scbi_fqbin 0.2.2 → 0.2.3

data/lib_fqbin_src/other/rd_extras_fbin.c

@@ -0,0 +1,45 @@
+#include "lib_fqbin.h"
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+
+/*******************************************************/
+/* main                                                */
+/*******************************************************/
+int main(int argc, char *argv[])
+{
+
+	char *fasta=NULL;
+	char *qual=NULL;
+	char *extras=NULL;
+	int size=5000;
+	int res=0;
+
+	if (argc!=3)
+	{
+	  printf("Usage %s fbin_file seq_name\n\n",argv[0]);
+	  return -1;
+	}
+ 
+
+
+	res=read_seq(argv[1],argv[2], &fasta, &qual, &extras);
+
+	if (res==0){
+	
+        // printf("Extras for seq: %s\n", argv[2]);
+
+		if (extras!=NULL) printf("%s\n",extras);
+		
+	}
+
+	//res=read_seq("prueba2gz.fbin","F143CJN01EN6AH", &fasta, &qual, &extras);
+	if ( fasta!=NULL ) {free(fasta);fasta=NULL;}
+	if ( qual!=NULL ) {free(qual);qual=NULL;}
+	if ( extras!=NULL ) {free(extras);extras=NULL;}
+
+	return res;
+}
+

data/lib_fqbin_src/read_fq.c

@@ -0,0 +1,143 @@
+
+#include "lib_fqbin.h"
+#include <stdio.h>
+#include <ctype.h>
+
+#include <unistd.h>
+
+
+// process a fastq file adding it to fbin file
+int find_in_fastq(char *fname, char *seq_name)
+{
+
+    // allocate strings
+    char *name;
+    if ((name = malloc(MAXSEQNAME)) == NULL) {
+        puts("Memory allocation error!");
+        return EXIT_FAILURE;
+    }
+    
+    char *fasta;
+    if ((fasta = malloc(MAXSEQLENGTH)) == NULL) {
+        puts("Memory allocation error!");
+        return EXIT_FAILURE;
+    }
+    
+    char *qual;
+    if ((qual = malloc(MAXSEQLENGTH)) == NULL) {
+        puts("Memory allocation error!");
+        return EXIT_FAILURE;
+    }
+    
+    char *comments;
+    if ((comments = malloc(MAXSEQLENGTH)) == NULL) {
+        puts("Memory allocation error!");
+        return EXIT_FAILURE;
+    }
+    
+    static time_t curr_time=0;
+    static time_t prev_time=0;
+    
+    prev_time=time(NULL);
+    
+    FILE *fastq_file=NULL;
+    
+    
+    int valid=0;
+    int res=0;
+    int r=0;
+    // Open fasta and qual files
+    if (strcmp(fname,"-")==0){
+        fastq_file=stdin;
+    }else{
+
+        open_file(fname,&fastq_file);
+    }
+    
+    if (fastq_file==NULL){
+        printf("TRESb\n");
+    }
+        
+    // for each sequence on fastq file
+    while (valid=get_next_seq_fastq(fastq_file,&name,&fasta,&qual,&comments)){
+        if(valid==1)
+        {
+            r++;
+            if (strcmp(name,seq_name)==0)
+            {
+                printf("@%s %s\n%s\n", name,comments, fasta);
+                printf("+%s\n%s\n",name,qual);
+                break;
+            }
+
+        }else{
+            fprintf(stderr,"Invalid sequence found %s. Aborting import.\n",name);
+            res=-1;
+            break;
+        }
+        
+        // if ((r%10000)==0) {
+        // }
+        
+    }
+
+    curr_time=time(NULL);    
+    printf("\nEnd fastq processing. %d seqs in %.0f s. Rate: %8.2f seqs/s\n",r,difftime(curr_time,prev_time),r/difftime(curr_time,prev_time));
+
+    // free mem
+    free(name);
+    free(fasta);
+    free(qual);
+    free(comments);
+    
+    // close files
+    fclose(fastq_file);
+    
+    return res;
+}
+
+void usage(){
+    printf("Usage: read_fq fastq_file seq_name\n\n");
+    
+    exit(-1);
+    
+}
+
+
+
+/*******************************************************/
+/* main                                                */
+/*******************************************************/
+int main(int argc, char *argv[])
+{
+    
+    int ch;
+
+    while ((ch = getopt(argc, argv, "h")) != -1) {
+            switch (ch) {
+
+            case 'h':
+                    usage();
+                    break;
+            case '?':
+            default:
+                    usage();
+            }
+    }
+
+    argc -= optind;
+    argv += optind;
+    
+    
+  // check params
+  if (argc<2)
+  {
+    usage();
+    return -1;
+  }
+
+  int res=find_in_fastq(argv[0],argv[1]);
+
+  return res;
+}
+

data/lib_fqbin_src/read_fqbin.c

@@ -0,0 +1,101 @@
+#include "lib_fqbin.h"
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include <unistd.h>
+
+
+void usage(){
+    printf("Usage: read_fqbin [-f][-e][-E] fqbin_file seq_name\n\n");
+    printf("    -f    Output sequence in fasta format\n");
+    printf("    -e    Output extras for sequence\n");
+    printf("    -E    Output only extras for sequence\n");
+    
+    exit(-1);
+    
+}
+
+
+/*******************************************************/
+/* main                                                */
+/*******************************************************/
+int main(int argc, char *argv[])
+{
+
+	char *fasta=NULL;
+	char *qual=NULL;
+	char *extras=NULL;
+	int size=5000;
+	int res=0;
+
+    int ch;
+
+    int output_fasta = 0;
+    int output_extras = 0;
+    int only_extras = 0;
+
+    while ((ch = getopt(argc, argv, "feEh")) != -1) {
+            switch (ch) {
+            case 'f':
+                    output_fasta = 1;
+                    break;
+            case 'e':
+                    output_extras = 1;
+                    break;
+            case 'E':
+                    output_extras = 1;
+                    only_extras = 1;
+                    break;
+    
+            case 'h':
+                    usage();
+                    break;
+            case '?':
+            default:
+                    usage();
+            }
+    }
+
+    argc -= optind;
+    argv += optind;
+    // printf("argc: %d", argc);
+    // printf("argv: %s", argv[0]);
+
+
+	if (argc!=2)
+	{
+        usage();
+	  return -1;
+	}
+
+  res=read_seq(argv[0],argv[1], &fasta, &qual, &extras);
+
+  if (res==-2)
+  {
+    printf("Index file does not exist for: %s.index\n", argv[0]);
+    return res;
+  }
+
+  if (res==0){
+  
+      if (!only_extras){
+           if (output_fasta){
+               printf(">%s\n%s\n", argv[1], fasta);
+           }else{
+               printf("@%s\n%s\n", argv[1], fasta);
+             printf("+%s\n%s\n",argv[1],qual);
+           }
+   }
+      if ((extras!=NULL) && (output_extras)) printf ("EXTRAS:%s\n",extras);
+   
+  }
+
+	//res=read_seq("prueba2gz.fqbin","F143CJN01EN6AH", &fasta, &qual, &extras);
+	if ( fasta!=NULL ) {free(fasta);fasta=NULL;}
+	if ( qual!=NULL ) {free(qual);qual=NULL;}
+	if ( extras!=NULL ) {free(extras);extras=NULL;}
+	return res;
+}
+

data/lib_fqbin_src/sort_index

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+# La entrada a fichero es el nombre del fichero sin extensión
+
+mv $1 $1.bkp
+echo "UMACOMPRESSEDFORMAT 1 0 0 999999999999 999999999999" > $1
+zgrep -v UMACOM $1.bkp | sort -k 1 >> $1
+gzip $1
+mv $1.gz $1.sorted

data/lib_fqbin_src/test.rb

@@ -0,0 +1,13 @@
+require 'scbi_fastq'
+
+fqr=FastqFile.new(ARGV.shift)
+
+r=0
+ntcount=0
+fqr.each do |f,q,n|
+	r+=1
+	ntcount+=f.length+q.length
+  # puts f,q,n
+end
+puts "Total seqs: #{r}\n";
+puts "Total NT: #{ntcount}\n";

data/scbi_fqbin.gemspec

@@ -0,0 +1,25 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'scbi_fqbin/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "scbi_fqbin"
+  spec.version       = ScbiFqbin::VERSION
+  spec.authors       = ["dariogf"]
+  spec.email         = ["dariogf@scbi.uma.es"]
+  spec.summary       = %q{Read/write compressed fastq or fasta files in fqbin format}
+  spec.description   = %q{Read/write compressed fastq or fasta files in fqbin format}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+
+  spec.add_runtime_dependency "ffi"
+  spec.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+end

data/test/build.rake

@@ -0,0 +1,15 @@
+desc "build lib"
+task :build do
+  chdir "libfbin_src" do
+    sh "make"
+  end
+end
+
+desc "Install lib"
+task :install do
+  chdir "libfbin_src" do
+    sh "sudo make install"
+  end
+end
+
+

data/test/no_test_fill_file.rb

@@ -0,0 +1,66 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestFillfile < Test::Unit::TestCase
+
+  def setup
+  end
+  
+	TEST_FILE='/tmp/fbinfile';
+  	
+  	SEQ_FASTA='ACTG'
+		SEQ_QUAL=[25]
+	  SEQ_NAME='SEQ'
+	  SEQ_EXTRAS='SOME EXTRAS IN SEQ'
+  	 
+  	 
+  def fill_file(n)
+  	fb=Fastabin.new(TEST_FILE,'w')
+  	n.times do |c|
+  	  i = c+1
+  		fb.add_seq(SEQ_NAME+i.to_s,SEQ_FASTA*i,(SEQ_QUAL*i*SEQ_FASTA.length).join(' '),SEQ_EXTRAS)  		
+  	end
+
+  	fb.close
+  end
+  
+#
+#  def test_add100
+#		
+#    # make new file and fill with data
+#		fill_file(100)  	
+#		
+##  	fb=Fastabin.new(TEST_FILE,'r')
+##    assert(fb.count == 100)
+##    fb.close
+#  	
+#   end
+   
+     def test_read
+
+    	 # make new file and fill with data
+		  fill_file(10) 	
+		
+
+			fb=Fastabin.new(TEST_FILE,'r')
+			
+    	10.times do |c|
+    		i = c+1
+				n,s,q,e=fb.read_seq(SEQ_NAME+i.to_s)
+				#puts n,s.length,q.split(' ').length
+			  assert(SEQ_NAME+i.to_s==n)
+			  assert(SEQ_FASTA*i==s)
+			  assert((SEQ_QUAL*i*SEQ_FASTA.length).join(' ')==q)
+			  assert(SEQ_EXTRAS==e)
+			end
+			 
+			n,s,q,e=fb.read_seq(SEQ_NAME+'NO_EXIST')
+			assert(n.nil?)
+			 			 		  
+		  fb.close			
+   end
+
+   
+   
+   
+   
+end

data/test/old/app.rb

@@ -0,0 +1,43 @@
+require 'lib/scbi_fqbin/fbin_file'
+
+file='c/sample/f1.fbin'
+
+o = FbinFile.new(file,'r')
+
+
+name,fasta,qual,extras=o.next_sequence
+while !name.nil?
+  puts "Name:#{name}, fasta: #{fasta}"
+  name,fasta,qual,extras=o.next_sequence
+end
+
+puts "="*20
+
+o.each do |name,fasta,qual,extras|
+  puts "Name:#{name}, fasta: #{fasta}"
+end
+
+puts "="*20
+
+seq='FX9YN3P05C43XJ'
+name,fasta,qual,extras=o.read_sequence(seq)
+puts "Name:#{name}, fasta: #{fasta}"
+
+o.close
+
+
+# r=o.calculate_something(42,98.6)
+# puts r
+
+# c = MyLibrary.calculate_something(42, 98.6) # note FFI handles literals just fine
+# 
+# if ( (errcode = MyLibrary.error_code()) != 0)
+#   puts "error calculating something: #{errcode}"
+#   exit 1
+# end
+# 
+# objptr = MyLibrary.create_object("my object") # note FFI handles string literals as well
+# d = MyLibrary.calculate_something_else(c, objptr)
+# MyLibrary.free_object(objptr)
+# 
+# puts "calculated #{d}"