diff options
| -rw-r--r-- | doc/.cli.markdown.swo | bin | 0 -> 16384 bytes | |||
| -rw-r--r-- | doc/.cli.markdown.swp | bin | 0 -> 16384 bytes | |||
| -rw-r--r-- | doc/.install.markdown.swo | bin | 0 -> 12288 bytes | |||
| -rw-r--r-- | doc/.install.markdown.swp | bin | 0 -> 12288 bytes | |||
| -rw-r--r-- | doc/.matlab.markdown.swp | bin | 0 -> 16384 bytes | |||
| -rw-r--r-- | doc/install.markdown | 7 | ||||
| -rw-r--r-- | doc/matlab.markdown | 7 | ||||
| -rw-r--r-- | doc/python.markdown | 3 | ||||
| -rw-r--r-- | src/c/quikr.1 | 5 | ||||
| -rw-r--r-- | src/c/quikr.c | 1 |
10 files changed, 12 insertions, 11 deletions
diff --git a/doc/.cli.markdown.swo b/doc/.cli.markdown.swo Binary files differnew file mode 100644 index 0000000..cb4d4a8 --- /dev/null +++ b/doc/.cli.markdown.swo diff --git a/doc/.cli.markdown.swp b/doc/.cli.markdown.swp Binary files differnew file mode 100644 index 0000000..428a3b6 --- /dev/null +++ b/doc/.cli.markdown.swp diff --git a/doc/.install.markdown.swo b/doc/.install.markdown.swo Binary files differnew file mode 100644 index 0000000..94f5651 --- /dev/null +++ b/doc/.install.markdown.swo diff --git a/doc/.install.markdown.swp b/doc/.install.markdown.swp Binary files differnew file mode 100644 index 0000000..c676c32 --- /dev/null +++ b/doc/.install.markdown.swp diff --git a/doc/.matlab.markdown.swp b/doc/.matlab.markdown.swp Binary files differnew file mode 100644 index 0000000..c2e5b26 --- /dev/null +++ b/doc/.matlab.markdown.swp diff --git a/doc/install.markdown b/doc/install.markdown index eb0e8ce..3308f83 100644 --- a/doc/install.markdown +++ b/doc/install.markdown @@ -5,23 +5,24 @@ To use Quikr there are several prerequisites. + Mac OS X 10.6.8 or GNU/Linux + 4Gb of RAM minimum. Absolutely neccessary. + gcc that supports OpenMP -+ mlton the Standard-ML compiler ### Python Requirements ### +*the python version is out of date* + Python 2.7+ + Scipy + Numpy + BioPython +### Matlab Requrements ### ++ [dna\_utils](http://github.com/EESI/dna-utils/) must be installed + ### Mac Requirements ### + Mac OS X 10.6.8 (what we have tested) + GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation) -+ mlton the Standard-ML compiler + OpenMP libraries (libgomp, usually comes with gcc) ### Linux Requirements ### + GCC 4.7 or newer -+ OCaml compiler mlton + OpenMP libraries (libgomp, usually comes with gcc) We also have a Quikr implementation in Matlab so that you can easily integrate diff --git a/doc/matlab.markdown b/doc/matlab.markdown index 09b0103..87a3a4d 100644 --- a/doc/matlab.markdown +++ b/doc/matlab.markdown @@ -2,13 +2,6 @@ The Quikr implementation works in Matlab and also works in Octave, but the Octave version will run much slower. -You will need to install the generate_kmers tool into your $PATH (eg /usr/bin/) -this file is available in the src/python/ directory. If you use make to install -the quikr project, it will already be installed. To test this you can run: - - which generate_kmers - - ## Quikr Example ## This is an example of how to run Quikr. Before you try the example please make make sure that you are in the quikr's matlab directory (src/matlab/): diff --git a/doc/python.markdown b/doc/python.markdown index df086d8..cbc59d1 100644 --- a/doc/python.markdown +++ b/doc/python.markdown @@ -1,3 +1,5 @@ +*The python version is outdated. do not use! It is only here for historical purposes!* + # Python Documentation # The python version comes with scripts that can be used like the regular quikr program, and also a module called quikr so integration with python scripts @@ -12,6 +14,7 @@ If you want to use our quikr module, run help on the module: >>> import quikr >>> help(quikr) + ## Python Cannot Find XYZ ## Ensure that you have Python 2.7, Scipy, Numpy, and BIOpython installed diff --git a/src/c/quikr.1 b/src/c/quikr.1 index 4418a7f..7d0baf6 100644 --- a/src/c/quikr.1 +++ b/src/c/quikr.1 @@ -36,6 +36,9 @@ specify what size of kmer to use. (default value is 6) .B \-l, --lambda lambda value to use. (default value is 10000) .TP +.B \-r, --rare-percent +remove mers from classification if their values are less than the x percentile of values in the sample (default value is 10000) +.TP .B \-o, --output OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output) .TP @@ -52,7 +55,7 @@ quikr -i sample.fa -s rdp_sensing_matrix.gz -o frequencies.txt \fBmultifasta_to_otu\fP(1), \fBquikr_train\fP(1). .SH AUTHORS .B quikr -was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison +was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison <mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and Jean-Luc Bouchot. .SH REPORTING BUGS .TP diff --git a/src/c/quikr.c b/src/c/quikr.c index 01c5f63..de1f39a 100644 --- a/src/c/quikr.c +++ b/src/c/quikr.c @@ -115,6 +115,7 @@ int main(int argc, char **argv) { if(verbose) { printf("kmer: %u\n", kmer); + printf("rare: %lf\n", rare_percent); printf("lambda: %llu\n", lambda); printf("fasta: %s\n", input_fasta_filename); printf("sensing matrix: %s\n", sensing_matrix_filename); |