sequenceserver 0.8.3 → 0.8.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of sequenceserver might be problematic. Click here for more details.
- data/lib/blast.rb~ +200 -0
- data/lib/sequenceserver/database_formatter.rb~ +190 -0
- data/public/css/beige.css.css +254 -0
- data/public/css/beige.css~ +226 -0
- data/public/js/Scribl.min.js +53 -0
- data/public/js/sequenceserver.js~ +250 -0
- data/sequenceserver.gemspec +2 -2
- data/tests/database/nucleotide/head.fa +10 -0
- data/tests/database/nucleotide/head.faVno_parse.html +96 -0
- data/tests/database/nucleotide/head.faVparse.html +96 -0
- data/tests/database/nucleotide/headVno_parse.archive +151 -0
- data/tests/database/nucleotide/headVno_parse.archive.csv +1 -0
- data/tests/database/nucleotide/headVparse.archive +148 -0
- data/tests/database/nucleotide/headVparse.archive.csv +1 -0
- data/tests/database/nucleotide/no_parse.fa +5486 -0
- data/tests/database/nucleotide/no_parse.fa.nhr +0 -0
- data/tests/database/nucleotide/no_parse.fa.nin +0 -0
- data/tests/database/nucleotide/no_parse.fa.nsq +0 -0
- data/tests/database/nucleotide/no_parse.info +7 -0
- data/tests/database/nucleotide/parse.fa +5486 -0
- data/tests/database/nucleotide/parse.fa.nhr +0 -0
- data/tests/database/nucleotide/parse.fa.nin +0 -0
- data/tests/database/nucleotide/parse.fa.nog +0 -0
- data/tests/database/nucleotide/parse.fa.nsd +946 -0
- data/tests/database/nucleotide/parse.fa.nsi +0 -0
- data/tests/database/nucleotide/parse.fa.nsq +0 -0
- data/tests/database/nucleotide/parse.info +7 -0
- data/views/search.erb~ +164 -0
- metadata +56 -28
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data/views/search.erb~
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xml:lang="en" lang="en" xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<title>SequenceServer</title>
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<meta name="author" content="Anurag Priyam" />
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<meta name="author" content="Yannick Wurm" />
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<meta name="author" content="Cedric Wurm" />
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<meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
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<script type="text/javascript" src="/js/jquery.js"></script>
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<script type="text/javascript" src="/js/jquery.enablePlaceholder.min.js"></script>
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<script type="text/javascript" src="/js/search.js"></script>
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<link rel="stylesheet" media="screen" type="text/css" href="css/beige.css"/>
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</head>
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<body>
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<div class="container">
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<h1 class="banner">BLAST Sequence(s)</h1>
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<form method="post" action="/#result">
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<div class="horizontal">
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<div class="entryfield">
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<textarea name="sequence" id="sequence" rows="11" cols="" placeholder="Paste your sequence(s) here..." ></textarea>
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</div>
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<fieldset class="blastmethods box" >
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<div>
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<input type="radio" name="method" value="blastp" id="blastp" class="radiobutton" title="Protein query; protein database."/>
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<label for="blastp" title="Protein query; protein database.">blastp</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="tblastn" id="tblastn" class="radiobutton" title="Protein query; six-frame translated nucleotide database." />
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<label for="tblastn" title="Protein query; six-frame translated nucleotide database.">tblastn</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="blastn" id="blastn" class="radiobutton" title="Nucleotide query; nucleotide database."/>
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<label for="blastn" title="Nucleotide query; nucleotide database.">blastn</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="blastx" id="blastx" class="radiobutton" title="Translated nucleotide query; protein database."/>
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<label for="blastx" title="Six-frame translated nucleotide query; protein database.">blastx</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="tblastx" id="tblastx" class="radiobutton" title="Six-frame translated nucleotide query; six-frame translated nucleotide database"/>
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<label for="tblastx" title="Six-frame translated nucleotide query; six-frame translated nucleotide database">tblastx</label>
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</div>
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</fieldset>
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</div>
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<div class='horizontal'>
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<fieldset class="nucleotide rounded box databases">
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<h2>Nucleotide databases</h2>
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<!-- Database list is actually dynamically loaded -->
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<% settings.databases['nucleotide'].each_with_index do |db, i| %>
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<input type="checkbox" class="dbcheckbox" id="ndb<%=i%>" name="db[nucleotide][]" value="<%=i%>"/>
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<label for="ndb<%=i%>" class="dbdescription"><%= db.title or db.name %></label>
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<% end %>
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</fieldset>
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<fieldset class="protein rounded box databases">
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<h2>Protein databases</h2>
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<!-- Database list is actually dynamically loaded-->
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<% settings.databases['protein'].each_with_index do |db, i| %>
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<input type="checkbox" class="dbcheckbox" id="pdb<%=i%>" name="db[protein][]" value="<%=i%>"/>
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<label for="pdb<%=i%>" class="dbdescription"><%= db.title or db.name %></label>
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<% end %>
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</fieldset>
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</div>
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<div class="horizontal">
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<fieldset class="advanced box rounded">
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<span class="bigtext pointer" title="Click to show/hide advanced options.">Advanced parameters:</span>
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<input type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
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<pre class="smalltext">
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<%= ERB::Util.h %q|
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-evalue <Real>
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Expectation value (E) threshold for saving hits
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Default = `10'
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-word_size <Integer, >=2>
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Word size for wordfinder algorithm
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-gapopen <Integer>
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Cost to open a gap
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-gapextend <Integer>
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Cost to extend a gap
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-matrix <String>
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Scoring matrix name (normally BLOSUM62)
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-threshold <Real, >=0>
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Minimum word score such that the word is added to the BLAST lookup table
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-comp_based_stats <String>
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Use composition-based statistics for blastp / tblastn:
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D or d: default (equivalent to 2)
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0 or F or f: no composition-based statistics
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1: Composition-based statistics as in NAR 29:2994-3005, 2001
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2 or T or t : Composition-based score adjustment as in Bioinformatics
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21:902-911,
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2005, conditioned on sequence properties
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3: Composition-based score adjustment as in Bioinformatics 21:902-911,
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2005, unconditionally
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For programs other than tblastn, must either be absent or be D, F or 0
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Default = `2'
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-num_descriptions <Integer, >=0>
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Number of database sequences to show one-line descriptions for
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Default = `500'
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-num_alignments <Integer, >=0>
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Number of database sequences to show alignments for
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Default = `250'
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*** Query filtering options
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-seg <String>
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Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
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'no' to disable)
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Default = `no'
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-soft_masking <Boolean>
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Apply filtering locations as soft masks
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Default = `false'
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-lcase_masking
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Use lower case filtering in query and subject sequence(s)?
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*** Restrict search or results
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-gilist <String>
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Restrict search of database to list of GI's
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* Incompatible with: negative_gilist, seqidlist, remote, subject,
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subject_loc
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-seqidlist <String>
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Restrict search of database to list of SeqId's
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* Incompatible with: gilist, negative_gilist, remote, subject,
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subject_loc
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-negative_gilist <String>
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Restrict search of database to everything except the listed GIs
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* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
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-entrez_query <String>
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Restrict search with the given Entrez query
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* Requires: remote
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-db_soft_mask <String>
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Filtering algorithm ID to apply to the BLAST database as soft masking
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* Incompatible with: subject, subject_loc
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-culling_limit <Integer, >=0>
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If the query range of a hit is enveloped by that of at least this many
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higher-scoring hits, delete the hit
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* Incompatible with: best_hit_overhang, best_hit_score_edge
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-best_hit_overhang <Real, (>0 and <0.5)>
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Best Hit algorithm overhang value (recommended value: 0.1)
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* Incompatible with: culling_limit
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-best_hit_score_edge <Real, (>0 and <0.5)>
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Best Hit algorithm score edge value (recommended value: 0.1)
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* Incompatible with: culling_limit
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-max_target_seqs <Integer, >=1>
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Maximum number of aligned sequences to keep | %>
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</pre>
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</fieldset>
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<div class="submit_button">
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<input type="submit" value="BLAST!"/>
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</div>
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</div>
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</form>
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<div class="result prepend-top" id="result">
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<pre class='smalltext'>
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<%= @blast %>
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</pre>
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</div>
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<div class ="underbar">
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<p>© <a href='http://www.sequenceserver.com'>sequenceserver.com</a></p>
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</div>
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</div>
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</body>
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</html>
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: sequenceserver
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version: !ruby/object:Gem::Version
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version: 0.8.
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version: 0.8.4
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prerelease:
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platform: ruby
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authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2013-03-
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date: 2013-03-29 00:00:00.000000000 Z
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dependencies:
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name: bundler
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requirements:
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- - ~>
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version: 1.2
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version: '1.2'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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name: sinatra
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extensions: []
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extra_rdoc_files: []
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files:
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- lib/sequenceserver/blast.rb
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- lib/sequenceserver/customisation.rb
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- lib/sequenceserver/database.rb
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- lib/sequenceserver/database_formatter.rb
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- lib/sequenceserver/helpers.rb
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- lib/sequenceserver/helpers.rb
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- lib/sequenceserver/blast.rb
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- lib/sequenceserver/sinatralikeloggerformatter.rb
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- lib/sequenceserver/database_formatter.rb~
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- lib/sequenceserver/version.rb
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- lib/sequenceserver/database_formatter.rb
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- lib/sequenceserver/customisation.rb
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- lib/blast.rb~
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- views/_options.erb
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- public/css/custom.css
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- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
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- tests/database/nucleotide/headVno_parse.archive.csv
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- tests/database/nucleotide/head.faVparse.html
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- tests/database/nucleotide/parse.info
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- tests/database/nucleotide/headVparse.archive.csv
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- tests/database/nucleotide/headVparse.archive
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- tests/database/nucleotide/parse.fa.nsi
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- tests/database/nucleotide/headVno_parse.archive
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- tests/database/nucleotide/parse.fa.nsd
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- tests/database/nucleotide/parse.fa.nsq
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- tests/database/nucleotide/parse.fa.nhr
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- tests/database/nucleotide/head.faVno_parse.html
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155
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+
- tests/database/nucleotide/parse.fa.nog
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156
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+
- tests/database/nucleotide/no_parse.fa
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157
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+
- tests/database/nucleotide/parse.fa
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158
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+
- tests/database/nucleotide/no_parse.fa.nsq
|
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159
|
+
- tests/database/nucleotide/parse.fa.nin
|
|
160
|
+
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
|
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137
161
|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
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138
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|
- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
|
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139
|
-
- tests/database/nucleotide/
|
|
140
|
-
- tests/database/
|
|
141
|
-
- tests/database/
|
|
163
|
+
- tests/database/nucleotide/no_parse.fa.nin
|
|
164
|
+
- tests/database/nucleotide/head.fa
|
|
165
|
+
- tests/database/nucleotide/no_parse.info
|
|
166
|
+
- tests/database/nucleotide/no_parse.fa.nhr
|
|
142
167
|
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
|
|
168
|
+
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
|
|
143
169
|
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
|
|
170
|
+
- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
|
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144
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|
- tests/run
|
|
145
|
-
- tests/test_sequencehelpers.rb
|
|
146
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|
- tests/test_sequenceserver_blast.rb
|
|
147
173
|
- tests/ui.specs.todo
|
|
174
|
+
- tests/test_sequencehelpers.rb
|
|
148
175
|
- config.ru
|
|
149
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|
- example.config.yml
|
|
150
177
|
- LICENSE.txt
|
|
@@ -152,7 +179,8 @@ files:
|
|
|
152
179
|
- README.txt
|
|
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|
- Gemfile
|
|
154
181
|
- sequenceserver.gemspec
|
|
155
|
-
-
|
|
182
|
+
- !binary |-
|
|
183
|
+
YmluL3NlcXVlbmNlc2VydmVy
|
|
156
184
|
homepage: http://sequenceserver.com
|
|
157
185
|
licenses:
|
|
158
186
|
- SequenceServer (custom)
|
|
@@ -177,7 +205,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
177
205
|
version: '0'
|
|
178
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|
requirements: []
|
|
179
207
|
rubyforge_project:
|
|
180
|
-
rubygems_version: 1.8.
|
|
208
|
+
rubygems_version: 1.8.24
|
|
181
209
|
signing_key:
|
|
182
210
|
specification_version: 3
|
|
183
211
|
summary: BLAST search made easy!
|