From 1a570c3e4f4932674a751494c592738eaad6bc05 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Tue, 4 Feb 2014 16:45:27 -0500
Subject: add examples to readme.md

---
 README.md | 80 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 72 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index dd204a4..5786016 100644
--- a/README.md
+++ b/README.md
@@ -4,21 +4,85 @@
 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
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