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BLAST2COL

Section: User Commands (1)
Updated: September 2000
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NAME

blast2col - convert BLAST output format to col format.  

SYNOPSIS

blast2col
[-expect=expect] [-length=length] [-similarity=similarity] [-score=score] [-top=top] [-mismatch=mismatch] [-alignlen=alignlen] [-ignore=ignore] [file]
 

DESCRIPTION

blast2col converts BLAST output to col format. Input is either from file or stdin. The output is sent to stdout.

 

OPTIONS

blast2col accepts the following options:

--expect=expect
Sets maximum limit for expect value of hits to be converted. expect is a decimal number

--length=length
Sets minimum limit for alignment length of hits to be converted. length is an integer.

--similarity=similarity
Sets minimum limit for matches relative to length of hits to be converted. similarity is an integer from 0 to 1.

--score=score
Sets minimum limit for score value of hits to be converted. score is a decimal number

--top=top
Does not work.

--mismatch=mismatch
Sets maximum limit for number of mismatches of hits to be converted. mismatch is an integer.

--alignlen=alignlen
Sets minimum limit for alignment length relative to query length of hits to be converted. alignlen is an integer from 0 to 1.

--ignore=ignore
Specifies mismatches that should be ignored. ignore is a string of nucleotide pairs, separated by commas. E.g. `GT,TG' specifies that G-T mismatches (both ways) should be ignored when deciding which sequences to convert.

 

EXAMPLES

Convert blast file to col file.

blast2col foo.blast

Convert blast file to col file. Only convert hits that has at most 5 mismatches and has a length of at least 40, while 90% of the hit is matches.

blast2col --mismatch=5 --length=40 --similarity=0.9 foo.blast

 

BUGS

--top option does not work.

Report other bugs to col-bugs@bioinf.au.dk.  

AUTHOR

Bjarne Knudsen (bk@daimi.au.dk)  

SEE ALSO


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
BUGS
AUTHOR
SEE ALSO


Comments, questions, etc., email gorodkin@genome.ku.dk.


Last updated March 26th, 2007 by Jan Gorodkin