From 2dbf2b7b0850f09bd1afb64455f799f273c00686 Mon Sep 17 00:00:00 2001
From: Shaman Narayanasamy <shaman.narayanasamy@uni.lu>
Date: Fri, 12 Jun 2015 17:04:27 +0200
Subject: [PATCH] Add perl script to filter length
---
src/fasta_filter_length.pl | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
create mode 100755 src/fasta_filter_length.pl
diff --git a/src/fasta_filter_length.pl b/src/fasta_filter_length.pl
new file mode 100755
index 0000000..3a85ab1
--- /dev/null
+++ b/src/fasta_filter_length.pl
@@ -0,0 +1,21 @@
+## removesmalls.pl
+#
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $minlen = shift or die "Error: `minlen` parameter not provided\n";
+{
+ local $/=">";
+ while(<>) {
+ chomp;
+ next unless /\w/;
+ s/>$//gs;
+ my @chunk = split /\n/;
+ my $header = shift @chunk;
+ my $seqlen = length join "", @chunk;
+ print ">$_" if($seqlen >= $minlen);
+ }
+ local $/="\n";
+}
+
--
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