UNVERIFIED but progress on converting quikr.m to dna-utils

4 files changed, 13 insertions, 16 deletions

diff --git a/Makefile b/Makefile
index c4f5827..88b698b 100644
--- a/Makefile
+++ b/Makefile
@@ -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