diff options
| -rw-r--r-- | Makefile | 12 | ||||
| -rw-r--r-- | src/matlab/quikr.m | 4 | ||||
| -rw-r--r-- | src/matlab/quikrCustomTrained.m | 4 | ||||
| -rw-r--r-- | src/matlab/quikrTrain.m | 9 |
4 files changed, 13 insertions, 16 deletions
@@ -10,12 +10,12 @@ install: c @cp -vf src/c/quikr ${DESTDIR}${PREFIX}/bin/quikr @cp -vf src/c/multifasta_to_otu ${DESTDIR}${PREFIX}/bin/multifasta_to_otu @cp -vf src/python/generate_kmers ${DESTDIR}${PREFIX}/bin/generate_kmers - chmod -v 755 ${DESTDIR}${PREFIX}/bin/probabilities-by-read - chmod -v 755 ${DESTDIR}${PREFIX}/bin/count-kmers - chmod -v 755 ${DESTDIR}${PREFIX}/bin/quikr - chmod -v 755 ${DESTDIR}${PREFIX}/bin/quikr_train - chmod -v 755 ${DESTDIR}${PREFIX}/bin/multifasta_to_otu - chmod -v 755 ${DESTDIR}${PREFIX}/bin/generate_kmers + chmod -v 555 ${DESTDIR}${PREFIX}/bin/probabilities-by-read + chmod -v 555 ${DESTDIR}${PREFIX}/bin/count-kmers + chmod -v 555 ${DESTDIR}${PREFIX}/bin/quikr + chmod -v 555 ${DESTDIR}${PREFIX}/bin/quikr_train + chmod -v 555 ${DESTDIR}${PREFIX}/bin/multifasta_to_otu + chmod -v 555 ${DESTDIR}${PREFIX}/bin/generate_kmers @cp -vf src/c/quikr.1 ${DESTDIR}${PREFIX}/share/man/man1/quikr.1 @cp -vf src/c/quikr_train.1 ${DESTDIR}${PREFIX}/share/man/man1/quikr_train.1 @cp -vf src/c/multifasta_to_otu.1 ${DESTDIR}${PREFIX}/share/man/man1/multifasta_to_otu.1 diff --git a/src/matlab/quikr.m b/src/matlab/quikr.m index f295d2b..aa2a271 100644 --- a/src/matlab/quikr.m +++ b/src/matlab/quikr.m @@ -15,9 +15,9 @@ if nargin>1 error('too many input arguments');
end
-[status, counts]=unix(['count-kmers -r 6 -1 -u ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels
+[status, counts]=unix(['kmer_total_count -k 6 -i ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels
if status ~= 0
- error('count-kmers failed: ensure count-kmers is in your path.');
+ error('kmer_total_count failed: ensure kmer_total_count is in your path.');
end
counts=textscan(counts,'%f'); %convert into floats
diff --git a/src/matlab/quikrCustomTrained.m b/src/matlab/quikrCustomTrained.m index 9331e06..9a45256 100644 --- a/src/matlab/quikrCustomTrained.m +++ b/src/matlab/quikrCustomTrained.m @@ -15,9 +15,9 @@ if rows~=4^k error('Wrong k-mer size for input training matrix');
end
-[status, counts]=unix([sprintf('count-kmers -r %d -1 -u ', k) ' ' inputfasta]); %count the k-mers in the fasta file, in the forward direction, return the counts without labels.
+[status, counts]=unix([sprintf('kmer_total_count -k %d', k) ' -i ' inputfasta]); %count the k-mers in the fasta file, in the forward direction, return the counts without labels.
if status ~= 0
- error('count-kmers failed: ensure count-kmers is in your path.');
+ error('kmer_total_count failed: ensure kmer_total_count is in your path.');
end
counts=textscan(counts,'%f'); %read them in as floats.
diff --git a/src/matlab/quikrTrain.m b/src/matlab/quikrTrain.m index 86a994b..be4a85b 100644 --- a/src/matlab/quikrTrain.m +++ b/src/matlab/quikrTrain.m @@ -19,17 +19,14 @@ outputfilename=fullfile(pathtofile, [filename sprintf('-sensingmatrixK%d.txt',k) %crashes when unix() returns as many entries as ./probabilities-by-read
%does (on the order of ~2*10^10).
-kmerfilename=sprintf('%dmers.txt',k); %This contains the list of 6-mers to count. In future versions this will be computed locally instead of being read in.
-
-unix(['probabilities-by-read ' sprintf('%d',k) ' ' inputfasta ' <( generate_kmers ' sprintf('%d',k) ') > ' outputfilename]); %obtain the k-mer counts of the inputfasta read-by-read
+unix(['kmer_counts_per_sequence -k ' sprintf('%d',k) ' -i ' inputfasta '>' outputfilename]);
fid=fopen(outputfilename); %open the output file
-
-%A=textscan(fid,'%f'); %get all the counts
-%A=A{:};
A=fscanf(fid,'%f');
+
mat=sparse(reshape(A,4^k,length(A)/4^k)); %form into a matrix
mat=bsxfun(@rdivide,mat,sum(mat,1)); %column-normalize
+
fclose(fid); %close file
delete(outputfilename); %delete the file
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