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<h3>
Saira Hussain pushed to branch master
at <a href="https://salsa.debian.org/med-team/mcl">Debian Med / mcl</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/mcl/commit/d59032e3302762aac5041ef32a3e6c72122b711d">d59032e3</a></strong>
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<span>by Saira Hussain</span>
<i>at 2019-07-11T13:40:26Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update README with the testing workflow
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<h4>1 changed file:</h4>
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−
debian/tests/data/README
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<h4>Changes:</h4>
<li id="4d8bffeb70d7cbd4c77ded97a3a50b4af285e3e0">
<a href="https://salsa.debian.org/med-team/mcl/commit/d59032e3302762aac5041ef32a3e6c72122b711d#4d8bffeb70d7cbd4c77ded97a3a50b4af285e3e0"><strong>debian/tests/data/README</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">In order to get a FASTA file from all the Skunavirus genomes, the NCBI database was used:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Skunavirus,%20taxid:1623305</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Select Download, Select Data Type (Sequence Data/FASTA Format)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">The rest of the data is generated with this workflow in mind:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">1. Using the package prodigal to generate a database file</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">2. Using awk to filter this</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">3. Using mcl to generate protein families</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">4. Using a custom python script to do pairwise comparisons</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">5. Out of the files generated in the previous step, I am using mcl again to build clusters of genomes.</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">You can find more details inside the LMCLUST.sh</span></pre>
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