# HG changeset patch
# User yating-l
# Date 1495054172 14400
# Node ID 512ed6da23676c626be53d59240ede76d27bcee0

planemo upload

diff -r 000000000000 -r 512ed6da2367 bigbed_to_fa.xml
--- /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>
diff -r 000000000000 -r 512ed6da2367 bigbed_to_standard_bed.pl
--- /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;
+}
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.models_12_2.bb
Binary file test-data/contigs.models_12_2.bb has changed
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.models_12_2.fa
--- /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
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.models_6_2.bb
Binary file test-data/contigs.models_6_2.bb has changed
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.models_6_2.fa
--- /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
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.out.2bit
Binary file test-data/contigs.out.2bit has changed
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.trf_4.bb
Binary file test-data/contigs.trf_4.bb has changed
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.trf_4.hard.fa
--- /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
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.trf_4.nomask.fa
--- /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
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.trf_4.soft.fa
--- /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
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.trf_4_12.bb
Binary file test-data/contigs.trf_4_12.bb has changed
diff -r 000000000000 -r 512ed6da2367 test-data/contigs.trf_4_12.fa
--- /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
diff -r 000000000000 -r 512ed6da2367 tool_dependencies.xml
--- /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>
diff -r 000000000000 -r 512ed6da2367 ucsc_macros.xml
--- /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>