miga-base 0.7.10.2 → 0.7.11.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f3b350bb3e5dce2f0f8d0006d7f0693ff746c157006890a1250f30d71d89a523
-  data.tar.gz: 1d94e39c61bfe191388d309eeb992b995350f6191dc74d5c7b15ae9741bcca09
+  metadata.gz: 7b4a168130d732c670246cd4a874272e77e5f7d88fdef00e10d81ab8e5f9979a
+  data.tar.gz: '069e2dd280b4afecb67478612f1dee35bf2cada3ae57cbc61c6e70d0ef3bd233'
 SHA512:
-  metadata.gz: f2a47ca016873723f030c9435db7daa81c819a3f19c65ed7614c21d8d68d556af0dd7313b79d2678508a12762ecd36f7bd922f5cf45640b383c6aaadde91cdfe
-  data.tar.gz: e8218114c0e89d80eab2b6cf7eba5a1de6f26b7d27e3560af1da12fdfc9037f3557a5994e1b982cff35635cea3d23e18ef234758ef8e12b86fb56f782a41ef89
+  metadata.gz: a37fd7d69339c7a63d5ac38e0c232fed96d479c3f2f2bc67b2ee956bb908d8690a55f21a6fa0185c05f209139e16b6b2ddcd6b0f36fac471f9e0b4fd2c4a5f04
+  data.tar.gz: cb156656c79f1a765281f163691650e32f90056dc767827d4b3fe958b4042e6359b810f5a3249c6902bce042f6a457507a027836797c39328889d9cbbbc5c5d0

data/lib/miga/cli/action/stats.rb

@@ -38,7 +38,7 @@ class MiGA::Cli::Action::Stats < MiGA::Cli::Action
     end
     if cli[:key].nil?
       r[:stats].each do |k, v|
-        k_n = k == :g_c_content ? 'G+C content' : k.to_s.unmiga_name.capitalize
+        k_n = k.to_s.unmiga_name.sub(/^./, &:upcase)
         cli.puts "#{k_n}: #{v.is_a?(Array) ? v.join(' ') : v}"
       end
     else

data/lib/miga/common/format.rb

@@ -68,15 +68,20 @@ module MiGA::Common::Format
   # a FastA or FastQ file (supports gzipped files). The +format+ must be a
   # Symbol, one of +:fasta+ or +:fastq+. Additional estimations can be
   # controlled via the +opts+ Hash. Supported options include:
-  # - +:n50+: If true, it also returns the N50 and the median (in bp)
-  # - +:gc+: If true, it also returns the G+C content (in %)
-  # - +:x+: If true, it also returns the undetermined bases content (in %)
+  # - +:n50+: Include the N50 and the median (in bp)
+  # - +:gc+: Include the G+C content (in %)
+  # - +:x+: Include the undetermined bases content (in %)
+  # - +:skew+: Include G-C and A-T sequence skew (in %; forces gc: true).
+  #   See definition used here in DOI:10.1177/117693430700300006
   def seqs_length(file, format, opts = {})
+    opts[:gc] = true if opts[:skew]
     fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
     l = []
     gc = 0
     xn = 0
-    i = 0 # <- Zlib::GzipReader doesn't set `$.`
+    t  = 0
+    c  = 0
+    i  = 0 # <- Zlib::GzipReader doesn't set `$.`
     fh.each_line do |ln|
       i += 1
       if (format == :fasta and ln =~ /^>/) or
@@ -86,6 +91,10 @@ module MiGA::Common::Format
         l[l.size - 1] += ln.chomp.size
         gc += ln.scan(/[GCgc]/).count if opts[:gc]
         xn += ln.scan(/[XNxn]/).count if opts[:x]
+        if opts[:skew]
+          t += ln.scan(/[Tt]/).count
+          c += ln.scan(/[Cc]/).count
+        end
       end
     end
     fh.close
@@ -97,6 +106,12 @@ module MiGA::Common::Format
     o[:sd]  = Math.sqrt o[:var]
     o[:gc]  = 100.0 * gc / o[:tot] if opts[:gc]
     o[:x]   = 100.0 * xn / o[:tot] if opts[:x]
+    if opts[:skew]
+      at = o[:tot] - gc
+      o[:at_skew] = 100.0 * (2 * t - at) / at
+      o[:gc_skew] = 100.0 * (2 * c - gc) / gc
+    end
+
     if opts[:n50]
       l.sort!
       thr = o[:tot] / 2
@@ -132,9 +147,14 @@ class String
   end
 
   ##
-  # Replace underscores by spaces or dots (depending on context).
+  # Replace underscores by spaces or other symbols depending on context
   def unmiga_name
-    gsub(/_(str|sp|subsp|pv)__/, '_\\1._').tr('_', ' ')
+    gsub(/_(str|sp|subsp|pv)__/, '_\\1._')
+      .gsub(/g_c_(content)/, 'G+C \\1')
+      .gsub(/g_c_(skew)/, 'G-C \\1')
+      .gsub(/a_t_(skew)/, 'A-T \\1')
+      .gsub(/x_content/, &:capitalize)
+      .tr('_', ' ')
   end
 
   ##

data/lib/miga/result/stats.rb

@@ -21,28 +21,35 @@ module MiGA::Result::Stats
 
   def compute_stats_raw_reads
     stats = {}
+    seq_opts = { gc: true, x: true, skew: true }
     if self[:files][:pair1].nil?
-      s = MiGA::MiGA.seqs_length(file_path(:single), :fastq, gc: true, x: true)
+      s = MiGA::MiGA.seqs_length(file_path(:single), :fastq, seq_opts)
       stats = {
         reads: s[:n],
         length_average: [s[:avg], 'bp'],
         length_standard_deviation: [s[:sd], 'bp'],
         g_c_content: [s[:gc], '%'],
-        x_content: [s[:x], '%']
+        x_content: [s[:x], '%'],
+        g_c_skew: [s[:gc_skew], '%'],
+        a_t_skew: [s[:at_skew], '%']
       }
     else
-      s1 = MiGA::MiGA.seqs_length(file_path(:pair1), :fastq, gc: true, x: true)
-      s2 = MiGA::MiGA.seqs_length(file_path(:pair2), :fastq, gc: true, x: true)
+      s1 = MiGA::MiGA.seqs_length(file_path(:pair1), :fastq, seq_opts)
+      s2 = MiGA::MiGA.seqs_length(file_path(:pair2), :fastq, seq_opts)
       stats = {
         read_pairs: s1[:n],
         forward_length_average: [s1[:avg], 'bp'],
         forward_length_standard_deviation: [s1[:sd], 'bp'],
         forward_g_c_content: [s1[:gc], '%'],
         forward_x_content: [s1[:x], '%'],
+        forward_g_c_skew: [s1[:gc_skew], '%'],
+        forward_a_t_skew: [s1[:at_skew], '%'],
         reverse_length_average: [s2[:avg], 'bp'],
         reverse_length_standard_deviation: [s2[:sd], 'bp'],
         reverse_g_c_content: [s2[:gc], '%'],
-        reverse_x_content: [s2[:x], '%']
+        reverse_x_content: [s2[:x], '%'],
+        reverse_g_c_skew: [s2[:gc_skew], '%'],
+        reverse_a_t_skew: [s2[:at_skew], '%']
       }
     end
     stats
@@ -50,19 +57,22 @@ module MiGA::Result::Stats
 
   def compute_stats_trimmed_fasta
     f = self[:files][:coupled].nil? ? file_path(:single) : file_path(:coupled)
-    s = MiGA::MiGA.seqs_length(f, :fasta, gc: true, x: true)
+    s = MiGA::MiGA.seqs_length(f, :fasta, gc: true, x: true, skew: true)
     {
       reads: s[:n],
       length_average: [s[:avg], 'bp'],
       length_standard_deviation: [s[:sd], 'bp'],
       g_c_content: [s[:gc], '%'],
-      x_content: [s[:x], '%']
+      x_content: [s[:x], '%'],
+      g_c_skew: [s[:gc_skew], '%'],
+      a_t_skew: [s[:at_skew], '%']
     }
   end
 
   def compute_stats_assembly
     s = MiGA::MiGA.seqs_length(
-      file_path(:largecontigs), :fasta, n50: true, gc: true, x: true
+      file_path(:largecontigs), :fasta,
+      n50: true, gc: true, x: true, skew: true
     )
     {
       contigs: s[:n],
@@ -70,7 +80,9 @@ module MiGA::Result::Stats
       total_length: [s[:tot], 'bp'],
       longest_sequence: [s[:max], 'bp'],
       g_c_content: [s[:gc], '%'],
-      x_content: [s[:x], '%']
+      x_content: [s[:x], '%'],
+      g_c_skew: [s[:gc_skew], '%'],
+      a_t_skew: [s[:at_skew], '%']
     }
   end
 

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 10, 2]
+  VERSION = [0.7, 11, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 6, 30)
+  VERSION_DATE = Date.new(2020, 7, 1)
 
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.10.2
+  version: 0.7.11.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-06-30 00:00:00.000000000 Z
+date: 2020-07-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons