gfa 0.6.2 → 0.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: c8aec87b21fd9b1d7972228fa7118cf71b40f58a5dd20e385e6e80ef86b2ef92
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+  data.tar.gz: 2b17c35013f3c9dbdb99a20e060c2dde13732c139f0551f3ce5b65e317ad5d1918b84447570542b11b67f5d65387729606de914b18994c420e5fe8b41b9bf5af

data/bin/gfa-add-gaf

@@ -8,7 +8,7 @@ $LOAD_PATH.push File.expand_path('../../lib', File.realpath(__FILE__))
 
 require 'gfa'
 
-input_gfa, input_gaf, output, degree, threads = ARGV
+input_gfa, input_gaf, output, degree, pref, threads = ARGV
 
 unless degree
   $stderr.puts <<~HELP

data/bin/gfa-paths-to-fasta

@@ -8,29 +8,42 @@ $LOAD_PATH.push File.expand_path('../../lib', File.realpath(__FILE__))
 
 require 'gfa'
 
-input, output, threads = ARGV
+input, output, threads, orphan = ARGV
 
 unless output
   $stderr.puts <<~HELP
     Extract the sequences of the paths from a GFA to FastA file
 
-    gfa-merge <input> <output> [<threads>]
+    gfa-merge <input> <output> [<threads> [<orphan>]]
 
     <input>      Input GFA file to read
     <output>     Output FastA file to be created
     <threads>    If passed, parallelize process with these many threads
+    <orphan>     If set to 'yes', it also outputs the sequences of all
+                 segments that are not included in any path
   HELP
   exit(1)
 end
 
 $stderr.puts "Loading GFA: #{input}"
+orphan ||= 'no'
 gfa = GFA.load_parallel(input, (threads || 1).to_i)
 
 $stderr.puts "Saving path sequences: #{output}"
 File.open(output, 'w') do |fasta|
+  in_path = {}
   gfa.paths.set.each do |path|
     fasta.puts '>%s' % path.path_name.value
     fasta.puts path.sequence(gfa)
+    path.segment_names_a.each { |i| in_path[i] = true }
+  end
+
+  if orphan == 'yes'
+    gfa.segments.set.each do |segment|
+      next if in_path[segment.name.value]
+      fasta.puts '>S:%s' % segment.name.value
+      fasta.puts segment.sequence.value
+    end
   end
 end
 

data/lib/gfa/version.rb

@@ -1,5 +1,5 @@
 class GFA
-  VERSION       = '0.6.2'
+  VERSION       = '0.7.0'
   VERSION_ARRAY = VERSION.split(/\./).map { |x| x.to_i } # :nodoc:
   VERSION_MAJOR = VERSION_ARRAY[0] # :nodoc:
   VERSION_MINOR = VERSION_ARRAY[1] # :nodoc:

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gfa
 version: !ruby/object:Gem::Version
-  version: 0.6.2
+  version: 0.7.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-06 00:00:00.000000000 Z
+date: 2023-10-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rgl