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SequenceServer Individual Contributor License Agreement

Thank you for your interest in contributing to SequenceServer.
This contributor agreement ("Agreement") documents the rights granted by contributors to Us. To make this document effective, please sign it and send it to Us, following the instructions at . This is a legally binding document, so please read it carefully before agreeing to it. The Agreement may cover more than one software project managed by Us.
1. Definitions

"We" or "Us" means the maintaners of SequenceServer: Anurag Priyam and Dr. Yannick Wurm.
"You" means the individual who Submits a Contribution to Us.
"Contribution" means any work of authorship that is Submitted by You to Us in which You own or assert ownership of the Copyright. If You do not own the Copyright in the entire work of authorship, please follow the instructions in .
"Copyright" means all rights protecting works of authorship owned or controlled by You, including copyright, moral and neighboring rights, as appropriate, fo

yeban

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!DOCTYPE DASFEATURES SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
<DASGFF>
  <GFF version="1.0" href="http://localhost:4567/das/rubydas/features?segment=Si_gnF.scaffold02797:5943908,6066389;type=mRNA;type=exon;type=CDS;maxbins=3232">
    <SEGMENT id="Si_gnF.scaffold02797" version="1.0" start="5939256" stop="6066389">
      <FEATURE id="9216" label="maker-Si_gnF.scaffold02797-snap-gene-60.39-mRNA-1">
        <TYPE id="mRNA"/>
        <METHOD id="maker"/>
        <START>6003626</START>
        <END>6008125</END>

yeban

require 'ox'

Ox.parse(DATA.read)

__END__
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>tblastn</BlastOutput_program>
  <BlastOutput_version>TBLASTN 2.2.30+</BlastOutput_version>

yeban

#   Failed test 'bin/draw-basepair-track.pl compiled ok'
#   at tests/perl_tests/00.compile.t line 45.
# stdout: 
# stderr: Can't locate GD/Image.pm in @INC (you may need to install the GD::Image module) (@INC contains: /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5 /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/lib /Users/priyam/jbrowse/src/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thr

yeban

#!/usr/bin/env sh

set -x

cd

# Download chruby to ~/.chruby.
wget -O /tmp/chruby-0.3.9.tar.gz https://github.com/postmodern/chruby/archive/v0.3.9.tar.gz
tar xvf /tmp/chruby-0.3.9.tar.gz -C /tmp
rm /tmp/chruby-0.3.9.tar.gz

yeban

function usage()
io.stderr:write(string.format("Usage: %s <GFF file>\n" , arg[0]))
os.exit(1)
end

if #arg < 1 then
  usage()
  os.exit(1)
end

yeban

##gff-version 3
scaffold00002	.	contig	1	5659355	.	.	.	ID=scaffold00002;Name=scaffold00002
scaffold00002	maker	gene	5418413	5434733	.	+	.	ID=maker-scaffold00002-augustus-gene-54.23;Name=maker-scaffold00002-augustus-gene-54.23
scaffold00002	maker	mRNA	5418413	5434733	.	+	.	ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1;Parent=maker-scaffold00002-augustus-gene-54.23;Name=maker-scaffold00002-augustus-gene-54.23-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0.2|0.33|0.83|0.4|0.33|6|2271|1028
scaffold00002	maker	exon	5418413	5418704	.	+	.	ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1:exon:1799;Parent=maker-scaffold00002-augustus-gene-54.23-mRNA-1
scaffold00002	maker	exon	5419004	5419181	.	+	.	ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1:exon:1800;Parent=maker-scaffold00002-augustus-gene-54.23-mRNA-1
scaffold00002	maker	exon	5426189	5426463	.	+	.	ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1:exon:1801;Parent=maker-scaffold00002-augustus-gene-54.23-mRNA-1
scaffold00002	maker	exon	5428580	5428699	.	+	.	ID=maker-s

yeban

scaffold00002	repeatmasker	match	1244186	1244228	274	+	.	ID=scaffold00002:hit:1026:1.3.0.12;Name=species:R1_DPs|genus:LINE%2FR1;Target=species:R1_DPs|genus:LINE%2FR1 650 780 +
scaffold00002	repeatmasker	match_part	1244186	1244228	274	+	.	ID=scaffold00002:hsp:1026:1.3.0.12;Parent=scaffold00002:hit:1026:1.3.0.12;Target=species:R1_DPs|genus:LINE%2FR1 650 780 +
scaffold00002	repeatmasker	match	1261641	1261712	273	+	.	ID=scaffold00002:hit:1027:1.3.0.12;Name=species:GRANDE1_ZD-int|genus:LTR%2FGypsy;Target=species:GRANDE1_ZD-int|genus:LTR%2FGypsy 11010 11080 +
scaffold00002	repeatmasker	match_part	1261641	1261712	273	+	.	ID=scaffold00002:hsp:1027:1.3.0.12;Parent=scaffold00002:hit:1027:1.3.0.12;Target=species:GRANDE1_ZD-int|genus:LTR%2FGypsy 11010 11080 +
# [...]
scaffold00002	repeatrunner	protein_match	1241335	1241652	296	-	.	ID=scaffold00002:hit:1026:1.3.0.12;Name=gi|538540|pir||A40831;Target=gi|538540|pir||A40831 662 763 +
scaffold00002	repeatrunner	match_part	1241335	1241652	296	-	.	ID=scaffold00002:hsp:1026:1.3.

yeban

# Copyright (C) 2011 Anurag Priyam - MIT License
#
# cd to the project root (identified by the presence of a SCM directory, like
# .git, or .bzr)
#
# Install
# -------
#
# Put something like this in your .zshrc:
#

yeban

# Copyright (C) 2011 Anurag Priyam - MIT License

module Jekyll

  # Jekyll plugin to generate tag clouds.
  #
  # The plugin defines a `tag_cloud` tag that is rendered by Liquid into a tag
  # cloud:
  #
  #     <div class='cloud'>