blob: 37ee59c0fdb18dc1fa3af42dae3d5924f081b6ff (
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|
#!/usr/bin/perl -w
use strict;
my $name="";
my $sequence="";
my $infile = $ARGV[0];
my $outfile = $ARGV[1];
open(LIB, $infile);
open(CLIB, ">", $outfile);
while (<LIB>)
{
if (m/^>/)
{
if (not $name eq "")
{
if ($sequence eq "")
{
print "---------------------------------------------------------------------------------------\n";
print "Empty sequence: " . $name . "\n";
}
else
{
if ($sequence =~ m/^[ACGTNWSYRMHKXDVB]*$/)
{
$sequence =~ s/[WSYRMHKXDVB]/N/g;
if (not $sequence =~ m/NNNN/)
{
print CLIB $name;
print CLIB $sequence . "\n";
}
else
{
print "---------------------------------------------------------------------------------------\n";
print "Too many N's: " . $name;
}
}
else
{
print "---------------------------------------------------------------------------------------\n";
print "Invalid entry: " . $name;
$sequence =~ s/[ACGTN]//g;
print "Reduced sequence:\n";
print $sequence . "\n";
}
$sequence = "";
}
}
$name = $_;
}
else
{
$sequence .= uc($_);
$sequence =~ s/\n//g;
}
}
|
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