#!/usr/bin/perl

while (<DATA>) {
    next if (/^#/ or /^\s*$/);
    chomp;
    @t = split /\t/;
# your code goes here
}

__DATA__
# your data goes here

##</code><code>##

#!/usr/bin/perl

use strict;
use warnings;

my %hash = (
    1 => 'A',
    2 => 'T',
    3 => 'G',
    4 => 'C',
    12 => 'W', 21 => 'W',
    13 => 'R', 31 => 'R',
    14 => 'M', 41 => 'M',
    23 => 'K', 32 => 'K',
    24 => 'Y', 42 => 'Y',
);

while ( <DATA> ) {
    next if ( /^#/ or /^\s*$/ );
    chomp;
    my @t = split /\t/;

    my $seq = my $report = '';
    my $countref = ( $t[8] =~ tr/.,// );
    if ( $countref / $t[7] > 0.95 ) {
        $seq .=$t[2];
    }
    else {
        $t[8] =~ s/[.,]/$t[2]/g;
        my %ratio;
        my @letters = qw/a t g c/;
        $report = " $t[1] : ";
        for my $p ( @letters ) {
            my $count = eval "lc( '$t[8]' ) =~ tr/$p//";
            $ratio{$p} = $count / $t[7];
            $report .= sprintf( "%s %5.3f ", uc( $p ), $ratio{$p} );
        }

        my $countnut = 0;
        my @ncode;
        for my $i ( 0 .. $#letters ) {
            if ( $ratio{ $letters[$i] } >= 0.05 ) {
                push @ncode, $i + 1;
                $countnut++;
            }
            my $ccode = join ("", @ncode);

            if ( ! exists( $hash{$ccode} )) {
                $seq .= "N";
            }
            else {
                $seq .= $hash{$ccode};
            }
        }
    }
    printf( "Data_line %5d : t1= %5s ; report= %s; seq= %s\n",
            $., $t[1], $report, $seq );
}

__DATA__
#t0	t1	t2	t3	t4	t5	t6	t7	t8	t9
2L	1	G	A	48	48	26	7	AAaaAAA	ACCCD?@
2L	2	A	A	48	0	26	7	..,,...	AACC@BC
2L	3	T	K	18	18	26	7	.Ggg...	ACCCCCC
2L	4	C	C	57	0	37	16	.,..,,.,a.,,,,,^F,	CBCCBBC@3CCBBD=?
2L	5	C	C	54	0	37	17	.,..,,.,a.,,,,,,^F,	CDCCDACB9CCA@B?@D
2L	6	c	C	78	0	37	17	.,..,,.,,.,,,,,,,	CBCCBAC>9CBB@BA?A
2L	7	c	C	45	0	37	19	.,..,,.,,.+1A,,,,t,,^F,^Ft	CDCCDAC>;CBCBD*?DAA
2L	7	*	*/*	55	0	37	19	*	A	18	1	0	0	0
2L	8	a	A	162	0	21	45	,-4gtct,-4gtct,,....,,,,,,.,.,,,,.,,,,,,,,...,.,.,,,,.,,,	CCCCA<;=/CCACDBCBCCCCDCCCCBBCCBDCCCCCDCDDCCAB
2L	8	*	*/*	173	0	21	45	*	-gtct	43	2	0	0	0
2L	9	g	G	87	0	37	20	.,..,,.,,.,,,,,,,,,^F,	CDCCCAC?BCBBCD?<DBBB
2L	10	a	A	87	0	37	20	.,..,,.,,.,,,,,,,,,,	CBCDABC>BCACBB:AC?4C
2L	11	g	G	90	0	37	21	.,..,,.,,.,,,,,,,,,,^F.	CDCCCAC@@CDDCC<:DBABC
2L	12	c	C	117	0	14	31	...,,*.,,-2gt.,,.,,.,..........,,..	;B6CCBBCBCACDCCCB@DCDCC8CCCABCC
2L	12	*	*/-gt	21	21	14	31	*	-gt	30	1	0	0	0
2L	13	g	G	90	0	37	21	.,..,,.,,.,,,,,,,,,,.	CDCCCAC?:CDB5?<>BB>BC
2L	14	t	T	45	0	37	6	..,,,.-1T	CCCCCC
2L	14	*	-t/-t	56	59	37	6	-t	*	1	5	0	0	0
2L	15	t	T	93	0	37	22	.,..,,.,,.,,,G,,,,,,.^F.	CDCDDDC<@CBB5B@ABC<ACC
2L	16	G	G	178	0	36	50	.$,$,$,$,,,,,.,,,,..,.,,...,,,,.,,...,....,...,,,$,,,.,	BCCCCCCCCCCCCBDBCBCCB>8CCCCBCCBDBC8>ACCBB6CC?CCC6C
2L	17	A	A	59	0	36	45	,$,$,,,C,,,c..,.,,C..,,,,.,,...,....,..C,,,,,$.,	CCCCCBCCCBB8CACC>@;CCCCDCCCDAC-5ABCAA2CCCC?1A
2L	18	w	T	54	54	37	9	tTTTTttTT	CCDCCDCCC
2L	18	*	A/+A	65	279	37	9	A	*	8	1	0	0	0
2L	19	g	G	54	0	37	9	....,,...	>>@@CC>BB
2L	20	c	C	57	0	37	10	....,,...^F,	CACCCC?CBB
2L	21	t	T	57	0	37	10	....,,...,	BCDCCCCCB?
2L	650	t	T	48	0	34	7	..,.,,+4caaa,+4caaa	C?CCA=?
2L	650	*	*/*	9	0	34	7	*	+CAAA	5	2	0	0	0
2L	654	A	A	48	0	34	7	.$.$,.,+1g,,	DBC?CCA
2L	654	*	*/*	19	0	34	7	*	+G	6	1	0	0	0
2L	2332	g	G	60	0	14	33	.,...,,.-13GGCGCGCGTGCGC.,,A,,A,,A,..........aa..	DCBBBBDBCCCCBCCCDCBDCBCCCACCBABCC
2L	2332	*	*/*	61	0	14	33	*	-ggcgcgcgtgcgc	32	1	0	0	0
2L	3334	a	A	163	0	15	49	..$,..,,,t,.T,,,..,,,,T,-7attattt,,-7attattt,,,,,,....,,......,.,,..	BBCA>BCCCC:CCCC>ACCCCBCCCCBCCCCCCDCCCCCCCCBCBCDCC
2L	3334	*	*/-attattt	27	27	15	49	*	-attattt	47	2	0	0	0
2L	3928	c	C	32	0	0	11	,,-4tctt,,.-4TCTT...-4TCTT.^!.^!,	CCC8CCCCBCA
2L	3928	*	*/-tctt	157	157	0	11	*	-tctt	8	3	0	0	0