bio-gadget 0.4.0 → 0.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a8b08f5a256d452f6399fe4484d6a18811bc3b58
-  data.tar.gz: 532b1903529b32c549eb321e363d0dc8e8efaf27
+  metadata.gz: 83130daa98cf1f04006aba7a9602b52a036d8d9c
+  data.tar.gz: 3c99911a518cacaa4ee0661bbff1d007b506500b
 SHA512:
-  metadata.gz: 23f150133d857f16a9ff0a326201fb044ec167d51fcf5addc23cb445ef219b75ff84038d457c3325fe076ce024b91d3afa2ffa33dcbba3c33401b9c75dfaf0bb
-  data.tar.gz: edbfc69fcfa8f7db2003236fc8d7b01046a051955907ad45bb2939096b389d6c3a6f19c79d95dbf3212ed320a20c6f9bf477a5f57e3ce9a542ccedd52ab4e4e5
+  metadata.gz: 2869693a0cb2357c9d9bab623a6686475c96ef9b9e28e6498a3b8cbe66404f7d31cccbe3b09957436eab9c9c87442df37177b2ca3704244bd03f97d2bb09b9b8
+  data.tar.gz: 644f86a29aed0eebbf30031f54fe70b28ce607d8248b594d393396bee192e83aa30ea0faffebcc35ffd8bd294e36e3f1f6f99b5ba266b11cdc3f266db76a01c9

data/lib/bio-gadget/demlt.rb

@@ -8,14 +8,16 @@ module Bio
 
     namespace :bio
 
-    desc 'demlt BARCODE [FASTQ]', 'demultiplex fastq from STDIN by barcodes'
+    desc 'demlt BARCODE [FASTQ]', 'Demultiplex fastq from STDIN by barcodes. '
     option 'output-dir', :aliases => '-o', :type => :string, :default => '.'
-    option 'umi-length', :aliases => '-u', :type => :numeric, :default => 4
-    option 'cdna-length', :aliases => '-c', :type => :numeric, :default => 37
+    option 'umi-length', :aliases => '-u', :type => :numeric, :default => 4, :desc => '0 is no umi, means no PCR-amplicon removal.'
+    option 'cdna-length', :aliases => '-c', :type => :numeric, :default => 37, :desc => '-1 is no trimming by length.'
+    option 'g-trimming', :aliases => '-g', :type => :boolean, :default => false, :desc => "Trimming of 5'-end poly-G. Length of the trimmed Gs attached after the read name. This sets cdna-length option to -1."
     def demlt(bcfile, fastq=:stdin)
 
       ofs = options['umi-length']
-      len = options['cdna-length']
+      trim = options['g-trimming']
+      len = trim ? -1 : options['cdna-length']
 
       wells = Array.new
       bcs = Array.new
@@ -115,7 +117,7 @@ module Bio
         outpath = "#{options['output-dir']}/#{well}.fq.xz"
         pid = Kernel.fork {
           left = ofs+bclen
-          right = ofs+bclen+len-1
+          right = trim ? -1 : ofs+bclen+len-1
           preprocess = ofs > 0 ? <<"DEDUPandFORMAT"
 ruby -F'\\t' -anle 'f1=$F[1][0..#{right}];f2=$F[2][0..#{right}];puts([f1+f2, $F[0], f2, f1].join("\\t"))' #{fifo3paths[i]} \\
 | sort -k 1 -r | cut -f 2- | uniq -f 2 \\
@@ -124,6 +126,9 @@ DEDUPandFORMAT
           : <<"FORMAT"
 ruby -F'\\t' -anle 'puts(["@"+$F[0], $F[1][#{left}..#{right}], "+", $F[2][#{left}..#{right}].rstrip].join("\\n"))' #{fifo3paths[i]} \\
 FORMAT
+
+          preprocess += '| ruby -e \'require "bio-faster";Bio::Faster.new(:stdin).each_record(:quality=>:raw){|v|s=v[1].gsub(/^G+/,"");l=v[1].length-s.length;puts("@#{v[0]}|-G#{l}\\n#{s}\\n+\\n#{v[2][l,s.length]}")}\'' if trim
+
           exec preprocess+"| xz -z -c -e > #{outpath}"
         }
       }

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.4.0"
+    VERSION = "0.4.1"
 
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Shintaro Katayama
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-02 00:00:00.000000000 Z
+date: 2013-04-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thor