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Top Forums UNIX for Beginners Questions & Answers How to split a column based on |? Post 302999412 by Aia on Monday 19th of June 2017 11:06:26 PM
Old 06-20-2017
Quote:
Originally Posted by BioBing
Hi all,

Newbie here, so please bear over with my stupid question Smilie

I have used far too long time today on figuring this out, so I hope that someone here can help me move on.

I have some annotation data for a transcriptome where I want to split a column containing NCBI accession IDs into a column with GIs and REFs (I still want keep the rest of the columns - just split the IDs)

This is an example of a row in my data set:
Code:
TRINITY_DN17272_c0_g1_i1	gi|242003970|ref|XP_002422928.1|	57.5	127	54	0	2	382	65	191	1.2e-41	176.0

What I want:
Code:
TRINITY_DN17272_c0_g1_i1	242003970   XP_002422928.1   57.5	127	54	0	2	382	65	191	1.2e-41	176.0

I have tried the following:
Code:
cut -d'|' -f2,4 File.m8 | tr '|' '\t'

It splits perfectly - too perfectly because I loose everything else besides the two columns:
Code:
242003970   XP_002422928.1

Can someone please help me out?

Thanks! Birgitte
Since gi and ref seems to be always there, perhaps another suggestion:
Code:
perl -pe 's/\|?(?:\s+gi|ref)?\|\s*/\t/g' file

Output:
Code:
TRINITY_DN17272_c0_g1_i1        242003970       XP_002422928.1  57.5    127     54      02382     65      191     1.2e-41 176.0

This User Gave Thanks to Aia For This Post:
 

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