This repository contains general utilities for processing sequences in fasta files.
All of our tools use an alphebetical indexing scheme like this:
AAAA = 0
AAAC = 1
AAAG = 2
AAAT = 3
AACA = 4
...
this program will count each kmer in a fasta file, and print to standard out.
usage: kmer_total_count -i input_file -k kmer [-n] [-l] ...
count mers in size k from a fasta file
--input -i input fasta file to count
--kmer -k size of mers to count
--nonzero -n only print non-zero values
--label -l print mer along with value
Report all bugs to mutantturkey@gmail.com
Copyright 2014 Calvin Morrison, Drexel University.
If you are using any dna-utils tool for a publication
please cite your usage:
dna-utils. Drexel University, Philadelphia USA, 2014;
software available at www.github.com/EESI/dna-utils/
a basic example, where we specify the k-mer size and input file.
calvin@barnabas:~/dna-utils$ ./kmer_total_count -i SuperManSequences.fasta -k 8
2946
1161
14141
...
it also supports input from stdin, which is great for combining with compression programs
calvin@barnabase:~/dna-utils$ gzip -dc ~/super_big_fasta_file.fasta.gz | ./kmer_total_count -k 8
234523
121612
123161
294282
...
we can also have only nonzero results (great for large mers), which prints the index, then the value
calvin@barnabas:~/src/dna-utils$ ./kmer_total_count --nonzero -k 9 < ~/input/sample\=700013596.fa
no input file specified with -i, reading from stdin
0 3
1 2
3 3
5 1
...
lastly a useful tool is having the labels generated for us, so grepping, searching and other things are easier.
calvin@barnabas:~/src/dna/utils$ ./kmer_total_count -i ~/sample.fa -k 6 -l
AAAAAA 552
AAAAAC 246
...
TTTTTC 102
TTTTTG 924
TTTTTT 4961
Report all bugs to mutantturkey@gmail.com
Copyright 2014 Calvin Morrison, Drexel University.
If you are using any dna-utils tool for a publication please cite your usage:
dna-utils. Drexel University, Philadelphia USA, 2014; software available at www.github.com/EESI/dna-utils/