diff options
| author | Calvin <calvin@EESI> | 2013-05-14 21:51:40 -0400 |
|---|---|---|
| committer | Calvin <calvin@EESI> | 2013-05-14 21:51:40 -0400 |
| commit | 0773aaf89678b967588a902df1f5e6f9ccea393d (patch) | |
| tree | 40762e5df1da876d460d8695357ab0835645e8c6 /src/c/quikr_train.1 | |
| parent | 1d2becc9af591d37badfe0e77751bbb80932472f (diff) | |
release1.0
Diffstat (limited to 'src/c/quikr_train.1')
| -rw-r--r-- | src/c/quikr_train.1 | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/src/c/quikr_train.1 b/src/c/quikr_train.1 new file mode 100644 index 0000000..dd1493f --- /dev/null +++ b/src/c/quikr_train.1 @@ -0,0 +1,61 @@ +.TH quikr_train 1 quikr_train-2013-05 +.SH NAME +quikr_train \- train databases for use with Quikr +.SH SYNOPSIS +.B quikr_train +.RB [ \-i +.IR input] +.RB [ \-o +.IR output] +.RB [ \-k +.IR kmer ] +.RB [ \-v ] +.P +.BR quikr " ..." +.SH DESCRIPTION +.B quikr +The quikr_train is a utility to train a database for use with quikr. +Before running the quikr utility, you need to generate the sensing matrix or +download a pretrained one from our project's homepage. + +quikr_train returns a sensing matrix that can be used with the quikr +function. +.P +.SH OPTIONS +.TP +.B \-i, --input +the database of sequences to create the sensing matrix. (fasta format) +.TP +.B \-k, --kmer +specify what size of kmer to use. (default value is 6) +.TP +.B \-o, --output +the sensing matrix. (a gzip'd text file) +.TP +.B \-v, --verbose +verbose mode. +.SH EXAMPLES +Use quikr_train to generate a sensing matrix from rdp7.fasta. This uses 6mers by default. +.P +quikr_train -i rdp7.fa -o rd7_sensing_matrix.gz +.SH USAGE +If you do not have a .gz file on your output matrix name, it will be appended. +.SH "SEE ALSO" +\fBmultifasta_to_otu\fP(1), \fBquikr\fP(1). +.SH AUTHORS +.B quikr +was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison +<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, Jean-Luc Bouchot +.SH REPORTING BUGS +.TP +Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \ +operating system, current compiler, and test files to reproduce your issue. +.SH COPYRIGHT. +Copyright \(co 2013 by Calvin Morrison and Gail Rosen. Permission to use, +copy, modify, distribute, and sell this software and its documentation for +any purpose is hereby granted without fee, provided that the above copyright +notice appear in all copies and that both that copyright notice and this +permission noticeappear in supporting documentation. No representations are +made about the suitability of this software for any purpose. It is provided +"as is" without express or implied warranty. + |