From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 24 Jun 2013 10:55:33 +0000 (+0000)
Subject: fixed genbank and embl parsing of 5'UTR and 3'UTR
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=7029104c208f9013c0e8804737cc4f5da8bf7524

fixed genbank and embl parsing of 5'UTR and 3'UTR

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2187 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/embl.rb b/code_ruby/lib/maasha/embl.rb
index 6d9d6b5..66a53c0 100644
--- a/code_ruby/lib/maasha/embl.rb
+++ b/code_ruby/lib/maasha/embl.rb
@@ -152,7 +152,7 @@ class EMBLFeatures
 
   def each
     while @entry[@i] and @entry[@i][0 ... 2] != "SQ"
-      if @entry[@i] =~ /^FT\s{3}([A-Za-z_-]+)/
+      if @entry[@i] =~ /^FT\s{3}([53'A-Za-z_-]+)/
         if want_feat? $1
           record = {}
 
@@ -160,7 +160,7 @@ class EMBLFeatures
 
           @j = @i + 1
 
-          while @entry[@j] and @entry[@j][0 ... 2] == "FT" and @entry[@j] !~ /^FT(\s{19}\/|\s{3}[A-Za-z_-])/
+          while @entry[@j] and @entry[@j][0 ... 2] == "FT" and @entry[@j] !~ /^FT(\s{19}\/|\s{3}[53'A-Za-z_-])/
             loc << @entry[@j].split(/\s+/, 2).last
             @j += 1
           end
@@ -186,7 +186,7 @@ class EMBLFeatures
     quals = {}
     k     = 0
 
-    while @entry[@j] and @entry[@j][0 ... 2] == "FT" and @entry[@j] !~ /^FT\s{3}[A-Za-z_-]/
+    while @entry[@j] and @entry[@j][0 ... 2] == "FT" and @entry[@j] !~ /^FT\s{3}[53'A-Za-z_-]/
       if @entry[@j] =~ /^FT\s{19}\/([^=]+)="([^"]+)/
         qual = $1
         val  = $2
@@ -194,7 +194,7 @@ class EMBLFeatures
         if want_qual? qual
           k = @j + 1
 
-          while @entry[k] and @entry[k][0 ... 2] == "FT" and @entry[k] !~ /^FT(\s{19}\/|\s{3}[A-Za-z_-])/
+          while @entry[k] and @entry[k][0 ... 2] == "FT" and @entry[k] !~ /^FT(\s{19}\/|\s{3}[53'A-Za-z_-])/
             val << @entry[k].split(/\s+/, 2).last.chomp('"')
             k += 1
           end
diff --git a/code_ruby/lib/maasha/genbank.rb b/code_ruby/lib/maasha/genbank.rb
index b1c9f87..795de75 100644
--- a/code_ruby/lib/maasha/genbank.rb
+++ b/code_ruby/lib/maasha/genbank.rb
@@ -147,7 +147,7 @@ class GenbankFeatures
 
   def each
     while @entry[@i] and @entry[@i] !~ /^ORIGIN/
-      if @entry[@i] =~ /^\s{5}([A-Za-z_-]+)/
+      if @entry[@i] =~ /^\s{5}([53'A-Za-z_-]+)/
         if want_feat? $1
           record = {}
 
@@ -155,7 +155,7 @@ class GenbankFeatures
 
           @j = @i + 1
 
-          while @entry[@j] and @entry[@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+          while @entry[@j] and @entry[@j] !~ /^(\s{21}\/|\s{5}[53'A-Za-z_-]|[A-Z])/
             loc << @entry[@j].lstrip
             @j += 1
           end
@@ -181,7 +181,7 @@ class GenbankFeatures
     quals = {}
     k     = 0
 
-    while @entry[@j] and @entry[@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
+    while @entry[@j] and @entry[@j] !~ /^\s{5}[53'A-Za-z_-]|^[A-Z]/
       if @entry[@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
         qual = $1
         val  = $2
@@ -189,7 +189,7 @@ class GenbankFeatures
         if want_qual? qual
           k = @j + 1
 
-          while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+          while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[53'A-Za-z_-]|[A-Z])/
             val << @entry[k].lstrip.chomp('"')
             k += 1
           end