SYNOPSIS
dnaindex [ option ... ]DESCRIPTION
dnaindex builds an index for a dna file. Dna files must be indexed to be useable with anfo(1), it is possible to have multiple indices for the same dna file.
OPTIONS
- -V, --version
-
Print version number and exit.
- -o file, --output file
-
Write output to
file. file
customarily ends in
.idx.
Default is
genomename_wordsize.idx.
- -g file, --genome file
-
Read the genome from
file.
This file name is also stored in the resulting index so it can be found
automatically whenever the index is used. It is therefore best if
file
is just a file name without path.
- -G dir, --genome-dir dir
-
Add
dir
to the genome search path. This is useful if the genome to be indexed
is not yet in the place where it will later be used.
- -d text, --description text
-
Add
text
as description to the index. This is purely informative.
- -s size, --wordsize size
-
Set the wordsize to
size.
A smaller wordsize increases precision at the expense of higher
computational investment. The default is 12, which with a stride of 8
yields a good compromise.
- -S num, --stride num
-
Set the stride to
num.
Only one out of
num
possible words of dna is actually indexed. A smaller stride increases
precicion at the expense of a bigger index. The default is 8, which in
conjunction with a wordsize of 12 yields a good compromise.
- -l lim, --limit lim
-
Prevents the indexing of words that occur more often than
lim
times. This can be used to ignore repetitive seeds and save the space
to store them. A good default depends on the size of the genome being
indexed, something like 500 works for the human genome with wordsize 12
and stride 8.
- -h, --histogram
-
Produce a histogram of word frequencies. This can be used to get an
indea how the frequency distribution to select an appropriate value for
--limit.
- -v, --verbose
-
Print a progress indicator during operation.
NOTES
dnaindex is limited to genomes no longer than 4 gigabases due to its use of 32 bit indices. The index is quite large, so depending on parameters, a 64 bit platform is needed for genomes in the gigabase range.
If a genome contains IUPAC ambiguity codes, the affected seeds need to be expanded. If there are many ambiguity codes in a small region, that results in an unacceptably large index.
ENVIRONMENT
- ANFO_PATH
-
Colon separated list of directories searched for genome files.
FILES
/etc/popt- The system wide configuration file for popt(3). dnaindex identifies itself as "dnaindex" to popt.
~/.popt
- Per user configuration file for popt(3).
BUGS
None known.