagcttTTAAATTAAAAATTTATAAAACTTAACTAATTGTTAAGATGG +Ccgttttaaaatcgtattaagcacatgagtttcgacatatgtacgagagt +tagtctgattataagggaaaacaaaaaaatttacagcactgtaaagatta +cgttcacggtcctttacctgcaatcttgtgctattcaacactgggtaaac +gatcttctgtctctatttttctcatgtgaaaggactacgggtcagaatat +agagaagggtGGGGTACAGCGAATTCACGAATTCGTGTGTTCAATTATCT +ATTTGTACGTATTACCAtccgtctatacttctgtctgcttctctgtaaac +aagtcactcagttttaaagctatcCAGACAAAATCATTTTTTAGGCATTA +AACATGGACACATGCTTATTAGGCAGTTCCTAGTACTTCCTAGTACTTAT +TAAGCACTTGAAATAACTTAAAAGGAAATCCTAACTGAAAACGAAAAATG +TTTGTCAAAAGGCAGTGTACGTAACGGATGTTTGCAAGCTCAACCAAAAT +CTTACTTGTGAAAACTACTTTTTATATTATCGTTTACAAGATAATCTTAA +ATTTCTTTATTAAATAGATTAGATGAGATAACATTTAATGAGTACGCCCA +TAAACGAAGCCCATTAAATAAGGTAATTCAGAAATATAAAAGAGTAAATT +GCGACTCAATTAAATACTTTATAAAAAAAAGGATGATAATACAAAGATGA +GTGAAAGAGATATGGATTCAACTTTCTTGTTGCCACATACACATCTTTAT +AAGCCTGACGAGGTAATAACACTCTTATAA +>CG31997-RB +ATGGGTTTCCATTTTCATTTTGATATTTTGCTCCTCATTTTACTCTTAAC +TCTAATAGCTCCTTTTTGTATTGCGGCTGAACAAAAAGTGTTGAAAGATG +AAACTGCCAATGTTGGTGAAATACGAATTTTTAAACGCCTTATTCCTGCT +GATGTTCTGAGAGGTACGTAGTAAACAAATTATTTTGCTACTTACACACG +ATAGATGTATTGAATAATTTCAATAGTATTCTACAGGTAAAAATGTTATT +TGAATTAAGCGAACAAGATTTTACATTGAAAAATGTACATGTGTAATAAA +ATATTTCATATTGCCTATTAATCCCTTTCTGACACACATAAATGCATAAT +GCAAAAATCCATCCGTCCCATCTATTCGATGAGTCATCCTTAAACAGCTT +ATCAAGGCTTAATTATGAATGATTTTTATAGAAAAATTGTAACGGAGATA +GTGACTAAAAATAGTTAGCCTGTAACTTTAATTTTTTAGTTTACGATCTT +TTTATTATTAAATCATTTCATTCATTTTAAAGTAAACTATTATGAGTTGA +GTTTGTTAATTGGTTAAAAGCAACTTAGCCCTTCTTTATTTTTACTTTGT +CCATTTTAGGTGCAGTTTATAACAACGTTTTTTTAAGCCTTgtacttaaa +tcttttaacagtttgactagttatcctattctctgtagtgtgacagatag +tatcagaatttattGTTAATGCCCAAAGCAAGACAAATAGAAAACAAGGG +AATTTGAGATATTCCAAAAAAGATCTTGTGGTATAATGAAGTTAAATTTA +AAATAACAAAGTTGTTCATAATAACACAGAAACATCGACGACTTCTTCTC +CACCTTACCAGCATCTTCCGGACGCATGCTATTTAACTGCGCATACCAAT +ATGACAACAAGAGTAGGTTAGGGAAAGGGGTTGTTCCGCTGATGCTGTAG +GAAGTCCGGTCAGCATACTTTACATGACCATGCTGACAATAAACAATGAA +AATGCTCCAAGAAGAATGAAGTTAGCTCCCGGTATAGTGTGACCCCTAGA +CCAGAAAAAAGACTTAACCATTTTATAGGATTCTTTTTCGTAATGTTTTA +AGAAAATTTTGTATAGCATCTCCGTGTTTTGTCGGaagtatatatattct +tgataaagattactagccgagtagaactagccatgtttgtATAGTTTCCA +AGACGTCTGCGTTCTGCTAGATTTTTTTTATAGCTGTGTTGGCTAGTGAT +CCTGATAAAGAATACTTTTTCTACGAGTAACGAGTGTAAAAATTATAAAA +ACCCAACCACCCAAGAAAATATCTGCCTTCGCCACTCTTTTTAATATCCT +TGTGACAGTTCAAAAAATATAAGAACATTAAAAAAGTCACAAAACTTTTT +TTTTAGATTTTCCGGCGATGTGCTTTGCTTCCACTCGATGCGCTACTGTT +GAACCAGGGAAGACTTGGGACTTAACTCCGTTCTGCGGTCGTTCTACTTG +CGTGCAAAATGAGGAAAATGAAACAAAGTAAAGTATTAACAAAATTTATA +TTTTGTTACTGTAACGATTATAAATTAATTTCAATAGAAAATAATATTAC +ATTTGTTCTTAGGCTTTTGGAACTAGTAGAAGACTGTGGCCCATTGCCAC +TGGCAAACGACAAATGTAAGTTGGACACTGAGAAGACAAATAAAACGGCT +TCGTTTCCTTACTGCTGCCCCATCTTCACATGTGAGCCTGGCGTTGCATT +GGAATATCCTGAGGTTGGAAAGGAAAATGACAAAAAGAATGTTGAGTGA +>Arl4-RA +ATGGGGGCAACCATGGTAAAACCTCTGGTAAAAAACGGAAATTTTTTAGA +CGCATTGCCTTCTCAGGTATTTTAACTACTGTTTCCAAACTATAATATAA +CAAATACTGTTTTTTTAAGGCAACCCTCCATGTAGTAATGTTAGGCTTGG +ACTCTGCGGGGAAAACCACTGCATTATACAGACTTAAGTTCGATCAGTAT +TTAAACACGGTGCCGACTATTGGTTTTAATTGCGAAAAAGTTTGTGACTA +TGAAATCGTTGACTAAACACAAATATACAAAAATCTTATATTTCTTAGGT +TCAAGGTACTATTGGTAAGGCTAAAGGAGTTCATTTTCTTGTTTGGGATG +TTGGAGGTCAAGAAAAACTAAGACCTCTTTGGAGAAGCTATACACGGTAT +TATAAAAACATTATTCAAAATCTTGTTACATATGTATCCTTAAATTGGTT +TTAGCTGCACCGATGGAATTTTGTTTGTTATCGATTCGGTCGATACGGAA +CGAATGGAAGAAGCAAAAATGGAGTTGATGCGTACCGCTAAATGTCCTGA +TAATCAGGTAAGTAAAAACAGAAGCTCACTGCTTAAATGATGTACAGCGT +TCTTTAAACTTTGACGCTGTTTAGCAGTGTATTTAAAGGGAATAATTAAA +ATACCAAGTTATCAAATGAAAAATAAAAGTGTCTAGAACAAGATTTACCT +CTTATTGACATTCAAAGTCCATAACCGACTAGGTTAAACATCAAAAAACG +GGAAACTAGAATAAAATATACCTTTTTAATATTACCCAGAATATGCGTGA +GGCATCCTAGTAATCAAATAGTACATAGTCATCTCAAGGTAGAGCgaggg +agatggatatatgcaataattgatcacccgcaacgacggcgaacttgctt +ttaaacttttaatggatggtccgatttggaccattGCATTGACTCTTTTA +GTAATTCTCTAAAAGTGTTTTCGCAAGCAGCGTTTGTTTTCAGCGTTGTC +GTTTATGGgcgtcagagtgggcgtgggattctgaaataaactggcgatgt +cccaaaacctcaagaatctgcatgcaaatcccaacgatcttacttacaga +tgtatagattccgatatctttgcgttcgtacggacagagatagatagatc +gactcggcttatgttgctgaatactttattaggtcggtaacgctATTTCT +TAAGATGCGAGCGACTGTATATATGTAGTTGTAAAGCATACAGATAAATA +TTATAAGAAGTCTGGGTAGAGATAGGATAACCCATCGGCGACCTATCGAT +TGGCGTTCTACATAAAGGTTAGGTGTTTGTCAATGGGTTAGGCGTTACAA +ACACATTAATACCTATCTTTTCAGTTTCAGTTTTCAACATAACTCGCAAA +TAAATGTTAACCGATTCGTGCGGTCTCAAAATAAGAATTCGTCACTGAGG +CTTTGAGTAAAAAGTCCAAGAGTAACCGATTGAATTGCTCGTATACAAAT +TTGGCTCGCGCTCAGCCGAAGAACAGTTTTTCTGTTTTCACTTGGTCTGC +TCATTCTCGGACCGTTTGCTCGCGATCGATTCAAAAGTCTTTTGCGTAGT +ATGTGTGTACATATGTGAAGTTTCGTGGGTTCTACGCGTGCATCTGGCTT +GTAAAAATTGACTATTCATTTTTTAATAAAAATAATTAATATATAAGTTA +GAAATTTGAAAAATTCACTTCAGAAAAATTTCAAGAAATTTTTTTTTTTT +TAAATTGCATGTACATTTGTTCAGCAAATGGGATGTCCGTTTTTCGCTCG +TGACATTTCATGACAATTTTTCGATGACAGCCATGTTACCACGCATGTCT +TATCCCTTCCTTATCACACGTGGCAAAAAATTTAAAAATATGTCCTTTGA +TATGTCACCTAAGAAAGTATAGAATATTTCGTCATCGCGACACCTGAGTC +ATGGGTGATTTCTTCTATGACTTTATACCATTGCGGACGGTATAaaaatg +caattggaagtttgcaacgaaggaaatgtttccgaccccataaagtatat +atattcttgatcagcgtcactagacgagtcgatctagcccgtctgtccgt +ccgtctgtctgtccgttactacgcaaagtagtctctcagttatgaagata +tcgggctgaaactttcccaaaagtcttctttctattgcaggttccatatg +aactatcggggaaaaaattaaaaaattatatctttggtgttttttaacat +ataaacttctaagctaggaattaacattttttaaatagttctgaatttta +aattaaattatataaaaaatcggacgactatatcatatagccgccatatg +aacgatcggaaaattagtggtaaaataaaatgaaaaaattaaatcttcgt +ggttttttaacatacaaccttctaagattagaaataacatttttaaatta +gtcctgaatctcgaattcaattttatcaaaacttagtaacaattggaaaa +ttagtgttaaaataatatgaaatattatatcttcggtttttttaacattt +aatcttctaagctaggaaataaaattttttaattagttctgaatttcgaa +ttaaattttgtcaaaatcggaagactatatcatatagctgtcataggaac +gataggaaaaatggtggcaaaataatatataacaaattgtagctttagtg +ctttttgacaaataaccttcttagcttggaaataacattttttaattagt +tctgaatttacaaacttcggcaagggtatacaaacttcggcttgctgaag +ttaacttcctttcttgttttgttaGTTTATTATCGACGATCTCATACATC +TGTCTGAGTCTTGCAAATCTTTGGTCAATGCTTCGGCTGAAGCAGGCATA +CACCCCTAACGAAAAGTTATAAAGCGAAAGAAAGTGACTTTATACGTAAT +TAAAAGACTACAATCAAATGTGATTGTGTTTTCGCTTTGTCGTTCTACTC +TATTCTTGAGTTTACCGCAAGCCTCTCTAGTGTGTTGTTGTTGGTCGTAA +CTGCGGTATTATCTTTTTTACTGCAAACATTCGCACGTACGAAAAGCTTA +TCGCTGACCAAACTGCACGCTGCGTTTTCTACATCTACTCTGTTTATCTA +CGCGTATATAACTGACGCTTATAACAACAACATACTACATACTGCCTGCT +GCATCAAAGCAAGCCTTTTAAATGGCAAAATCACAGCCCACAATTTGTTG +CTGGATTTATGACAAATATTTAGGATTAGGATTTTAGGATCTATCTGATT +GGTTTGTAAAGGCTGAATCTAATTTTAAAGGTAGAATTCTGCGGTCAGAG +GCAGCTGGCGGGCTCAGTGCCGATGCTACTTTGGAACTGTTGCTGCCAAT +TCTACGTCGTGCGCTGCTGCTCTTGGCTCCCCTTATGATCCAACACTTGG +GTCATCACGTTTAACACTCAGCTACAGAACCAGTGCAGTTCAGttatgtc +cccgtctcagcatggctttttgaaactgagttcaacgtctacgaatctct +tggaatttacttcaatcatcagaaactcttttaaaaacaattatccaact +gatgtaatttttacagacttcagtaaggcttgcgactccgtgaactatcg +gttattATTGAAAAACTTAATCTTATACTTTTCTAATCACGTTGATTAAG +TGGATTTTGACATATTTATCGAACCGGACTCAGAGAGTAGCTTTTAAAAG +CTCAACCTCTAACATTGTCCATATCCATGtcgtgtgtttggtcacctcaa +tatgcaaagtatcagaaccttgtcgcatcggtatagaaacagttcctttt +gtttgcactacgtggttaaaactgggaaacccaacgtaacctaccatctt +acgcggacagactgcggcttctgaacctgccctccctcaaggatcgtcgg +acCTTCCACGGCGTAATGTTCCTTTAGAAACTAATCACTGATCTTGTAAA +TTCAAGCTACCTTCTCGGTCAAATACAGTTGTCCATTTCTGTAAGTCACT +TTCGACGTATCACCTTAAATATTTGTGAAACGAATTTTTATTTACATGAT +CCATTTGTAGTATAATGAAATGTACTATTTAATATTCACTGAATGCTCTG +TATATCTGAATGTAAAAAACATCCCAACCCACCTGTCTATACCCCCGCCC +ACTTAATGTGAGACGGGTACTTTGTTTATGTTGGCAGATATTTGATGACT +TCAATAAAATAAATGAAATGAAAAAAAATTTTGAGTGCCAATTTAATAAG +TGAGCATGATAATGACAATACATACACATAGGATCAATTTTGCGGGATGT +GAAAACAAGAAGATTGTAAATATTATTAAAAGATTCAGTATGAGTGTGTT +TAAAATCAGGTGAGTAGTTTTCATATAATTATTCTAATCTTATAGGAATC +AATATATTTGTGTTTTAATGCAATTCTCAAAAACCGCACGTACATACATT +TGTATATATATTTAGAATGCAGTTGGTGGTTACATTTACGCAGGAATGTG +TATCTTGTGTTACTGCGGTCTTACATACAGGGGTGGTCAAAAGTATTTTT +TATTtgcaaaaaaatattttcaaagatcatttttcttatattttttatga +ttttttgaaggtaacaatgtcggaaaaatacgtatttgtaaacattttca +aaaaatcaaaacaaatataatcaacattttttttttaaatcctttttcaa +gttttattattattgttttttaagaaacttttttcatctaaaaattttag +ttttcaagacaaggaaaAAAGTTTaaaaagtagattttcacaaaaattcg +ctcttttcaataaatatcaaatgagttaagaaaagaatagtatcattcaa +acggcatttaaattaattcaattgataccaaatgttaaacgaatcatgtt +caagtttcgagtatattttcttatgtaggcatattagtgcctgagtcctg +aaaaggacttgggccgagggagaggcgtccgatgttcaggcaccattttt +gcaggcataagctacgtcgtattcgggtcgtgggatcttggtaagcctct +ctcctctccaacataacaaaaataaatatttaaagtgcctaaaaaaataa +tattagagcgtaaaggtcgtcagtcgttagtccacacatattaataacag +cctataaaaaaaaactttttagactgcacgaataAAAAAAAGAaaaagac +tgctgctgttaagaataccaattcacttaaacacaaaaaatatatatatg +cctgaggcacgcgtcgtccgtaacgctggtagtgagactcgttttcgcta +attgtttatcaggatcagcactaccgattcacttgatttaaatgtatttc +aatgcatttttgaatgcttcccatgtttttttattttatttgctttgccc +accactttttcgacatatgctgtcggtcactaagcctctgatcgtatgag +aatttcgagtactgcggctacaagcatcccagtatgtcgaatgtcgtcct +tgcggttgatattggctccttttttgattataatgggggcggtggtccga +cacatgaaaatcttttgagctataggtatcctccttaagggctgctggac +cctggtggctgatcctggaggataggactccggggacgactgccctggaa +aggtcgcctttccttggagccggcggcttccgtcagcaagaccccagaat +gggttctctcccattttctaattgtcttttataccctagtacagctttta +cttagctgccagtttggagcggataaagtaggtgttcccacctagggtta +ctatatctcggtatccaatatctttggagtcaacgggtggctgttgcact +ttgccagctaccggaatatggttaccagtaggtcgatcgtggccgttgtt +ctagccacgcgacaccagtgaAAATACTTTTGACCACCCTTGTATACACT +GCACATATAAATGTATATAATATGTAAGCACTGACGATGACATCGCTTGT +TATTTTGTAATTCATTTTTTTTATTCAAGTTTTTTGTTTGTGGACACAAC +GGATTTGGACGAAAATGCGGATTTGAGTAAGTAGATATTACAAATTATAT +AATAATATTAAAAAAAATAGTACTAAGACGTCTTTCTTTCAGACTCCAAG +GATTGTCTAAGCTTAGAGCAAATATTATTACTTTAATTTAATAAAGATCC +TTTTATCAAATAAAAATTGAAAACAAATGTGTTTTTTTCATTTTTGGTCG +TAAGATTAAAAATATATTCGTGTCATGTTGATACTAAAGTCCTATCAATT +TGACCCAAAAAACGACCTTCTTATACCCCGAATCCGTTTTAAATTACTGC +TAAATAGTGTCCATATGACCACATATTCTTACTAAAAATGCCAATACGTG +GTTTTTTTTTGTCACCAAAAGGGTCAAAAAGATATTTTGGAAAAAATATG +AAAATGACACTAAAATTGTGTGAATTAGATGTTCTTCGTATCAGATATTT +TTTGACACTTTTTTGAGTGCTGAAATGTgtacattgttaaatgttgtata +tagaaattttatttataatttagagttacctctataattgtttgcttcca +cattgctaccctttttgtgtagaggaattataaacgatttcttccacata +ttgggaaattgtgaagattcttaagataaggtaaataatttaaggggctt +gagaatAAGGCTATGATAAATTAGTTAGAACAAACCGAAAGAATTTAACT +TTAAAACGATTTAAATTTTGTATAACAAAGAGTTATGCACGGCAAAACTA +GACCGAGCACAAGATTGAGAACCAGTATCCCTTTCAATGAGTGTAAACTC +TTTATTTATTATTTGAGACTGACAGATAGTAAAAGGGAACAGAAGAATTG +GAGAACGAACTTACTATAGAAAATATTTTTTGCATCATTCTTATTTCTGG +ATCTCGAGTGCAGGATGATATGGACCTTTGGGTTGAGTAAGAGGTGCTTC +TTTCGACACAAACACGCAGTCCGAAATAGTTACAAAAAACAGGTCTAGTA +AACGGCAAAGTTTTATTCCAATAACTTTAAATTTGAGGGACTAAATAAat +aaagtatatatatccttgattagcatcactagacgagtcgatttagacat +gtctgccgtccgcctgtatgccgtttctacgcaaactaatctctaagttt +taaagctattgggctgaaactttacttcttttgcaagtagtatataaTAc +ataagaataatcggaaaaaaacaattttaaaaaattataacttttgtgtt +atttaacatgtaaccccataggcttggaaataacattttttaattagttc +tgaatgtcgaattttattttatcaaaatcggacgactatatcatatagtt +gccacagagacgatcagaaaatctgtgggaaaataacataaaatgaatta +aagcttcggtgttctcgacatattatcctatactattgggaatatcattt +tttgtatttttaagaatttagaatttaatttgttacaaataggaccactc +caacgtgtagctgtcaaagaaacgatcagacaaacaatgaaataattaat +aaatttttttttttatattactgaagctgacaacaatactttaaaacgta +atatggtgttactttcattaatcataactgctagggtatacaaacttcgg +attgctgaagattactttcttttttgGAATAGTTATAATTTTTTAAAATT +GGAAAAAACAGCGTATGCTTGATTAATACTTTAAAacctcttctttcaaa +atacctttttttgacgacacctattatttaatttcttaaaaataaaaaca +agttaaattaaaaaaaAACATAGGTTTTGAGCCAAATcttcctacctctg +gaaatagggctaggcactttctctactagcagcttactgtatctcatcct +cagctctgtagctcatcctcagcacagttcttatatcgcctGACGGCACC +GTAATAACAACAGTTATCCTTGTCGCGACACGGTCGTCCTGTCATAAAAG +CGTTCCAGCCACGGCGGTACCCAGAAGGGTCCACTTTGGTTAGACATAAA +CAATGTGTTTGCTGAAAAGCAAATATAACGGttattactttgacgtttta +taacatagatttactcttgaaaatatcaatattataatatttcagaattt +cgaaaacaaattttcaaaaatcggacgacattgtgttatagctgtcatCA +TAACAAACGCATAATAAGATTAAAAATAATATAAATCCCGTTTTTTCCTT +TACATGTACTTTAATAAATTAAAAtgtaattagtttttagttttctaaaa +atcggaaagctcttgacctacaatgctctcaatgagaacaaAGCCGAATT +TAGTTTCTCGGTATTTGGTTAAGTACACGACAACCTTAATTATTTTATAA +AAAGGTTTTCAAAAAATGTGCATCCTATAATCTCTTTCAGGAAGCAGAGG +GAGCTGCAAGGCGGAGATAGAGATGGAAATATTTGGAAATAAAAAGGGTT +GACATAAGCAAGCACAAAAAGTTTTTTTCCTACGAAGGCATTTTTAATTC +ATTAAATTATTATTTATGCCTTATTATATAACAGCTTCTTTCGCAGCGCA +AGTTTGGATGCCATGAACATTAACTTTAAACTGGGCACGTTTGGATTAGT +GGTCGGACAGACAGACGCCTCATAGTCACCAAAGTGTTAAAAAATTACAC +AAAATACTTAATGCTGTTTTTAATATAATGGGCGAAATTAAACGGTTACA +TTATAATTGTTGAAGATATATATTTTCTAAATTTCACCTAAATTGGTTTG +GGTGCAATTTGCGATATAACTGAAACACAGATTTACCAATCAAATTTTTT +ATGAAAACGTCTTTTAAAAAACGTATCCATTTAAAATATTTTTGATTGCT +CTGTAATAAGTTAAAAGATTAGTCTTTGTTTTTGCAAAAGAGATTATCGG +TTAATAAAAGCGTTTGGTGTCTAGATTAATAAAAAATCGTTTTTGGAACA +GTTTGTTATAAATTGGGAAGCGTCAATAAATCTCGGCAATGTTTGCATTT +ATAAAAATCTAATTAAAGGAATATAAATAGTGTCTATCAATGCATTTGGT +GACTTTGATGATAGATGTATAtatatatatttagtagatcgtgtattcgt +cacagaaaattatatcagagcttttgtttgttcgaaagtgcgatcgtcac +tatatttacttcattattcctgtttgatttcagaactttttgttttatat +ttaaacaaatcatgttaaaaaggcattcacatttcaaaatacctttctaa +acacatgtagctgtaacagttcgttgttactggtgtacaaaatgtagctt +tttatacctgttttcacgccaaactatgaagttttccccaaagtgctaga +agtaaagtttcttctattaagctatttaagatgatctaaaatttttagTT +TCTTCAAGTAGGGTGTAagtgtcagatgatctgaactggtaaatgttaat +attttcgttgttaattatttagaaatggttttttatacaagaacgtgtcg +tatgtcataagttgaggaatctcaagggctctgcacttcaaaattaaagg +tgaaatcgttagagccgttttgagaaatcagaaaaaagacaaaaaaatat +atatataaaaaaaagcgttgaaccataattttaaacggtggtattaggac +aaatcgtgtttaaaaggcgtacatagtatttcgaaatacctttctaagaa +cgtataTATATATATATATATAAATATATATATATATATAtatattgagc +tgtttaacatcgtctagaattttcaaaactctaaaataaccttttgggac +aaactgacaagtaaaataaaattttaattttcagaggaccgcgaaaatct +tattttgcgtattacttttgacaaagcacccgcttttgaggtgtcattcg +gcgcgtattttaattgagaaaacaactaggtggatagccgggggtaattg +tccccaccagccccaaaagaccaaatttcaagtttaaccttttaccactt +ttgtcgaaaccaataaaattttttaaaagtcttggtatgcaattctttta +gcttttgcaatacattccgatttaggtatgactcgaaacaatcggattac +tctaaatttttatttctTCCCCAAAggtgcgcgtcgtcactacgtggact +gccgtccatagtgataTTCATAAACATACGGCTAAATTGAGTGGGCGGTT +CAGTCTTTTATGTACATACATATAAAGAAAGTAAACCACTAAAACGAAGT +TAATATAAAATAAAAACTATAACAAAACGAAATGCTTTATTTTTTATGTT +TTTCAAAGGGTGTTCCAGTGCTGATATTAGCAAATAAGCAAGATCTTCCA +AACGCGTGTGGTGCAATGGAGCTGGAAAAACTTTTAGGACTGAACGAGCT +TTATAACCCAGTGCCGAACATATCGATGCTAACTTGTTCCGACTCTTCTT +CCACCATCAATTTAATCGGATGTAGCAAGTCAAACCAAAGTATTACAGAA +ACCTCGTTAACAGAGCAAAGATCAAATCACCTGCATTCATCAATGATTCA +CATTAAACCTGCTCCTGAAAGTGACGAACAAAGGACTACGTTAAGTGGAG +AGGCGTTGTCTACATTCATATATCCGCATTCTGGCAAAGGTTCTGATGTG +AAGGACCAAAAAAATTCGCGTGATGGTAAAAACTGTTTTCATAACAAAAA +ACATAACAGGACCTTTTCCAACTCGATGCACTTTAGGGGGTGGTATATAC +AACCGACCTGTGCGATAACTGGCGAGGGACTTCAAGAAGGCCTAGAAGCT +CTTTATGATATGATATTGAAACGCCGGAAACTTAATAAATCTCATAAGAA +AAAACTGTAG +>CG2316-RA +ATGAGTGTCCTATCCAAATATGTTGACTGTTTTGCAGAAAAATGTGAACA +TAATGGGCTAACAAAACACGTTTTCAGCTATGCTCTTGTGACTAGTGCTA +TATTGGCACTTACTATCAAGGTGACTATCCCCTACGCGAAGAAAGGAATA +ACTCAAAATGGAAAACCCAAAGTCCACAATGGGACACTTACACCATTGGA +AGCAGATATTTCAGAGGAGGATTTAAAGCTAGCGGAGGCCGAAAAGTTGT +TAGTTGCTCAGCAGCAAAAAAAAAAATCAAATGATTTTGTTGAGCCAGGA +CTAAACCAAGAATTTTTGAAACAACTGAAAATGCTTTCAAAAATAATGAT +CCCACAGACCTTATGTTACGAAACTGGATTGCTGGCTGTTCATACATTTT +GCCTAATTTCTCGCACATTTCTTAGTATTTATGTGGCTGCTTTGGAGGGA +GCCCTTGTAAAATTCATAGTACGAAAAGACGTTAAACAATTTGCTCTTGT +ATTACTGAAATGGTTCGGGATTGCTATCCCTGCTACGTTTGTTAATTCCA +TGATACGGTTTCTTGAAAGTAAACTTGCTCTGGCTTTTCGGTAAATAACA +TATTTGAAACCTTAAGAAAGTATATACATAATTTTACTCTTTTATGTAGA +ACTCGACTGGTACGTCACTCATATCGTCTTTACTTTAAAAACCAAAATTA +TTATAGAGTATCGAATTTGGATGGACGCATTGAAAATGCGGATCACAGGT +AAGTTTTAAGGTTGCAACCTTTACATCCATCAGCTAATTAATTATTTAAA +AATGTATTTCTCTTATAGACTTACCGAAGATATTTCCGTGTTCGCTAGCT +CTGTAGCTCATTTGTATAGTAGCCTGACAAAACCATGTTTCGATCTAATG +CTTATTGGCTTGGCATTGATGAGATCCTCTAGAAAAATGAAAGCTAACAT +TATAACCGGTTAATTCGTATTTAATGAGTATGTATCATGCATAACTGAAT +ATTTTTTCCAACACGCAGGACCGGCTTTATCTGTTGGTGTTATTGCTCTA +ACAGCCCATATATTACGAATCGTGTCACCGAAGTTTGGACAGTTGGTATC +GGAAGAAGCCAATAGGTATGGCTACTTGAGGCACATTCACTCCCGCATAA +TAACTAATGCAGAAGAAATCGCCTTTTACGGTGGTCACAAAGTGAGTTTA +TCGTTTGTATTTAAAGTTTGCACCTTTGCACATTTGGAACATTTAGCATA +AGTTTTATGTAGAATACTATACAAGACTGTTTTTAACGTCACCTTTTACT +TTCTTATAAGACCGATTGGGAAGGCGCATGTATTTGGTGTTAAAGAAAGC +TCTTGTAAAGAGAAATAAGCGAAAAAGTCAAGCAATGACAGACACCAAGC +TGATTCAAAAGTAAAATTGGTTTTAATGTgttaatatatcttatacaaaa +acaagaagacaaagaataaatcttacatcagtaagccgaagtttctatac +ttttgccggtcttaggatggttgtaagtttccgatttttagaaaactaaa +aCGTCCCATTTCAATTaactatcgtatcaaacaaaaacacctcttaacga +ggcaacaataaaatgacgaccttcaacaataaaaagtcctgatatcaaat +tttgtgtcgaaaatgtgttatacaacctactaaataaatacattttctTT +ATTTTTTTACATTCCAAAATTGTTTTTAACTTACTaactggtagaactaa +tgtttcttacatttagatgttggatattatatgaaacttccaggaccttc +taataTATAGTTTGGAATCgcttttccagcagatgtaatgtgggcggcag +gcaaaattaagcgttttaacaatccgtgggcgttagagtgggcgtggcaa +acttttgtaagcagcaaagcagtattttagggcgccacctactggccact +tcagtcgatgttatgtgggcggcagacagttttaaccgattgtgggcgtg +gcacattttttttaagtcaatcgataggtattgatgagacacacatttca +gttaaaattttgtttctatcataaaaactgtaggcgctacagattttcgc +ggattgtgggcgttagagttggcgtggcaccccgctgaaagcccaggaat +ctgcatgccaagcttgactgttccagcacttatagtttccgagatctcaa +cgttcatacggacagacagacgatcaactcggctagtattcctgatcatg +aatatatatactttatggggtcgaaaacgcttctttctacctgttacata +ctttccgacgaatttataatacccttttactctacgagtaacgggtataa +aaacattgtaccataatttttaaacggtaggaattagacaaatcgtgttt +aaaaggcgtacatagtatttggaaatacatttctaacgacgcacagcaca +agcttcagtactacacattttacgggtatacaatgttgcaattttagctg +tttctcgccaaactagtcattccaaaagtaataaaactaatgtttcttat +attaagatgtttaacatcgtctaaaattttcNNNNNNNNNNNNNNNNNNN +Ngaaaattttagacgatgttaaacatcttaatataagaaacattagtttt +attacttttggaatgactagtttggcgagaaacagctaaaattgcaacat +tgtatacccgtaaaatgtgtagtactgaagcttgtgctgtgcgtcgttag +aaatgtatttccaaatactatgtacgcaaatattcataatttttaccttt +acatttttttaccactttttttcaaacgaattgattttttaagtcttggt +atgcaaCTGATGTTTCACTCGAAGCAATACTGTAGTTTTTCATTTTGTCA +CTTCGTCTCTACGGGGACTGCCGTTCACTGTGATGTTTTTAAAATCGTAA +AATTGTATTGGTCTAACTGAACATTTTATAACTATAATTATCAATAACTT +TTAAAAGTTATAAATGTACATTGTGGTTTCGTTCAAAATTAAATGAGCCT +TTCATCTAAAGTGATAGTTTTCTATACCAATAAACTTTCATGAGTTAAGT +TGGCTCCACGGAGCCTTGTCCTCAGAACTTTTGTTTCCGAAGTAAATTTC +ACTTTGATATAGCATAAAACAATACTTTCAATAGATGCAAGTATAAAGAG +TAGTAAAATCACTAAAGAACCAATCGGATTTCTCAAAAATACTATTTCAC +ATTTTTGATTAGCATGAAATATTTTCTATATATACTTTTTAAAAATTAAT +TAAAAAACTAAAATTTTCAAAAAGTGCtcggtttaaaaatgtttgtcttc +agctgtagttatcctattttttaatttcatttgtattaaatcttctgaaa +cctctaattttaataatattatagtaAAGAGAAgtccgattcggctggtt +ccgacttatatactacaatagatagctttataactgagcgactagttttc +gtagaaacggacggacagacgatcagacgtacatggctagatcttctcgt +atagtgatgttgattaaaaatatatatactttatggtgtcggaaacgtct +tcactgcgttgcaatctcttgacttaactcattttactctctgcaagggt +atacaaatcggacaactaataaagctgctatagaaacgatcggaTTTTTA +ATGTAatgttgttttcgacaaacatttacggcattaaattaaaatgtggg +gttatctttatataactgtgttaagttttagttttctaaaaatcgtaaag +ctgtagaccacaatacttatacggaaacgacctgcaaggatatagaaCAT +GCAACATATTGAGGAACATTTGTAAAGTTATTGTTACGTTCTTTTGTGTA +GAAGATTTTACGTTAGGATAAATATTTTTTTCAAATATCACATGAACGTA +ACAACATTATACATAGTAAAATACAATTTAACCAGCAATTTTGTTGTGCT +TACACTAGGAAATAATACATTTTTCATTTCATTGTTCTTAAATTTTTCTG +GCTGGTTTTTTCTTTTTTTTTATTTTATTCTACATTTTAAAATTTAaaaa +aatgtatattttttagggtagaagctaatacgttaagcaacaacgatgtt +ttaagtattttacatttaaaaaattatattttatcattcctgtgggagct +taggatatagtcgcctgaACGGTTGCGGTAATCCAGCTTGTTTAAAATAC +TAAGTGGTCTTTGGCCCATATACGTTGGAGAATTGCAAATACCGTGTCCC +TTGATTTACATTCCACAACGTCCATACATGTCAATTTGTAGTCTTTGCGA +CCAAATAATATACCCCGACACACGGGATGATATGAAACAGAAAGAAATAT +ATGAGATGATATGAAAGATATAGATGATATGAAAGATAAGATGAAAGATA +TAAGATGCATTTTGAAGTTGGTCAGCCTTGAACACATCGCCCAACGATAT +TCAATTTTAGATTTTTGTTTAAAGTTGATTAGTGAAAAATTGGTTATTGT +TTTCAGTGATATTTTTTAATTTTACCAGCCAATTTTTTTTGTGCCTACAC +TAGGAAAGCATACATTTTTCATTTCATTGTTCTTAAATTTTGCAGGCTGG +TTTTTCCTCTTTTTATTTTATTATAAATTTTTAAATattaaaaaatgtat +attccctagttaataagttaaaaaacaccgatgttataatttttttacat +taaaaaaatattttttatcactcctgtgggagcttaggatatagtcgcct +gatccgtgtcgttccgacttatatactacctgcaatagaaacacaatttt +tgggaaggtttaattctaatagttttaaaactgagagactcgactgcgtg +gaaacggggggatagaTCTACTGTGATTTTATTGTAATGTAAACAACCTG +TTATATGTTATAGGTAAGTTATAAATTTGTTAAAAAAGTAAATACTTTTT +TTATAACGAAATATGCATTGCATAGCCTTAGAGTCCAAAACGGTTTTAAA +CAAAAAATTTGGTAAAATGTAAACAAAAGGTATTCTTGTTATATGTTATA +GGTAAGTTATAAATTTGTTAAAAAAATAAATACTTTTTTTATAACGTTAT +ATGCATTGCATAGCCTAAGAGTCCAAAACGCTTTTAAACAAAAAATTTGC +AACGGTCTTTTTTATAATTTTATATTTTTAGGTGGAGATGCAGCAGCTAC +GGCAGGCATACAACCGTCTAGTAAATCAAATGACTACAATTTTTAACCAA +AAACTTTGGTTTATTATGCTTGAACAATTTTTTATGAAATATGTTTGGTC +CGGTACTGGAATGATTATGGTGTCACTTCCTATTCTGACAGGCAGTGACG +TAGGATCTGCATCAAAGCCCGACTCGGCCATTACGGAGTCGCGTGTTAGC +GAACGTACGCAGTATTTAACAACAGCTAGAAATTTACTAATTTCTGCAGC +AGACGCTATTGAGCGATTGATGTCTTCTTACAAAGAAATTGTGTCGCTTG +CTGGATACACTTATCGCGTGGCTGGCATGATGGATGTGTTCGAGGAAACT +GCACAGGGACTCTACTGCAAGGCGAGTGTAATAGATAACAATCAGTCAAA +AGGAATTATAGAGCACCGTAACGGAAAGCCAATAGCAAAGGGTCGCATTA +TTTACTCAGATGATCCGGAAAATATGTCAATAAACTTACGTGCAGTGCCA +GTAGTGACACCAAACTGTGATATAGTTGTACCGAAACTTACATTGTGCAT +CGAGCCTGGGGTGCATTTGTTAATAACTGGGCCGAACGGTTGTGGTAAAT +CCAGCTTGTTTAGAATACTAAGTGGTCTTTGGCCCATATACGCTGGAGAA +TTGCAAATACCGCGGCCCGTAAAAGATATTCCTTGTATGTTTTACATTCC +ACAACGTCCATACATGTCAATTGGTAGTCTTTGCGACCAAATTATATACC +CCGACACACGGGATGATATGAAACGCAAAGAAATATCTGAAAATGAGTTA +AGATGCATTTTGAAGTTGGTCAGCCTTGAACACATCGCCCAACGGTATTC +AATTTTAGATTTTTGTTTAAAGTTTATAAGTGATAAATTTATTATTATTT +TCAGTGATAGTTTTGACGTTGTTCGTGATTGGAAGGATATATTATCTGGA +GGTGAAAAACAACGTATGGCGATAGCTCGCTTGTTTTACCACAAGTAAGA +ACAAATCAATGTCCTTCATTTTTTAGTATCCAAGCTTCAAAATCGCTTTA +CTTTATCGCGGAACTTTAATTGCAACTCATTTTTTGACTCCAAAGCTGAT +ATTAGAAATGTTTTATATAAATCTTTGGGTATTGCAAAAACAATTCAATT +ACagaaatccgaggacttttttgggaaggaaggaaaatttaattgaaacg +aaactttcgggtttaattgttatatttttttattaaaatatctgtcatat +tattcctggtataagcatttcgccgaggcgcctccattgtgcatgtgtcg +tgcggcgTTTATAATGAGGGTCGCATTTTTCATTTGAATAAAGAAAACAA +AAATATGTTTTTTTTTTAAAGTATATTTATTAGTTAAACCAAGTATATTa +ctataagattattaaatcccgaaaataataaattttatctcgttttcata +ggacgtttcccttaatttgtaataatgaaaaacgagaaatcgcacttcaa +agttttccagccgctcggccttactcacaatttcgcctgtaactttaaaa +atatttcgaatttggatagtttgggtatacatttgcgctaaaaaggaaaa +tagatttttttaagccttgaaagcatgttccttctAGGTAGATGTTGACT +TTAGAGGTTCGGGAACGAAAATCATAATTTTTTTTACTAAATTTTAATTG +AATGAATAAAAAACAAAAGCATTTGCAACCCTAGTCAACATCAGCGTAAC +GACTTTAAAGATAACAATTCGCGTGATATAGTATATATTTATACTAGTAT +ACCTTTATTCTAGCATTGAATTAATGTATGTTTTTCTTCTAGGCCACGTT +ATGCCCTACTTGATGAATGTACGAGCGCAGTGTCTATAGACGTTGAAAGC +TCAATATATGAAATTGCTAAAGGCATGGGAATTACGCTGTTGACTATAAC +ACACAGGCCTACCTTATGGTAAGAATTAATTATTTGAACTTTGTCCTAAT +TAAATAAACATTCTGCTTTAGGAAATACCACACACATATATTGGAGTTCG +ACGGCCTTGGCAACTGGCAGTTTAGAAAAATGAATGAAGATGAGCAACAA +AAGGAACTATTCCTTTCTTAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.trf_4.hard.fa Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,84 @@ +>trf_1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_2 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_3 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNN +>trf_4 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNN +>trf_5 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNN +>trf_6 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_7 +NNNNNTATATATATATATATATTTATATATATATATATANNNN +>trf_8 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_9 +NNNNNTATATATATATATATATTTATATATATATATATANNNN +>trf_10 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_11 +TATATATATATATCCTGTTCTATATATATAGAACCTGT +>trf_12 +CAAATTTTTTGTTTAAAAGCGTTTTGGACTCTTAGGCTATGCAATGCATA +TAACGTTATAAAAAAAGTATTTATTTTTTTAACAAATTTATAACTTACCT +ATAACATATAACAAGAATACCTTTTGTTTACATTTTACCAAATTTTTTGT +TTAAAACCGTTTTGGACTCTAAGGCTATGCAATGCATATTTCGTTATAAA +AAAAGTATTTACTTTTTTAACAAATTTATAACTTACCTATAACATATAAC +A +>trf_13 +TCATCTTATCTTTCATATCATCTATATCTTTCATATCATCTCATATATTT +C +>trf_14 +TTTCATATCATCTATATCTTTCATATCATCTCATATATTTCTTTCTGTTT +CATATCATC +>trf_15 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_16 +TATGTATAAACAATGTTCATACTTATGTGTAAACAATGTTCATACTTATG +TGT +>trf_17 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_18 +TATAATTTTGGGAATATAATNNNNNNNNNNNNNNNNNNN +>trf_19 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNN +>trf_20 +ACACTTAAGACATGTTTAACAACAACACTTAAAAAATGTTTAACAACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.trf_4.nomask.fa Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,84 @@ +>trf_1 +AATGATGCATTTAAATGCTGCATTTAAATG +>trf_2 +ACAGACAGACGGACGAACAGACGGACGGACG +>trf_3 +GAAGTGTCGCCGAAGTCACTCCTGGAAGTGTCGCCGAAGTGACTTTGAGA +AGTGCCGCCGAAGTG +>trf_4 +GAAGTGTCGCCGAAGTCACTCCTGGAAGTGTCGCCGAAGTGACTTCGAGA +AGTGCCGCCGAAGTG +>trf_5 +ATAATTTGTTTCATATTATTTCCCACCCAATTTTCGGATCGTTCCTATGA +CAGCTATATGATATAGTCGTCAGATTTTGTAAAAGTTTAATTCAAAACCA +AATAAAAAATGCTATTTCCAAGCGTAGAAGGTTATACGTTAAAAAACACC +GAAGATATAATTTTTCCATATTATTTTGCCACTAATTTTCCGTTTGTTCC +TATGGGAGCTATATGATATAGGTATCCGATTTTGATAAAATGTAATTCAA +AATTCAGAACTAATTTAAAAATGTTATATCCATGCTTAGAAAGCTATATG +TTTAAAATAACCCAAAGATAATTTTTTCTTATTATTTTACCACTAATTTT +TCGATCCTTCATATGGCAGCAATATGATATAGTCGTCCGATTTCGATAAA +AATTGAATTCGAAATTCTGAACTAATTAAAAATGGTTATCTCCAAGCTTA +GAAGGTTATATGTTAAAAA +>trf_6 +AACATTTTTAAATTAGTTCTGAATTTCGTATCAAATTTTATTAAAATCGG +CCGACTATATCATATAGCTCCCATAGCAACAATCGGAAAATTAGTGGTAA +AATAATATTCAAAAATTATATCTTCGGTGTTTTTTAACTTATAACCTCCT +ACGCTTGGAAATAACATTTTTTATTTGGTTTTGAATTACGAATTACATTT +TATCAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATGGTAA +AATTAGTAGAAAAAACATGAAATAAAAAAATTATATCTTTGGTGTTTTTA +ACATATAACTTGAAAGCTTAAAAATAACATTTTTTAATTAGTTCTGAATT +TAAATTTAAATTTTATTAAAATCGGAAGACCATATCATATAGCTGTCATA +GGAACGATCGGAAAATTGGTGGGAAATAAT +>trf_7 +ATATATATATATATATATATATTTATATATATATATATATATA +>trf_8 +GCTGAGGATGAGCTACAGAGCTGAGGATGAGATACAG +>trf_9 +ATATATATATATATATATATATTTATATATATATATATATATA +>trf_10 +GCTGAGGATGAGCTACAGAGCTGAGGATGAGATACAG +>trf_11 +TATATATATATATCCTGTTCTATATATATAGAACCTGT +>trf_12 +CAAATTTTTTGTTTAAAAGCGTTTTGGACTCTTAGGCTATGCAATGCATA +TAACGTTATAAAAAAAGTATTTATTTTTTTAACAAATTTATAACTTACCT +ATAACATATAACAAGAATACCTTTTGTTTACATTTTACCAAATTTTTTGT +TTAAAACCGTTTTGGACTCTAAGGCTATGCAATGCATATTTCGTTATAAA +AAAAGTATTTACTTTTTTAACAAATTTATAACTTACCTATAACATATAAC +A +>trf_13 +TCATCTTATCTTTCATATCATCTATATCTTTCATATCATCTCATATATTT +C +>trf_14 +TTTCATATCATCTATATCTTTCATATCATCTCATATATTTCTTTCTGTTT +CATATCATC +>trf_15 +TTTTAATTACATTTTATCAAAATCGGACGACTATATCATACAGCTGCCAT +TGAACGATCGGAAAATAAGTGGTCAAATAATATGAAAAACTTATATCTTC +GGTGACTTTAACATATAACTTCCAATGCTTGGAAATACAATTTTTAATTG +GTTTTCAATTTCGAATTAAATTTTATTAAAATCGGACGACTATATATATA +GCTGCCATAAATACGATCGGAAAATTAGTCGGAAAATATAAAAAAATTAT +ATCTTTGGTGTTTTTTAACATATAACCTTCTAAACTTGAAAATAACATTT +TTTAATTAGTTCTAAATTTTGAATTAAATTTTATCAAAATCGGTTAACTA +TATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGGAAAATA +>trf_16 +TATGTATAAACAATGTTCATACTTATGTGTAAACAATGTTCATACTTATG +TGT +>trf_17 +AATACAATACAATTTTTAATACAATACAATTTT +>trf_18 +TATAATTTTGGGAATATAATATATTGGGAATATAATTTT +>trf_19 +AATTATCCGATCGTTCCTATGACAGCTATATGATATAGTCGTCCGATTTT +AATAAAATTTAATTCGAAATTCAGAATTAATTAAAAAATGTTTTTTTTAA +GCTTATAAGGTTATATGTTAAAAAACACTAAAGATATAATTTTAATTTAT +GTTTTCCGACTAATTTTCCGATCGTTCCTATGGCAGTTATATGATATAAT +CGTCCGATTTTGATAAAATGTAATTCGAAATTCAAAACCAAATAAAAAAT +GTTATTTCCAAGCGTAGGAGGTCATAAGTTAAAAAACACCGAAGATATAA +TTTTTCAATATTATTCACCATTAATTTTCCGATTGTTCCTATGGGAGCTA +TAAGATATAGTCGACCGATTTTGATAAAATTTAATTCGAAATTCAGAACT +AATTTAAAAGTGTTATATCCAAACTTAAAAAAGTATATCTTATAAAACAC +GAAAGATAATAATTTTTTTTTTTTTTTTTAATTTTACTCGATAGTTCCTA +TGGGAGCTATAAGATATAGTTGTCCGAT +>trf_20 +ACACTTAAGACATGTTTAACAACAACACTTAAAAAATGTTTAACAACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.trf_4.soft.fa Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,84 @@ +>trf_1 +aatgatgcatttaaatgctgcatttaaatg +>trf_2 +acagacagacggacgaacagacggacggacg +>trf_3 +gaagtgtcgccgaagtcactcctggaagtgtcgccgaagtgactttgaga +agtgccgccgaagtg +>trf_4 +gaagtgtcgccgaagtcactcctggaagtgtcgccgaagtgacttcgaga +agtgccgccgaagtg +>trf_5 +ataatttgtttcatattatttcccacccaattttcggatcgttcctatga +cagctatatgatatagtcgtcagattttgtaaaagtttaattcaaaacca +aataaaaaatgctatttccaagcgtagaaggttatacgttaaaaaacacc +gaagatataatttttccatattattttgccactaattttccgtttgttcc +tatgggagctatatgatataggtatccgattttgataaaatgtaattcaa +aattcagaactaatttaaaaatgttatatccatgcttagaaagctatatg +tttaaaataacccaaagataattttttcttattattttaccactaatttt +tcgatccttcatatggcagcaatatgatatagtcgtccgatttcgataaa +aattgaattcgaaattctgaactaattaaaaatggttatctccaagctta +gaaggttatatgttaaaaa +>trf_6 +aacatttttaaattagttctgaatttcgtatcaaattttattaaaatcgg +ccgactatatcatatagctcccatagcaacaatcggaaaattagtggtaa +aataatattcaaaaattatatcttcggtgttttttaacttataacctcct +acgcttggaaataacattttttatttggttttgaattacgaattacattt +tatcaaaatcggacgactatatcatatagctgccataggaacgatggtaa +aattagtagaaaaaacatgaaataaaaaaattatatctttggtgttttta +acatataacttgaaagcttaaaaataacattttttaattagttctgaatt +taaatttaaattttattaaaatcggaagaccatatcatatagctgtcata +ggaacgatcggaaaattggtgggaaataat +>trf_7 +atataTATATATATATATATATTTATATATATATATATAtata +>trf_8 +gctgaggatgagctacagagctgaggatgagatacag +>trf_9 +atataTATATATATATATATATTTATATATATATATATAtata +>trf_10 +gctgaggatgagctacagagctgaggatgagatacag +>trf_11 +TATATATATATATCCTGTTCTATATATATAGAACCTGT +>trf_12 +CAAATTTTTTGTTTAAAAGCGTTTTGGACTCTTAGGCTATGCAATGCATA +TAACGTTATAAAAAAAGTATTTATTTTTTTAACAAATTTATAACTTACCT +ATAACATATAACAAGAATACCTTTTGTTTACATTTTACCAAATTTTTTGT +TTAAAACCGTTTTGGACTCTAAGGCTATGCAATGCATATTTCGTTATAAA +AAAAGTATTTACTTTTTTAACAAATTTATAACTTACCTATAACATATAAC +A +>trf_13 +TCATCTTATCTTTCATATCATCTATATCTTTCATATCATCTCATATATTT +C +>trf_14 +TTTCATATCATCTATATCTTTCATATCATCTCATATATTTCTTTCTGTTT +CATATCATC +>trf_15 +ttttaattacattttatcaaaatcggacgactatatcatacagctgccat +tgaacgatcggaaaataagtggtcaaataatatgaaaaacttatatcttc +ggtgactttaacatataacttccaatgcttggaaatacaatttttaattg +gttttcaatttcgaattaaattttattaaaatcggacgactatatatata +gctgccataaatacgatcggaaaattagtcggaaaatataaaaaaattat +atctttggtgttttttaacatataaccttctaaacttgaaaataacattt +tttaattagttctaaattttgaattaaattttatcaaaatcggttaacta +tatcatatagctgtcataggaacgatcggaaaattggtgggaaaata +>trf_16 +TATGTATAAACAATGTTCATACTTATGTGTAAACAATGTTCATACTTATG +TGT +>trf_17 +aatacaatacaatttttaatacaatacaatttt +>trf_18 +TATAATTTTGGGAATATAATatattgggaatataatttt +>trf_19 +aattatccgatcgttcctatgacagctatatgatatagtcgtccgatttt +aataaaatttaattcgaaattcagaattaattaaaaaatgttttttttaa +gcttataaggttatatgttaaaaaacactaaagatataattttaatttat +gttttccgactaattttccgatcgttcctatggcagttatatgatataat +cgtccgattttgataaaatgtaattcgaaattcaaaaccaaataaaaaat +gttatttccaagcgtaggaggtcataagttaaaaaacaccgaagatataa +tttttcaatattattcaccattaattttccgattgttcctatgggagcta +taagatatagtcgaccgattttgataaaatttaattcgaaattcagaact +aatttaaaagtgttatatccaaacttaaaaaagtatatcttataaaacac +gaaagataataatttttttttttttttttaattttactcgatagttccta +tgggagctataagatatagttgtccgat +>trf_20 +ACACTTAAGACATGTTTAACAACAACACTTAAAAAATGTTTAACAACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.trf_4_12.fa Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,84 @@ +>trf +aatgatgcatttaaatgctgcatttaaatg +>trf +acagacagacggacgaacagacggacggacg +>trf +gaagtgtcgccgaagtcactcctggaagtgtcgccgaagtgactttgaga +agtgccgccgaagtg +>trf +gaagtgtcgccgaagtcactcctggaagtgtcgccgaagtgacttcgaga +agtgccgccgaagtg +>trf +ataatttgtttcatattatttcccacccaattttcggatcgttcctatga +cagctatatgatatagtcgtcagattttgtaaaagtttaattcaaaacca +aataaaaaatgctatttccaagcgtagaaggttatacgttaaaaaacacc +gaagatataatttttccatattattttgccactaattttccgtttgttcc +tatgggagctatatgatataggtatccgattttgataaaatgtaattcaa +aattcagaactaatttaaaaatgttatatccatgcttagaaagctatatg +tttaaaataacccaaagataattttttcttattattttaccactaatttt +tcgatccttcatatggcagcaatatgatatagtcgtccgatttcgataaa +aattgaattcgaaattctgaactaattaaaaatggttatctccaagctta +gaaggttatatgttaaaaa +>trf +aacatttttaaattagttctgaatttcgtatcaaattttattaaaatcgg +ccgactatatcatatagctcccatagcaacaatcggaaaattagtggtaa +aataatattcaaaaattatatcttcggtgttttttaacttataacctcct +acgcttggaaataacattttttatttggttttgaattacgaattacattt +tatcaaaatcggacgactatatcatatagctgccataggaacgatggtaa +aattagtagaaaaaacatgaaataaaaaaattatatctttggtgttttta +acatataacttgaaagcttaaaaataacattttttaattagttctgaatt +taaatttaaattttattaaaatcggaagaccatatcatatagctgtcata +ggaacgatcggaaaattggtgggaaataat +>trf +atataTATATATATATATATATTTATATATATATATATAtata +>trf +gctgaggatgagctacagagctgaggatgagatacag +>trf +atataTATATATATATATATATTTATATATATATATATAtata +>trf +gctgaggatgagctacagagctgaggatgagatacag +>trf +TATATATATATATCCTGTTCTATATATATAGAACCTGT +>trf +CAAATTTTTTGTTTAAAAGCGTTTTGGACTCTTAGGCTATGCAATGCATA +TAACGTTATAAAAAAAGTATTTATTTTTTTAACAAATTTATAACTTACCT +ATAACATATAACAAGAATACCTTTTGTTTACATTTTACCAAATTTTTTGT +TTAAAACCGTTTTGGACTCTAAGGCTATGCAATGCATATTTCGTTATAAA +AAAAGTATTTACTTTTTTAACAAATTTATAACTTACCTATAACATATAAC +A +>trf +TCATCTTATCTTTCATATCATCTATATCTTTCATATCATCTCATATATTT +C +>trf +TTTCATATCATCTATATCTTTCATATCATCTCATATATTTCTTTCTGTTT +CATATCATC +>trf +ttttaattacattttatcaaaatcggacgactatatcatacagctgccat +tgaacgatcggaaaataagtggtcaaataatatgaaaaacttatatcttc +ggtgactttaacatataacttccaatgcttggaaatacaatttttaattg +gttttcaatttcgaattaaattttattaaaatcggacgactatatatata +gctgccataaatacgatcggaaaattagtcggaaaatataaaaaaattat +atctttggtgttttttaacatataaccttctaaacttgaaaataacattt +tttaattagttctaaattttgaattaaattttatcaaaatcggttaacta +tatcatatagctgtcataggaacgatcggaaaattggtgggaaaata +>trf +TATGTATAAACAATGTTCATACTTATGTGTAAACAATGTTCATACTTATG +TGT +>trf +aatacaatacaatttttaatacaatacaatttt +>trf +TATAATTTTGGGAATATAATatattgggaatataatttt +>trf +aattatccgatcgttcctatgacagctatatgatatagtcgtccgatttt +aataaaatttaattcgaaattcagaattaattaaaaaatgttttttttaa +gcttataaggttatatgttaaaaaacactaaagatataattttaatttat +gttttccgactaattttccgatcgttcctatggcagttatatgatataat +cgtccgattttgataaaatgtaattcgaaattcaaaaccaaataaaaaat +gttatttccaagcgtaggaggtcataagttaaaaaacaccgaagatataa +tttttcaatattattcaccattaattttccgattgttcctatgggagcta +taagatatagtcgaccgattttgataaaatttaattcgaaattcagaact +aatttaaaagtgttatatccaaacttaaaaaagtatatcttataaaacac +gaaagataataatttttttttttttttttaattttactcgatagttccta +tgggagctataagatatagttgtccgat +>trf +ACACTTAAGACATGTTTAACAACAACACTTAAAAAATGTTTAACAACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ucsc_twobit" version="340"> + <repository changeset_revision="cd2adf686498" name="package_ucsc_twobit_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="ucsc_bigbed" version="340"> + <repository changeset_revision="dd9b230c079d" name="package_ucsc_bigbed_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsc_macros.xml Wed May 17 16:49:32 2017 -0400 @@ -0,0 +1,44 @@ +<macros> + <xml name="requirements_twobit"> + <requirements> + <requirement type="package" version="340">ucsc_twobit</requirement> + <yield /> + </requirements> + </xml> + <xml name="environment_LC_COLLATE"> + <environment_variables> + <!-- Sort uppercase letters before lowercase (required by UCSC tools) --> + <environment_variable name="LC_COLLATE">C</environment_variable> + <yield /> + </environment_variables> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{Kent01062002, +author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler, and David}, +title = {The Human Genome Browser at UCSC}, +volume = {12}, +number = {6}, +pages = {996-1006}, +year = {2002}, +doi = {10.1101/gr.229102}, +URL = {http://genome.cshlp.org/content/12/6/996.abstract}, +eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html}, +journal = {Genome Research} +} + </citation> + <yield /> + </citations> + </xml> + + <token name="@OPTIONAL_PARAM_FUNC@"> +<![CDATA[ + #def optional_param($_flag, $_flag_value, $_sep="=") + #if str($_flag_value) and str($_flag_value).strip(): + ${_flag}${_sep}${_flag_value} + #end if + #end def +]]> + </token> +</macros>