fahash1
Sequence hash builder for reverse e-pcr
Usage
fahash [-hV]
-b
hash-file
[-w
wdsize]
[-f
period]
[-F
fragment_min,fragment_max]
[-k]
[-c
cachesize]
[{-v
1 | 2}]
famap-file ...
fahash [-hV]
-T
hash-file
[-o
outfile]
Overview
The program fahash is part of the e-PCR suite and is used to build hash-files, and output word usage statistics for reverse e-PCR searches.
Options
-
-b hash-file -
Build hash tables (hash-file) from sequence files,
-
-T hash-file -
Print word usage statistics for hash-file
-
-o outfile -
Write output to file `outfile'
build-options:
-
-w wordsize -
Set word size when building hash tables
-
-f period -
Set discontiguity when building hash tables
-
-k -
Skip repeats when building hash-file
-
-F min,max -
Set watermarks for fragment size (in Mb) (version 1 only)
-
-c cachesize -
Set cache size (version 2 only)
-
-v ver -
Use format version (1|2, 2 is default)
Examples
famap -tN -b genome.famap org/chr_*.fa
fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
See famap(1) and re-pcr(1)
Releases
Unchanged in 9 releases since Debian 5.0 (Lenny).