From dfe5663c3a055cc0f6d0d2c4c6c84ffca30736c7 Mon Sep 17 00:00:00 2001
From: Eduardo Eyras <eae@sanger.ac.uk>
Date: Thu, 22 May 2003 12:21:54 +0000
Subject: [PATCH] added method to clip sequences on both ends, the length to be
clipped is passed as an argument
---
modules/Bio/EnsEMBL/Utils/PolyA.pm | 81 ++++++++----------------------
1 file changed, 20 insertions(+), 61 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/PolyA.pm b/modules/Bio/EnsEMBL/Utils/PolyA.pm
index b16a593647..59fc71c1af 100644
--- a/modules/Bio/EnsEMBL/Utils/PolyA.pm
+++ b/modules/Bio/EnsEMBL/Utils/PolyA.pm
@@ -124,6 +124,20 @@ sub mask{
############################################################
+# $seq is a string and $length is the length we want to clip from both ends
+
+sub clip_ends{
+ my ($self,$seq,$length) = @_;
+
+ my $seq_length = length( $seq );
+ my $subseq = substr( $seq, $length, $seq_length - 2*$length );
+
+ return $subseq;
+}
+
+
+
+############################################################
sub _find_polyA{
my ($self, $seq) = @_;
my $new_seq;
@@ -137,7 +151,6 @@ sub _find_polyA{
my $t_count = $check_polyT =~ tr/Tt//;
my $a_count = $check_polyA =~ tr/Aa//;
-
#### polyA ####
if ( $a_count >= 5 && $a_count > $t_count ){
@@ -293,76 +306,22 @@ sub has_polyA_track{
my $length = length($seq);
# is it a polyA or polyT?
- my $check_polyT = substr( $seq, 0, 6 );
+ my $check_polyT = substr( $seq, 0, 10 );
- my $check_polyA = substr( $seq, -6 );
+ my $check_polyA = substr( $seq, -10 );
+ print STDERR "polyA: $check_polyA\n";
+
my $t_count = $check_polyT =~ tr/Tt//;
my $a_count = $check_polyA =~ tr/Aa//;
-
- my $length_to_mask = 0;
- #### polyA ####
- if ( $a_count >= 5 && $a_count > $t_count ){
-
- # we calculate the number of bases we want to chop
- my $length_to_mask = 0;
-
- # we start with 3 bases
- my ($piece, $count ) = (3,0);
-
- # count also the number of Ns, consider the Ns as potential As
- my $n_count = 0;
-
- # take 3 by 3 bases from the end
- while( $length_to_mask < $length ){
- my $chunk = substr( $seq, ($length - ($length_to_mask + 3)), $piece);
- $count = $chunk =~ tr/Aa//;
- $n_count = $chunk =~ tr/Nn//;
- if ( ($count + $n_count) >= 2*( $piece )/3 ){
- $length_to_mask += 3;
- }
- else{
- last;
- }
- }
- }
- #### polyT ####
- elsif( $t_count >=5 && $t_count > $a_count ){
-
- # calculate the number of bases to chop
- my $length_to_mask = -3;
-
- # we start with 3 bases:
- my ($piece, $count) = (3,3);
-
- # count also the number of Ns, consider the Ns as potential As
- my $n_count = 0;
-
- # take 3 by 3 bases from the beginning
- while ( $length_to_mask < $length ){
- my $chunk = substr( $seq, $length_to_mask + 3, $piece );
- #print STDERR "length to mask: $length_to_mask\n";
- #print "chunk: $chunk\n";
- $count = $chunk =~ tr/Tt//;
- $n_count = $chunk =~ tr/Nn//;
- if ( ($count+$n_count) >= 2*( $piece )/3 ){
- $length_to_mask +=3;
- }
- else{
- last;
-
- }
- }
- }
-
- if ( $length_to_mask >= 5 ){
+ ## testing with this short cut
+ if ( $a_count >=7 || $t_count >=7 ){
return 1;
}
else{
return 0;
}
-
}
--
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