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authorCalvin Morrison <mutantturkey@gmail.com>2014-02-04 16:45:27 -0500
committerCalvin Morrison <mutantturkey@gmail.com>2014-02-04 16:45:27 -0500
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This repository contains general utilities for processing sequences in fasta files.
-### Tools included ###
+## Tools included ##
+All of our tools use an alphebetical indexing scheme like this:
-kmer_total_count - this program will count each kmer in a fasta file, and print to standard out.
+ AAAA = 0
+ AAAC = 1
+ AAAG = 2
+ AAAT = 3
+ AACA = 4
+ ...
+
+
+### kmer_total_count
+
+this program will count each kmer in a fasta file, and print to standard out.
#### Usage
- kmer_total_count filename kmer_size
+ 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/
+
+#### Examples
+
+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
+ ...
- # Example
- calvin@barnabas:~/dna-utils$ ./kmer_total_count SuperManSequences.fasta 8
-
-the order of the array corresponds to AAAA, AAAC, AAAG, AAAT and so on
+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
+
+### kmer_counts_per_sequence
+
-usage: kmer_total_count -i input_file -k kmer [-n] [-l] ...
#### Licensing and Citation
Report all bugs to mutantturkey@gmail.com