From b27f4ea2ab2523f3f2eb706345a224534e0e413a Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Tue, 11 Jun 2013 10:26:52 -0400
Subject: small edits to man page
---
src/c/multifasta_to_otu.1 | 2 +-
src/c/quikr.1 | 2 +-
src/c/quikr_functions.c.1 | 153 ++++++++++++++++++++++++++++++++++++++++++++++
src/c/quikr_train.1 | 2 +-
4 files changed, 156 insertions(+), 3 deletions(-)
create mode 100644 src/c/quikr_functions.c.1
(limited to 'src/c')
diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1
index 29fe5d7..2a00d5c 100644
--- a/src/c/multifasta_to_otu.1
+++ b/src/c/multifasta_to_otu.1
@@ -79,7 +79,7 @@ make_3d_plots.py -i <quikr_otu_project_name>_weighted.txt -o <3d_pcoa_plotdirect
.SH AUTHORS
.B multifasta2otu
was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison
-<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, Jean-Luc Bouchot
+<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and Jean-Luc Bouchot.
.SH REPORTING BUGS
.TP
Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \
diff --git a/src/c/quikr.1 b/src/c/quikr.1
index 937109b..9b32667 100644
--- a/src/c/quikr.1
+++ b/src/c/quikr.1
@@ -58,7 +58,7 @@ quikr -i sample.fa -f rdp7.fa -s rdp_sensing_matrix.gz -o frequencies.txt
.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
+<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and Jean-Luc Bouchot.
.SH REPORTING BUGS
.TP
Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \
diff --git a/src/c/quikr_functions.c.1 b/src/c/quikr_functions.c.1
new file mode 100644
index 0000000..31afb3b
--- /dev/null
+++ b/src/c/quikr_functions.c.1
@@ -0,0 +1,153 @@
+#include <stdio.h>
+#include <stdio.h>
+#include <errno.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <math.h>
+#include <zlib.h>
+
+int count_sequences(char *filename) {
+ char command[512];
+ int sequences = 0;
+ FILE *grep_output;
+
+ sprintf(command, "grep -c ^\\> %s", filename);
+ grep_output = popen(command, "r");
+ if(grep_output == NULL) {
+ fprintf(stderr, "Could not execute %s\n", command);
+ exit(EXIT_FAILURE);
+ }
+
+ fscanf(grep_output, "%d", &sequences);
+
+ pclose(grep_output);
+ return sequences;
+}
+
+
+void normalize_matrix(double *matrix, int height, int width) {
+ int x = 0;
+ int y = 0;
+ for(x = 0; x < height; x++) {
+
+ double row_sum = 0;
+
+ for(y = 0; y < (width); y++)
+ row_sum = row_sum + matrix[width * x + y];
+ for(y = 0; y < (width); y++)
+ matrix[width * x + y] = matrix[width * x + y] / row_sum;
+ }
+}
+
+
+double *load_count_matrix(char *filename, int width, int kmer) {
+
+ double *count_matrix = malloc((width)*sizeof(double));
+ char count_command[512];
+ int x = 0;
+ char *line = NULL;
+ size_t len = 0;
+
+ if(count_matrix == NULL) {
+ fprintf(stderr, "could not allocate enough memory for the count matrix (%d x double) \n", width);
+ exit(EXIT_FAILURE);
+ }
+
+ // create out count matrix
+ sprintf(count_command, "count-kmers -r %d -1 -u %s", kmer, filename);
+ FILE *count_output = popen(count_command, "r");
+ if(count_output == NULL) {
+ fprintf(stderr, "could not execute \"%s\"", count_command);
+ exit(EXIT_FAILURE);
+ }
+
+ // set first element to zero.
+ count_matrix[0] = 0;
+
+ // get our first line
+ getline(&line, &len, count_output);
+ count_matrix[1] = atoi(line);
+
+ // iterate over the rest of the lines
+ for(x = 2; x < width; x++) {
+ getline(&line, &len, count_output);
+ count_matrix[x] = atoi(line);
+ }
+
+ pclose(count_output);
+
+ return count_matrix;
+}
+
+
+double *load_sensing_matrix(char *filename, int height, int width) {
+
+ int x = 0;
+ int y = 0;
+
+ gzFile sensing_matrix_fh = NULL;
+
+ double *sensing_matrix = malloc(height * width * sizeof(double));
+ if(sensing_matrix == NULL) {
+ fprintf(stderr, "Could not allocate memory for the sensing matrix\n");
+ }
+
+ sensing_matrix_fh = gzopen(filename, "r");
+ if(sensing_matrix_fh == NULL) {
+ fprintf(stderr, "could not open %s", filename);
+ exit(EXIT_FAILURE);
+ }
+
+ // read our sensing matrix in
+ for(x = 0; x < height; x++) {
+ for (y = 1; y < width; y++) {
+ char buffer[14];
+ gzgets(sensing_matrix_fh, buffer, 14);
+ sensing_matrix[width*x + y] = atof(buffer);
+ }
+ }
+
+ gzclose(sensing_matrix_fh);
+
+ return sensing_matrix;
+}
+
+char **load_headers(char *filename, int sequences) {
+ char command[512];
+ char *line= NULL;
+ int x = 0;
+ FILE *grep_output;
+ size_t len = 0;
+
+ sprintf(command, "grep ^\\> %s", filename);
+ grep_output = popen(command, "r");
+ if(grep_output == NULL) {
+ fprintf(stderr, "Could not execute %s\n", command);
+ exit(EXIT_FAILURE);
+ }
+
+ char **headers = malloc(sequences * sizeof(char *));
+ if(headers == NULL) {
+ fprintf(stderr, "could not allocated enough memory\n");
+ exit(EXIT_FAILURE);
+ }
+
+ for(x = 0; x < sequences; x++) {
+
+ char *header = malloc(256 * sizeof(char));
+ if(header == NULL) {
+ fprintf(stderr, "could not allocated enough memory\n");
+ exit(EXIT_FAILURE);
+ }
+ getline(&line, &len, grep_output);
+ sscanf(line + 1, "%s", header);
+ headers[x] = header;
+ }
+
+ pclose(grep_output);
+
+ return headers;
+}
+
diff --git a/src/c/quikr_train.1 b/src/c/quikr_train.1
index dd1493f..6a058cd 100644
--- a/src/c/quikr_train.1
+++ b/src/c/quikr_train.1
@@ -45,7 +45,7 @@ If you do not have a .gz file on your output matrix name, it will be appended.
.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
+<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and Jean-Luc Bouchot.
.SH REPORTING BUGS
.TP
Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \
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