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Top Forums UNIX for Beginners Questions & Answers How to split a column based on |? Post 302999387 by BioBing on Monday 19th of June 2017 09:45:58 AM
Old 06-19-2017
How to split a column based on |?

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
 

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SPLIT(1)						    BSD General Commands Manual 						  SPLIT(1)

NAME
split -- split a file into pieces SYNOPSIS
split [-a suffix_length] [-b byte_count[k|m] | -l line_count -n chunk_count] [file [name]] DESCRIPTION
The split utility reads the given file and breaks it up into files of 1000 lines each. If file is a single dash or absent, split reads from the standard input. file itself is not altered. The options are as follows: -a Use suffix_length letters to form the suffix of the file name. -b Create smaller files byte_count bytes in length. If 'k' is appended to the number, the file is split into byte_count kilobyte pieces. If 'm' is appended to the number, the file is split into byte_count megabyte pieces. -l Create smaller files line_count lines in length. -n Split file into chunk_count smaller files. If additional arguments are specified, the first is used as the name of the input file which is to be split. If a second additional argument is specified, it is used as a prefix for the names of the files into which the file is split. In this case, each file into which the file is split is named by the prefix followed by a lexically ordered suffix using suffix_length characters in the range ``a-z''. If -a is not speci- fied, two letters are used as the suffix. If the name argument is not specified, 'x' is used. STANDARDS
The split utility conforms to IEEE Std 1003.1-2001 (``POSIX.1''). HISTORY
A split command appeared in Version 6 AT&T UNIX. The -a option was introduced in NetBSD 2.0. Before that, if name was not specified, split would vary the first letter of the filename to increase the number of possible output files. The -a option makes this unnecessary. BSD
May 28, 2007 BSD
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