gfa 0.6.0 → 0.6.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 28ef77ca42b374e58c983f474d44801060dadb2df912230e431cf40ee8f1386c
+  metadata.gz: 8069525ab289a4299c4d51df9a58a083df95292cd7bc59b83516ac4c5e7508f2
+  data.tar.gz: c1398a889d1f49431bfa01b196084ee9c448c60426fb179801151e7731538c03
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-  data.tar.gz: 32f081a9cf35219f05cb21654011a32a1645f13cbf1d7dda320ebef0b7d893523943cd71f8c9f8a310f1021b6adfaa99b1f863d498be1bbb77bf0a5e04779efd
+  metadata.gz: d97f574a6081727f5687e259a954881351bf7767ec36d1f5ac8b2e6eef939a59a9406077619b306d9782e99357ec2cb98536b4e73474a9aad75c61614c7f7d13
+  data.tar.gz: 385a463ad705401ec083375b917d3654633f44e3828fcc93546422fb80712fc4bc22dbc2dd128dbdf1db44a8c60ed4d7a31df558db8786eb1fca12225a29b2ab

data/bin/gfa-add-gaf

@@ -18,11 +18,13 @@ unless degree
     <input-gaf>  Input GAF file to read
     <output>     Output GFA file to write
     <degree>     Maximum degree of separation between the segment set in the GAF
-                 and any other included segments. If 0, only segments are
-                 included. If 1, only the target segments, records linking to
-                 them, and segments linked by those records. Any integer > 1
-                 includes additional expansion rounds for those linked segments.
-                 Use -1 to include the complete original GAF without subsetting.
+                 and any other segments included in the output GFA.
+                 - -1: include the complete original GAF without subsetting.
+                 - 0: only segments in the GAF are included.
+                 - 1: only the target segments in the GAF, records linking to
+                   them, and segments linked by those records are included.
+                 - Any integer > 1: include additional expansion rounds for
+                   those linked segments.
     <pref>       A prefix to name all recorded paths
                  By default: Based on the GAF file name
     <threads>    If passed, parallelize process with these many threads

data/bin/gfa-paths-to-fasta

@@ -26,4 +26,11 @@ end
 $stderr.puts "Loading GFA: #{input}"
 gfa = GFA.load_parallel(input, (threads || 1).to_i)
 
+$stderr.puts "Saving path sequences: #{output}"
+File.open(output, 'w') do |fasta|
+  gfa.paths.set.each do |path|
+    fasta.puts '>%s' % path.path_name.value
+    fasta.puts path.sequence(gfa)
+  end
+end
 

data/lib/gfa/graph.rb

@@ -146,7 +146,7 @@ class GFA
 
   def internally_linking_records(segments, edges)
     $stderr.puts '- Gathering internally linking records'
-    segments = Hash[segments.set.map { |i| [i.name.value, true]}]
+    segments = Hash[segments.map { |i| [i.name.value, true]}]
     edges.select { |record| record.segment_names_a.all? { |s| segments[s] } }
   end
 

data/lib/gfa/record/path.rb

@@ -42,4 +42,59 @@ class GFA::Record::Path < GFA::Record
 
     segment_names_a.any? { |name| segment.name == name }
   end
+
+  ##
+  # Array of GFA::Field::String with the sequences from each segment featuring
+  # the correct orientation from a +gfa+ (which *must* be indexed)
+  #
+  # TODO: Distinguish between a direct path (separated by comma) and a
+  # jump (separated by semicolon). Jumps include a distance estimate
+  # (column 6, optional) which could be used to add Ns between segment
+  # sequences (from GFA 1.2)
+  def segment_sequences(gfa)
+    raise "Unindexed GFA" unless gfa.indexed?
+    segment_names.value.split(/[,;]/).map do |i|
+      orientation = i[-1]
+      i[-1] = ''
+      segment = gfa.segments[i]
+
+      case orientation
+        when '+' ; segment.sequence
+        when '-' ; segment.rc
+        else ; raise "Unknown orientation: #{orientation} (path: #{path_name})"
+      end
+    end
+  end
+
+  ##
+  # Produce the contiguous path sequence based on the segment sequences and
+  # orientations from a +gfa+ (which *must* be indexed)
+  #
+  # TODO: Estimate gaps (Ns) from Jump distances (see +segment_sequences+)
+  #
+  # TODO: Attempt reading CIGAR values from the path first, the corresponding
+  # links next, and actually performing the pairwise overlap as last resort
+  #
+  # TODO: Support ambiguous IUPAC codes for overlap evaluation
+  def sequence(gfa)
+    segment_sequences(gfa).map(&:value)
+      .inject('') { |a, b| a + after_overlap(a, b) }
+  end
+
+  private
+    ##
+    # Find the overlap between sequences +a+ and +b+ (Strings) and return
+    # only the part of +b+ after the overlap. Assumes that +a+ starts
+    # at the same point or before +b+. If no overlap is found, returns +b+
+    # in its entirety.
+    def after_overlap(a, b)
+      (0 .. a.length - 1).each do |a_from|
+        a_to = b.length + a_from > a.length ? a.length : b.length + a_from
+        b_to = b.length + a_from > a.length ? a.length - a_from : b.length
+        if a[a_from .. a_to - 1] == b[0 .. b_to - 1]
+          return b[b_to .. b.length].to_s
+        end
+      end
+      b
+    end
 end

data/lib/gfa/record/segment.rb

@@ -32,4 +32,12 @@ class GFA::Record::Segment < GFA::Record
   def length
     sequence.value.length
   end
+
+  ##
+  # Returns the reverse-complement of the sequence (as a Z field)
+  def rc
+    GFA::Field::String.new(
+      sequence.value.upcase.reverse.tr('ACGTURYSWKMBDHVN', 'TGCAAYRSWMKVHDBN')
+    )
+  end
 end

data/lib/gfa/version.rb

@@ -1,5 +1,5 @@
 class GFA
-  VERSION       = '0.6.0'
+  VERSION       = '0.6.2'
   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: 0.6.0
+  version: 0.6.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-05 00:00:00.000000000 Z
+date: 2023-10-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rgl