ncbi_blast_results_parser 0.1.0
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- data/.gitignore +17 -0
- data/Gemfile +3 -0
- data/LICENCE +20 -0
- data/README.md +30 -0
- data/Rakefile +8 -0
- data/lib/ncbi_blast_results_parser.rb +39 -0
- data/lib/ncbi_blast_results_parser/rid_parser.rb +22 -0
- data/lib/ncbi_blast_results_parser/status_parser.rb +15 -0
- data/lib/ncbi_blast_results_parser/version.rb +3 -0
- data/ncbi_blast_results_parser.gemspec +25 -0
- data/spec/fixtures/ready_response.html +135 -0
- data/spec/fixtures/rid_response.html +553 -0
- data/spec/fixtures/unknown_response.html +135 -0
- data/spec/fixtures/waiting_response.html +135 -0
- data/spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb +22 -0
- data/spec/lib/ncbi_blast_results_parser/status_parser_spec.rb +29 -0
- data/spec/lib/ncbi_blast_results_parser_spec.rb +24 -0
- data/spec/spec_helper.rb +8 -0
- metadata +115 -0
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<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
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// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
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bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
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bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
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src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
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href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to sign in"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Sign In]</a> <a
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href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to register for an account"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Register]</a></td></tr></table></div>
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<a class="skp" href="#content-wrap">Jump to Page Content</a>
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<li class="first "><a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
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<li class="recent "><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
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<li class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
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<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
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<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
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<a href="Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=">blastn suite</a>/
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<strong>Formatting Results - HZMF5DEN015</strong>
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<a id="frmPage" class="WAITING" href="#" submitForm="reformat">[Formatting options] </a>
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</div>
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<h3 id="jtitle" >Job Title: </h3>
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QBlastInfoBegin
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//--></SCRIPT>
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<table id="statInfo" class="WAITING">
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<tr><td>Request ID</td><td> <b>HZMF5DEN015</b></td></tr>
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<tr class="odd"><td>Status</td><td>Searching</td></tr>
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<tr><td>Submitted at</td><td>Sat Feb 16 13:37:25 2013</td></tr>
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<tr class="odd"><td>Current time</td><td>Sat Feb 16 13:37:26 2013</td></tr>
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<tr><td>Time since submission</td><td>00:00:01</td></tr>
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</table>
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<p class="WAITING">This page will be automatically updated in <b>2</b> seconds</p>
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<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
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<input name="ALIGNMENTS" type="hidden" value="200"><input name="ALIGNMENT_TYPE" type="hidden" value="Pairwise"><input name="DESCRIPTIONS" type="hidden" value="100"><input name="FORMAT_OBJECT" type="hidden" value="Alignment"><input name="FORMAT_TYPE" type="hidden" value="XML"><input name="OLD_BLAST" type="hidden" value="false"><input name="OVERVIEW" type="hidden" value="yes"><input name="RID" type="hidden" value="HZMF5DEN015"><input name="SEARCH_DB_STATUS" type="hidden" value="31"><input name="USER_TYPE" type="hidden" value="2"><input name="_PGR" type="hidden" value="0">
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<a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
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<a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
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<a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
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title='NCBI intellectual property statement'>Copyright</a> |
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<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
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title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> |
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title='NLM privacy policy'>Privacy</a> |
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<a href='http://www.ncbi.nlm.nih.gov/About/accessibility.html'
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title='About using NCBI resources with assistive technology'>Accessibility</a> |
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<a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
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title='How to get help, submit data, or provide feedback'>Contact</a> |
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title='How to get help, submit data, or provide feedback'>Send feedback</a>
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<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
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// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
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bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
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bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
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src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
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href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to sign in"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Sign In]</a> <a
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href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to register for an account"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Register]</a></td></tr></table></div>
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</div>
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<a class="skp" href="#content-wrap">Jump to Page Content</a>
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<ul id="nav">
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<li class="first "><a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
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<li class="recent "><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
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<li class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
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<li class= "last documentation "> <a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>
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<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
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<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
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<a href="Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=">blastn suite</a>/
|
|
52
|
+
<strong>Formatting Results - HZMF5DEN015</strong>
|
|
53
|
+
</div>
|
|
54
|
+
<div class="inlineDiv resHeader">
|
|
55
|
+
<a id="frmPage" class="WAITING" href="#" submitForm="reformat">[Formatting options] </a>
|
|
56
|
+
</div>
|
|
57
|
+
<h3 id="jtitle" >Job Title: </h3>
|
|
58
|
+
|
|
59
|
+
<div id="content">
|
|
60
|
+
<!--<ul id="msg" class="msg"><li class=""><p class=""></p><p class=""></p><p class=""></p></ul> -->
|
|
61
|
+
<ul id="msg" class="msg"><li class=""></li></ul>
|
|
62
|
+
<p><!--
|
|
63
|
+
QBlastInfoBegin
|
|
64
|
+
Status=WAITING
|
|
65
|
+
QBlastInfoEnd
|
|
66
|
+
--></p>
|
|
67
|
+
|
|
68
|
+
<SCRIPT LANGUAGE="JavaScript"><!--
|
|
69
|
+
var tm = "2000";
|
|
70
|
+
if (tm != "") {
|
|
71
|
+
setTimeout('document.forms[0].submit();',tm);
|
|
72
|
+
}
|
|
73
|
+
//--></SCRIPT>
|
|
74
|
+
<table id="statInfo" class="WAITING">
|
|
75
|
+
<tr><td>Request ID</td><td> <b>HZMF5DEN015</b></td></tr>
|
|
76
|
+
<tr class="odd"><td>Status</td><td>Searching</td></tr>
|
|
77
|
+
<tr><td>Submitted at</td><td>Sat Feb 16 13:37:25 2013</td></tr>
|
|
78
|
+
<tr class="odd"><td>Current time</td><td>Sat Feb 16 13:37:26 2013</td></tr>
|
|
79
|
+
<tr><td>Time since submission</td><td>00:00:01</td></tr>
|
|
80
|
+
</table>
|
|
81
|
+
<p class="WAITING">This page will be automatically updated in <b>2</b> seconds</p>
|
|
82
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
|
|
83
|
+
<input name="ALIGNMENTS" type="hidden" value="200"><input name="ALIGNMENT_TYPE" type="hidden" value="Pairwise"><input name="DESCRIPTIONS" type="hidden" value="100"><input name="FORMAT_OBJECT" type="hidden" value="Alignment"><input name="FORMAT_TYPE" type="hidden" value="XML"><input name="OLD_BLAST" type="hidden" value="false"><input name="OVERVIEW" type="hidden" value="yes"><input name="RID" type="hidden" value="HZMF5DEN015"><input name="SEARCH_DB_STATUS" type="hidden" value="31"><input name="USER_TYPE" type="hidden" value="2"><input name="_PGR" type="hidden" value="0">
|
|
84
|
+
<input name="_PGR" type="hidden" value="0" >
|
|
85
|
+
<input name="CMD" type="hidden" value="Get">
|
|
86
|
+
|
|
87
|
+
</form>
|
|
88
|
+
|
|
89
|
+
</div><!-- /#content -->
|
|
90
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat">
|
|
91
|
+
<input name="QUERY_INFO" type="hidden" value="" />
|
|
92
|
+
<input name="ENTREZ_QUERY" type="hidden" value="" />
|
|
93
|
+
<input name="CDD_RID" type="hidden" value="" />
|
|
94
|
+
<input name="CDD_SEARCH_STATE" type="hidden" value="" />
|
|
95
|
+
<input name="RID" type="hidden" value="HZMF5DEN015" />
|
|
96
|
+
<input name="STEP_NUMBER" type="hidden" value="" />
|
|
97
|
+
<input name="CMD" type="hidden" value="Web"/>
|
|
98
|
+
<input NAME="PAGE_TYPE" type="hidden" value="BlastFormatting"/>
|
|
99
|
+
|
|
100
|
+
<!-- TO DO: test all of those changes -->
|
|
101
|
+
<!-- Psi blast params PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
|
|
102
|
+
<!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
|
|
103
|
+
<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
|
|
104
|
+
</form>
|
|
105
|
+
</div><!-- /#content-wrap -->
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
<div id="footer">
|
|
109
|
+
<div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
|
|
110
|
+
<p id="orgns">
|
|
111
|
+
<a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
|
|
112
|
+
<a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
|
|
113
|
+
<a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
|
|
114
|
+
<a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
|
|
115
|
+
</p>
|
|
116
|
+
|
|
117
|
+
<p>
|
|
118
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
|
|
119
|
+
title='NCBI intellectual property statement'>Copyright</a> |
|
|
120
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
|
|
121
|
+
title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> |
|
|
122
|
+
<a href='http://www.nlm.nih.gov/privacy.html'
|
|
123
|
+
title='NLM privacy policy'>Privacy</a> |
|
|
124
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/accessibility.html'
|
|
125
|
+
title='About using NCBI resources with assistive technology'>Accessibility</a> |
|
|
126
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
|
|
127
|
+
title='How to get help, submit data, or provide feedback'>Contact</a> |
|
|
128
|
+
<a href='mailto:blast-help@ncbi.nlm.nih.gov'
|
|
129
|
+
title='How to get help, submit data, or provide feedback'>Send feedback</a>
|
|
130
|
+
</p>
|
|
131
|
+
</div>
|
|
132
|
+
</div><!--/#wrap-->
|
|
133
|
+
</body>
|
|
134
|
+
|
|
135
|
+
</html>
|
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
require_relative '../../spec_helper'
|
|
2
|
+
|
|
3
|
+
describe NCBIBlastResultsParser::RIDParser do
|
|
4
|
+
|
|
5
|
+
# Parser Setup
|
|
6
|
+
let(:rid_parser) { NCBIBlastResultsParser::RIDParser.new }
|
|
7
|
+
let(:parser) { Nokogiri::HTML::SAX::Parser.new(rid_parser) }
|
|
8
|
+
|
|
9
|
+
# RID Response
|
|
10
|
+
let(:response) { File.read(File.expand_path('../../fixtures/rid_response.html', File.dirname(__FILE__))) }
|
|
11
|
+
|
|
12
|
+
it 'parses an RID response' do
|
|
13
|
+
parser.parse(response)
|
|
14
|
+
rid_parser.rid.must_equal 'BUCSAKD101R'
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
it 'parses the suggested wait time' do
|
|
18
|
+
parser.parse(response)
|
|
19
|
+
rid_parser.wait.must_equal 17
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
end
|
|
@@ -0,0 +1,29 @@
|
|
|
1
|
+
require_relative '../../spec_helper'
|
|
2
|
+
|
|
3
|
+
describe NCBIBlastResultsParser::StatusParser do
|
|
4
|
+
|
|
5
|
+
# Parser Setup
|
|
6
|
+
let(:status_parser) { NCBIBlastResultsParser::StatusParser.new }
|
|
7
|
+
let(:parser) { Nokogiri::HTML::SAX::Parser.new(status_parser) }
|
|
8
|
+
|
|
9
|
+
# Status Responses
|
|
10
|
+
let(:ready) { File.read(File.expand_path('../../fixtures/ready_response.html', File.dirname(__FILE__))) }
|
|
11
|
+
let(:waiting) { File.read(File.expand_path('../../fixtures/waiting_response.html', File.dirname(__FILE__))) }
|
|
12
|
+
let(:unknown) { File.read(File.expand_path('../../fixtures/unknown_response.html', File.dirname(__FILE__))) }
|
|
13
|
+
|
|
14
|
+
it 'parses a ready response' do
|
|
15
|
+
parser.parse(ready)
|
|
16
|
+
status_parser.status.must_equal 'READY'
|
|
17
|
+
end
|
|
18
|
+
|
|
19
|
+
it 'parses a waiting response' do
|
|
20
|
+
parser.parse(waiting)
|
|
21
|
+
status_parser.status.must_equal 'WAITING'
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
it 'parses an unknown response' do
|
|
25
|
+
parser.parse(unknown)
|
|
26
|
+
status_parser.status.must_equal 'UNKNOWN'
|
|
27
|
+
end
|
|
28
|
+
|
|
29
|
+
end
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
require_relative '../spec_helper'
|
|
2
|
+
|
|
3
|
+
describe NCBIBlastResultsParser do
|
|
4
|
+
|
|
5
|
+
# Parser Setup
|
|
6
|
+
let(:parser) { NCBIBlastResultsParser }
|
|
7
|
+
|
|
8
|
+
# Responses
|
|
9
|
+
let(:rid_response) { File.read(File.expand_path('../fixtures/rid_response.html', File.dirname(__FILE__))) }
|
|
10
|
+
let(:ready_response) { File.read(File.expand_path('../fixtures/ready_response.html', File.dirname(__FILE__))) }
|
|
11
|
+
|
|
12
|
+
it 'parses a request id' do
|
|
13
|
+
parser.rid(rid_response).must_equal 'BUCSAKD101R'
|
|
14
|
+
end
|
|
15
|
+
|
|
16
|
+
it 'parses a suggested wait time' do
|
|
17
|
+
parser.wait(rid_response).must_equal 17
|
|
18
|
+
end
|
|
19
|
+
|
|
20
|
+
it 'parses a status' do
|
|
21
|
+
parser.status(ready_response).must_equal 'READY'
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
end
|
data/spec/spec_helper.rb
ADDED
metadata
ADDED
|
@@ -0,0 +1,115 @@
|
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
|
2
|
+
name: ncbi_blast_results_parser
|
|
3
|
+
version: !ruby/object:Gem::Version
|
|
4
|
+
version: 0.1.0
|
|
5
|
+
prerelease:
|
|
6
|
+
platform: ruby
|
|
7
|
+
authors:
|
|
8
|
+
- Gareth Rees
|
|
9
|
+
autorequire:
|
|
10
|
+
bindir: bin
|
|
11
|
+
cert_chain: []
|
|
12
|
+
date: 2013-02-17 00:00:00.000000000 Z
|
|
13
|
+
dependencies:
|
|
14
|
+
- !ruby/object:Gem::Dependency
|
|
15
|
+
name: nokogiri
|
|
16
|
+
requirement: &70334262957880 !ruby/object:Gem::Requirement
|
|
17
|
+
none: false
|
|
18
|
+
requirements:
|
|
19
|
+
- - ! '>='
|
|
20
|
+
- !ruby/object:Gem::Version
|
|
21
|
+
version: '0'
|
|
22
|
+
type: :runtime
|
|
23
|
+
prerelease: false
|
|
24
|
+
version_requirements: *70334262957880
|
|
25
|
+
- !ruby/object:Gem::Dependency
|
|
26
|
+
name: minitest
|
|
27
|
+
requirement: &70334259121780 !ruby/object:Gem::Requirement
|
|
28
|
+
none: false
|
|
29
|
+
requirements:
|
|
30
|
+
- - ! '>='
|
|
31
|
+
- !ruby/object:Gem::Version
|
|
32
|
+
version: '0'
|
|
33
|
+
type: :development
|
|
34
|
+
prerelease: false
|
|
35
|
+
version_requirements: *70334259121780
|
|
36
|
+
- !ruby/object:Gem::Dependency
|
|
37
|
+
name: turn
|
|
38
|
+
requirement: &70334264495440 !ruby/object:Gem::Requirement
|
|
39
|
+
none: false
|
|
40
|
+
requirements:
|
|
41
|
+
- - ! '>='
|
|
42
|
+
- !ruby/object:Gem::Version
|
|
43
|
+
version: '0'
|
|
44
|
+
type: :development
|
|
45
|
+
prerelease: false
|
|
46
|
+
version_requirements: *70334264495440
|
|
47
|
+
- !ruby/object:Gem::Dependency
|
|
48
|
+
name: rake
|
|
49
|
+
requirement: &70334264471540 !ruby/object:Gem::Requirement
|
|
50
|
+
none: false
|
|
51
|
+
requirements:
|
|
52
|
+
- - ! '>='
|
|
53
|
+
- !ruby/object:Gem::Version
|
|
54
|
+
version: '0'
|
|
55
|
+
type: :development
|
|
56
|
+
prerelease: false
|
|
57
|
+
version_requirements: *70334264471540
|
|
58
|
+
description: Parses useful information from the HTML response of an NCBI Blast
|
|
59
|
+
email:
|
|
60
|
+
- gareth@garethrees.co.uk
|
|
61
|
+
executables: []
|
|
62
|
+
extensions: []
|
|
63
|
+
extra_rdoc_files: []
|
|
64
|
+
files:
|
|
65
|
+
- .gitignore
|
|
66
|
+
- Gemfile
|
|
67
|
+
- LICENCE
|
|
68
|
+
- README.md
|
|
69
|
+
- Rakefile
|
|
70
|
+
- lib/ncbi_blast_results_parser.rb
|
|
71
|
+
- lib/ncbi_blast_results_parser/rid_parser.rb
|
|
72
|
+
- lib/ncbi_blast_results_parser/status_parser.rb
|
|
73
|
+
- lib/ncbi_blast_results_parser/version.rb
|
|
74
|
+
- ncbi_blast_results_parser.gemspec
|
|
75
|
+
- spec/fixtures/ready_response.html
|
|
76
|
+
- spec/fixtures/rid_response.html
|
|
77
|
+
- spec/fixtures/unknown_response.html
|
|
78
|
+
- spec/fixtures/waiting_response.html
|
|
79
|
+
- spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb
|
|
80
|
+
- spec/lib/ncbi_blast_results_parser/status_parser_spec.rb
|
|
81
|
+
- spec/lib/ncbi_blast_results_parser_spec.rb
|
|
82
|
+
- spec/spec_helper.rb
|
|
83
|
+
homepage: ''
|
|
84
|
+
licenses: []
|
|
85
|
+
post_install_message:
|
|
86
|
+
rdoc_options: []
|
|
87
|
+
require_paths:
|
|
88
|
+
- lib
|
|
89
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
|
90
|
+
none: false
|
|
91
|
+
requirements:
|
|
92
|
+
- - ! '>='
|
|
93
|
+
- !ruby/object:Gem::Version
|
|
94
|
+
version: '0'
|
|
95
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
96
|
+
none: false
|
|
97
|
+
requirements:
|
|
98
|
+
- - ! '>='
|
|
99
|
+
- !ruby/object:Gem::Version
|
|
100
|
+
version: '0'
|
|
101
|
+
requirements: []
|
|
102
|
+
rubyforge_project:
|
|
103
|
+
rubygems_version: 1.8.15
|
|
104
|
+
signing_key:
|
|
105
|
+
specification_version: 3
|
|
106
|
+
summary: Parses useful information from the HTML response of an NCBI Blast
|
|
107
|
+
test_files:
|
|
108
|
+
- spec/fixtures/ready_response.html
|
|
109
|
+
- spec/fixtures/rid_response.html
|
|
110
|
+
- spec/fixtures/unknown_response.html
|
|
111
|
+
- spec/fixtures/waiting_response.html
|
|
112
|
+
- spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb
|
|
113
|
+
- spec/lib/ncbi_blast_results_parser/status_parser_spec.rb
|
|
114
|
+
- spec/lib/ncbi_blast_results_parser_spec.rb
|
|
115
|
+
- spec/spec_helper.rb
|