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Full Discussion: modify one column
Top Forums Shell Programming and Scripting modify one column Post 302531407 by phil_heath on Thursday 16th of June 2011 05:06:42 PM
Old 06-16-2011
modify one column
Hi,

I have an output that looks unusual and it is very large so I cannot do it manually.

Basically it looks like this:


Code:
U	>c93[org=S_paradoxus][moltype=genomic][contig=c93]	57866	R
U	>c38[org=S_paradoxus][moltype=genomic][contig=c38]	66265	R
U	>c261[org=S_paradoxus][moltype=genomic][contig=c261]	80401	R
U	>c169[org=S_paradoxus][moltype=genomic][contig=c169]	12250	R
U	>c348[org=S_paradoxus][moltype=genomic][contig=c348]	2661	F
U	>c425[org=S_paradoxus][moltype=genomic][contig=c425]	38762	R
U	>c351[org=S_paradoxus][moltype=genomic][contig=c351]	44504	R
U	>c421[org=S_paradoxus][moltype=genomic][contig=c421]	8212	F
U	>c467[org=S_paradoxus][moltype=genomic][contig=c467]	3648	F
U	>c84[org=S_paradoxus][moltype=genomic][contig=c84]	33028	R
U	>c6[org=S_paradoxus][moltype=genomic][contig=c6]	4765	R

It is a tab separated file and I want it to modify the second column (basically simplify it) to look like this:

Code:
U	c93	57866	R
U	c38	66265	R
U	c261	80401	R
U	c169	12250	R
U	c348	2661	F
U	c425	38762	R
U	c351	44504	R
U	c421	8212	F
U	c467	3648	F
U	c84	33028	R
U	c6	4765	R

Thanks

Phil
 

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LEARN ABOUT DEBIAN

ssake

SSAKE(1)						      General Commands Manual							  SSAKE(1)

NAME

       ssake - assembling millions of very short DNA sequences

SYNOPSIS

       Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension.

OPTIONS

       -f     Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must now be separated by ":"

       -s     Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)

       -m     Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)

       -o     Minimum number of reads needed to call a base during an extension (default -o 3)

       -r     Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

       -t     Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)>

       -p     Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

       -v     Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

       -b     Base name for your output files (optional)

       ============ Options below only considered with -p 1 ============

       -d     Mean distance expected/observed between paired-end reads (default -d 200, optional)

       -e     Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

       -k     Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

       -a     Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.70, optional)

       -z     Minimum contig size to track paired-end reads (default -z 50, optional)

       -g     Fasta file containing unpaired sequence reads (optional)

SEE ALSO

       /usr/share/doc/ssake/SSAKE.readme between

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							  SSAKE(1)
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