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Anurag Priyam yeban

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yeban / subpart.gff
Last active August 29, 2015 14:02
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
yeban / gt_segfault.gff
Created July 19, 2014 04:27
This file has been truncated, but you can view the full file.
##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
yeban / gff3_to_json.lua
Last active August 29, 2015 14:06 — forked from satta/gff3_to_json.lua
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
yeban / ruby-setup.sh
Last active August 29, 2015 14:07
#!/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
yeban / jb_pl_test_output
Created November 21, 2014 16:13
# 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
yeban / ox_invalid_format_elements_overlap.rb
Created June 3, 2015 05:35
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
yeban / features.xml
Last active August 29, 2015 14:25
<?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
yeban / gfl-merb-run-method.rb
Created June 14, 2009 11:51
def run!
if request.params[:'openid.mode']
response = consumer.complete(request.send(:query_params), "#{request.protocol}://#{request.host}" + request.path)
case response.status.to_s
when 'success'
ax_response = ::OpenID::AX::FetchResponse.from_success_response(response) #modified
result = on_success!(response, ax_response)
Merb.logger.info "\n\n#{result.inspect}\n\n"
result
when 'failure'
@yeban
yeban / gfl-merb-on-success-find-user.rb
Created June 14, 2009 11:44
def on_success!(response, ax_response)
debugger
email=ax_response.data["http://schema.openid.net/contact/email"]
if user = find_user_by_email(email)
user
else
user=user_class.new({:email=>email})
user.save
user
end
@yeban
yeban / slim.theme
Created June 15, 2009 06:19
# yeban theme for SLiM
# by Anurag Priyam
# Messages (ie: shutdown)
msg_color #FFFFFF
msg_font Monaco:size=18:bold:dpi=75
msg_x 50%
msg_y 40%
msg_shadow_color #702342
msg_shadow_xoffset 1