Getting back into gear, I am assisting Andrew ID some targets from a salmonid transcriptome. With said transcriptome I am taking the blast output and getting some protein names sans SQLshare.

The tldr can be seen here, but if you have the time I will point out the key code aspects and leave you with a tabular file.


First we had the good ol tr.

Annotation_1D4BD559.png

Then I went ahead and downloaded the newest version of Swiss-prot details


http://ift.tt/2ak6G8p;

Before joining I needed to sort.

Annotation_1D4BD5EC.png

And with the join I needed a few parameters

!join -t $'\t' -1 3 -2 1 \
blastx_sprot.sort \
/Users/sr320/git-repos/nb-2016/uniprot-reviewed.sort

And because we need to get to Excel
!open blastx-join-uniprot-info.tab -a "Microsoft Excel"

Volia a tab file is created that can be examined further.

from half-shell http://ift.tt/2ajge08

The Little Things
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