bio-gadget 0.4.8 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 895f8bc130d316f85d376f85647c420b9152409e
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data/.gitignore

@@ -1,21 +1,11 @@
-*.gem
-*.rbc
-.bundle
-.config
-.yardoc
-Gemfile.lock
-InstalledFiles
-_yardoc
-coverage
-doc/
-lib/bundler/man
-pkg
-rdoc
-spec/reports
-test/tmp
-test/version_tmp
-tmp
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
 *~
-.#*
-.fuse*
-
+.DS_Store

data/.travis.yml

@@ -0,0 +1,5 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.3.1
+before_install: gem install bundler -v 1.12.5

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2012 Shintaro Katayama
+Copyright (c) 2012-2016 Shintaro Katayama
 
 MIT License
 

data/README.org

@@ -12,24 +12,3 @@ To check all commands and the usages in this package
 
 : bio-gadget help
 
-Currently available commands are
-
-- dedup :: Deduplicate fastq (via STDIN)
-- demlt :: Demultiplex fastq by barcodes
-- femrg :: Extract and merge first exons
-- fqxz :: (Re)compression of *.fq(.gz|.bz2) files
-- pead :: Find peak within each exon from wigs by a mojority vote.
-- qvstat :: Statistics of quality values in *.qual file
-- rgt2mtx :: Convert cuffdiff read group tracking file into tab-separated matrix
-- wig5p :: Convert bam-format alignments into wig-format table
-- wigchr :: Extract wiggle track on specified chromosome
-
-* Contributing
-
-1. Fork it
-2. Create your feature branch (`git checkout -b my-new-feature`)
-3. (optional) Install gems (`bundle`)
-4. Add your feature
-5. Commit your changes (`git commit -am 'Added some feature'`)
-6. Push to the branch (`git push origin my-new-feature`)
-7. Create new Pull Request

data/Rakefile

@@ -1,2 +1,6 @@
-#!/usr/bin/env rake
 require "bundler/gem_tasks"
+require "rake/extensiontask"
+
+Rake::ExtensionTask.new "bio_gadget" do |ext|
+  ext.lib_dir = "lib/bio/gadget"
+end

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "test"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/bio-gadget.gemspec

@@ -1,22 +1,28 @@
-require File.expand_path('../lib/bio-gadget/version', __FILE__)
-
 Gem::Specification.new do |gem|
-  gem.authors       = ["Shintaro Katayama"]
-  gem.email         = ["shintaro.katayama@gmail.com"]
-  gem.description   = %q{Gadgets for bioinformatics}
+  gem.name          = 'bio-gadget'
+  gem.version       = '0.5.0'
+  gem.licenses      = ['MIT']
   gem.summary       = gem.description
-  gem.homepage      = "https://github.com/shka/ruby-bio-gadget"
+  gem.description   = %q{Gadgets for bioinformatics}
+  gem.authors       = ['Shintaro Katayama']
+  gem.email         = ['shintaro.katayama@gmail.com']
+  gem.homepage      = 'https://github.com/shka/ruby-bio-gadget'
+  gem.extensions    = %w[ext/bio_gadget/extconf.rb]
 
   gem.files         = `git ls-files`.split($\)
-  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.bindir        = 'exe'                                           
+  gem.executables   = gem.files.grep(%r{^exe/}).map{ |f| File.basename(f) }
   gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
-  gem.name          = "bio-gadget"
-  gem.require_paths = ["lib"]
-  gem.version       = Bio::Gadget::VERSION
+  gem.require_paths = ['lib']
 
-  gem.add_dependency 'thor'
-  gem.add_dependency 'parallel'
-  gem.add_dependency 'levenshtein-ffi'
-  gem.add_dependency 'bio-faster'
+  gem.add_development_dependency 'bundler', '~> 1.12'
+  gem.add_development_dependency 'rake', '~> 10.0'
+  gem.add_development_dependency 'rake-compiler'
+  gem.add_development_dependency 'minitest', '~> 5.0'
+
+  gem.add_dependency 'bio'
+  gem.add_dependency 'damerau-levenshtein'
   gem.add_dependency 'mkfifo'
+  gem.add_dependency 'parallel'
+  gem.add_dependency 'thor' , '~> 0.19.3'
 end

data/exe/bio-gadget

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require 'bio/gadget'
+
+module Bio
+  class Gadgets < Bio::Gadget
+    
+    register(Bio::Gadget::Fq1l, 'fq1l', 'fq1l [COMMAND]', 'Tools for oneline-fastq; fq1l in the alias')
+    register(Bio::Gadget::Strt, 'strt', 'strt [COMMAND]', 'Tools for STRT RNAseq; strt is the alias')
+    
+  end
+end
+
+Bio::Gadgets.start

data/exe/fq1l

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require 'bio/gadget'
+
+Bio::Gadget::Fq1l.start

data/exe/rbg

@@ -0,0 +1 @@
+exe/bio-gadget

data/exe/strt

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require 'bio/gadget'
+
+Bio::Gadget::Strt.start

data/ext/bio_gadget/bio_gadget.c

@@ -0,0 +1,313 @@
+#include <limits.h>
+#include <regex.h>
+#include <stdio.h>
+#include <string.h>
+#include "bio_gadget.h"
+
+VALUE bio_gadget_fq1l_i2i(vSelf, vFirst, vLast)
+     VALUE vSelf;
+     VALUE vFirst;
+     VALUE vLast;
+{
+  char line[BUFSIZE];
+  char index[BUFSIZE] = "";
+  char *acc;
+  char *seq;
+  char *sep;
+  char *qual;
+  unsigned long head;
+  unsigned long length;
+
+  head = NUM2INT(vFirst)-1;
+  length = NUM2INT(vLast)-head;
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    sep = strtok(NULL, "\t");
+    qual = strtok(NULL, "\t");
+    strcpy(index, seq+head);
+    index[length] = 0;
+    printf("%s%s\t%s\t%s\t%s", acc, index, seq, sep, qual);
+  }
+
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_nr_deg(vSelf)
+     VALUE vSelf;
+{
+  char line[BUFSIZE];
+  char *acc;
+  char *seq;
+  char *sep;
+  char *qual;
+  char pseq[BUFSIZE] = "";
+  unsigned long pseql = ULONG_MAX;
+  char regexs[BUFSIZE];
+  regex_t regexc;
+
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    sep = strtok(NULL, "\t");
+    qual = strtok(NULL, "\t");
+    if (strlen(seq) >= pseql) {
+      printf("%s\t%s\t%s\t%s", acc, seq, sep, qual);
+      strcpy(pseq, seq);
+      pseql = strlen(seq);
+    } else {
+      sprintf(regexs, "^%s", seq);
+      regcomp(&regexc, regexs, REG_NOSUB);
+      if (regexec(&regexc, pseq, 0, NULL, 0) == REG_NOMATCH) {
+	printf("%s\t%s\t%s\t%s", acc, seq, sep, qual);
+	strcpy(pseq, seq);
+	pseql = strlen(seq);
+      }
+    }
+    regfree(&regexc);
+  }
+  
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_nr_std(vSelf)
+     VALUE vSelf;
+{
+  char line[BUFSIZE];
+  char *acc;
+  char *seq;
+  char *sep;
+  char *qual;
+  char pseq[BUFSIZE] = "";
+
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    sep = strtok(NULL, "\t");
+    qual = strtok(NULL, "\t");
+    if (strcmp(pseq, seq) != 0) {
+      printf("%s\t%s\t%s\t%s", acc, seq, sep, qual);
+      strcpy(pseq, seq);
+    }
+  }
+  
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_slice(vSelf, vNth, vSlice)
+     VALUE vSelf;
+     VALUE vNth;
+     VALUE vSlice;
+{
+  char line[BUFSIZE];
+  unsigned int nth;
+  unsigned int slice;
+  unsigned long count;
+
+  nth = NUM2INT(vNth)-1;
+  slice = NUM2INT(vSlice);
+  count = 0;
+
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    if (count % slice == nth)
+      fputs(line, stdout);
+    count += 1;
+  }
+
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_t3(vSelf, vCmdIn, vLen, vMinLen, vPathOut)
+     VALUE vSelf;
+     VALUE vCmdIn;
+     VALUE vLen;
+     VALUE vMinLen;
+     VALUE vPathOut;
+{
+  char line[BUFSIZE];
+  char *acc;
+  char *seq;
+  char *sep;
+  char *qual;
+  int len;
+  unsigned long minlen;
+  unsigned long seqlen;
+  FILE *fp_in;
+  FILE *fp_out;
+
+  fp_in = RTEST(vCmdIn) ? popen(StringValueCStr(vCmdIn), "r") : stdin;
+  fp_out = RTEST(vPathOut) ? fopen(StringValueCStr(vPathOut), "w") : stdout;
+  len = NUM2INT(vLen);
+  minlen = NUM2INT(vMinLen);
+  
+  while(fgets(line, BUFSIZE, fp_in) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    seqlen = strlen(seq)-len;
+    if (seqlen > 0 && seqlen >= minlen) {
+      sep = strtok(NULL, "\t");
+      qual = strtok(NULL, "\t");
+      seq[seqlen] = 0;
+      qual[seqlen] = 0;
+      fprintf(fp_out, "%s\t%s\t%s\t%s\n", acc, seq, sep, qual);
+    }
+  }
+  fclose(fp_out);
+  fclose(fp_in);
+  
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_t3q(vSelf, vLQs, vMinLen)
+     VALUE vSelf;
+     VALUE vLQs;
+     VALUE vMinLen;
+{
+  char line[BUFSIZE];
+  char *acc;
+  char *seq;
+  char *sep;
+  char *qual;
+  char *lqs;
+  unsigned long minlen;
+  unsigned long seqlen;
+
+  lqs = StringValueCStr(vLQs);
+  minlen = NUM2INT(vMinLen);
+
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    sep = strtok(NULL, "\t");
+    qual = strtok(NULL, "\t\n");
+    seqlen = strcspn(qual, lqs);
+    if (seqlen > 0 && seqlen >= minlen) {
+      if (seqlen < strlen(qual)) {
+	seq[seqlen] = 0;
+	qual[seqlen] = 0;
+      }
+      printf("%s\t%s\t%s\t%s\n", acc, seq, sep, qual);
+    }
+  }
+  
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_t5(vSelf, vPattern, vMinLen)
+     VALUE vSelf;
+     VALUE vPattern;
+     VALUE vMinLen;
+{
+  char regexs[BUFSIZE];
+  regex_t regexc;
+  unsigned long minlen;
+  char line[BUFSIZE];
+  regmatch_t match[1];
+  char *acc;
+  char *seq;
+  char *sep;
+  char *qual;
+
+  sprintf(regexs, "^%s", StringValueCStr(vPattern));
+  regcomp(&regexc, regexs, REG_EXTENDED);
+
+  minlen = NUM2INT(vMinLen);
+
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    sep = strtok(NULL, "\t");
+    qual = strtok(NULL, "\t");
+    if(regexec(&regexc, seq, 1, match, 0) != REG_NOMATCH) {
+      seq += match[0].rm_eo;
+      qual += match[0].rm_eo;
+      if(strlen(seq) >= minlen)
+	printf("%s\t%s\t%s\t%s", acc, seq, sep, qual);
+    } else
+      printf("%s\t%s\t%s\t%s", acc, seq, sep, qual);
+  }
+
+  regfree(&regexc);
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_to(vSelf, vDraw, vSkip)
+     VALUE vSelf;
+     VALUE vDraw;
+     VALUE vSkip;
+{
+  char line[BUFSIZE];
+  unsigned int draw;
+  unsigned int skip;
+  unsigned int sum;
+  unsigned long count;
+
+  draw = NUM2INT(vDraw);
+  skip = NUM2INT(vSkip);
+  sum = draw + skip;
+  count = 0;
+
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    if (count % sum < draw)
+      fputs(line, stdout);
+    count += 1;
+  }
+
+  return Qnil;
+}
+
+VALUE bio_gadget_fq1l_u2i(vSelf, vFirst, vLast)
+     VALUE vSelf;
+     VALUE vFirst;
+     VALUE vLast;
+{
+  char line[BUFSIZE];
+  char index[BUFSIZE] = "";
+  char *acc;
+  char *acc1;
+  char *acc2;
+  char *seq;
+  char *sep;
+  char *qual;
+  unsigned long head;
+  unsigned long length;
+
+  head = NUM2INT(vFirst)-1;
+  length = NUM2INT(vLast)-head;
+  while(fgets(line, BUFSIZE, stdin) != NULL) {
+    acc = strtok(line, "\t");
+    seq = strtok(NULL, "\t");
+    sep = strtok(NULL, "\t");
+    qual = strtok(NULL, "\t");
+    strcpy(index, seq+head);
+    index[length] = 0;
+    acc1 = strtok(acc, " ");
+    acc2 = strtok(NULL, " ");
+    if(acc2 == NULL) {
+      printf("%s:%s\t%s\t%s\t%s", acc1, index, seq, sep, qual);
+    }
+    else {
+      printf("%s:%s %s\t%s\t%s\t%s", acc1, index, acc2, seq, sep, qual);
+    }
+  }
+
+  return Qnil;
+}
+
+
+VALUE rb_mBio_Gadget;
+
+void
+Init_bio_gadget(void)
+{
+  rb_mBio_Gadget = rb_define_module("BioGadget");
+  rb_define_module_function(rb_mBio_Gadget, "i2i", bio_gadget_fq1l_i2i, 2);
+  rb_define_module_function(rb_mBio_Gadget, "nr_deg", bio_gadget_fq1l_nr_deg, 0);
+  rb_define_module_function(rb_mBio_Gadget, "nr_std", bio_gadget_fq1l_nr_std, 0);
+  rb_define_module_function(rb_mBio_Gadget, "slice", bio_gadget_fq1l_slice, 2);
+  rb_define_module_function(rb_mBio_Gadget, "t3", bio_gadget_fq1l_t3, 4);
+  rb_define_module_function(rb_mBio_Gadget, "t3q", bio_gadget_fq1l_t3q, 2);
+  rb_define_module_function(rb_mBio_Gadget, "t5", bio_gadget_fq1l_t5, 2);
+  rb_define_module_function(rb_mBio_Gadget, "to", bio_gadget_fq1l_to, 2);
+  rb_define_module_function(rb_mBio_Gadget, "u2i", bio_gadget_fq1l_u2i, 2);
+}