custom_reference_database tagshttps://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/tags2021-04-06T14:07:55Zhttps://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/tags/v1.1v1.1<h2 data-sourcepos="1:1-1:14" dir="auto">
<a id="user-content-version-11" class="anchor" href="#version-11" aria-hidden="true"></a>VERSION 1.1</h2>
<ul data-sourcepos="3:1-7:42" dir="auto">
<li data-sourcepos="3:1-3:15">Documentation</li>
<li data-sourcepos="4:1-4:12">Unit tests</li>
<li data-sourcepos="5:1-5:10">Tutorial</li>
<li data-sourcepos="6:1-6:21">Fix taxdump edition</li>
<li data-sourcepos="7:1-7:42">
<code data-sourcepos="7:4-7:20">init_ncbi_taxdump</code> decompression option</li>
</ul>2021-04-06T14:07:55Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/tags/v0.3v0.3<h1 data-sourcepos="1:1-1:33" dir="auto">
<a id="user-content-version-03-dentifrice-astral" class="anchor" href="#version-03-dentifrice-astral" aria-hidden="true"></a>VERSION 0.3 <em data-sourcepos="1:15-1:33">Dentifrice Astral</em>
</h1>
<ul data-sourcepos="3:1-4:14" dir="auto">
<li data-sourcepos="3:1-3:141">new command <code data-sourcepos="3:16-3:32">init_ncbi_taxdump</code> to download and uncompress ncbi taxdump archive from <a href="ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz">ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz</a>
</li>
<li data-sourcepos="4:1-4:14">fix curation</li>
</ul>2021-03-26T14:05:43Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/tags/v0.2v0.2<h1 data-sourcepos="1:1-1:29" dir="auto">
<a id="user-content-version-02-tĂȘte-de-veau" class="anchor" href="#version-02-t%C3%AAte-de-veau" aria-hidden="true"></a>Version 0.2 <em data-sourcepos="1:15-1:29">TĂȘte de veau</em>
</h1>
<ul data-sourcepos="3:1-15:0" dir="auto">
<li data-sourcepos="3:1-3:87">New colon <code data-sourcepos="3:14-3:22">ncbi_rank</code> in curate.csv which gives the known rank level in NCBI taxonomy</li>
<li data-sourcepos="4:1-4:47">
<code data-sourcepos="4:4-4:12">ncbi_rank</code> is generated by <code data-sourcepos="4:32-4:38">curegen</code> command</li>
<li data-sourcepos="5:1-10:103">
<code data-sourcepos="5:4-5:20">validate --curate</code> handle <code data-sourcepos="5:31-5:39">ncbi_rank</code> command following:
<ul data-sourcepos="6:4-10:103">
<li data-sourcepos="6:4-6:119">
<code data-sourcepos="6:7-6:18">species_rank</code> value is <em data-sourcepos="6:30-6:38">species</em> then no need to create new node in NCBI, just apply the taxonomy name correction</li>
<li data-sourcepos="7:4-7:135">
<code data-sourcepos="7:7-7:18">species_rank</code> value is <em data-sourcepos="7:30-7:36">genus</em> then a new node is created in NCBI with <code data-sourcepos="7:79-7:90">current_name</code> as species name and <code data-sourcepos="7:114-7:118">genus</code> as parent node.</li>
<li data-sourcepos="8:4-10:103">
<code data-sourcepos="8:7-8:18">species_rank</code> value is <em data-sourcepos="8:30-8:37">family</em> then
<ul data-sourcepos="9:8-10:103">
<li data-sourcepos="9:8-9:95">new node with taxonomy name <code data-sourcepos="9:39-9:43">genus</code> is created at <em data-sourcepos="9:60-9:66">genus</em> rank with <code data-sourcepos="9:79-9:84">family</code> as parent</li>
<li data-sourcepos="10:8-10:103">new node with taxonomy name <code data-sourcepos="10:39-10:50">current_name</code> is created at <em data-sourcepos="10:67-10:75">species</em> rank with <code data-sourcepos="10:88-10:92">genus</code> as parent</li>
</ul>
</li>
</ul>
</li>
<li data-sourcepos="11:1-11:52">module arguments check ncbi_taxdump files argument</li>
<li data-sourcepos="12:1-12:45">module arguments check curate file argument</li>
<li data-sourcepos="13:1-15:0">Curation of taxonomy is factorised</li>
</ul>2021-03-26T12:35:24Zpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/tags/v0.1v0.1<h1 data-sourcepos="1:1-1:28" dir="auto">
<a id="user-content-version-01-empty-coffee" class="anchor" href="#version-01-empty-coffee" aria-hidden="true"></a>VERSION 0.1 <em data-sourcepos="1:15-1:28">Empty coffee</em>
</h1>
<p data-sourcepos="3:1-3:11" dir="auto">2 commands:</p>
<ul data-sourcepos="5:1-8:0" dir="auto">
<li data-sourcepos="5:1-5:110">
<code data-sourcepos="5:4-5:11">validate</code>: check a FASTA file against NCBI taxonomy and return valid FASTA records and faulty FASTA records</li>
<li data-sourcepos="6:1-8:0">
<code data-sourcepos="6:4-6:10">curegen</code>: create a curate CSV file to apply curation on faulty taxonomy records</li>
</ul>2021-03-26T14:06:03Zpeguerinpierre-edouard.guerin@cefe.cnrs.fr