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#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Getopt::Long;
use Bio::Align::Utilities qw(:all);
#Var initializatoin
my ($input, $ingap, $output, $outgap, $flat, $aln_format, $min);
#Set a few default settings
$min = 1;
$aln_format = "fasta";
#Command line parameter space settings
"i=s" => \$input, #Path to alignment object(s)
"j=s" => \$ingap, #Path to gaps file
"o=s" => \$output, #Output file path
"p=s" => \$outgap, #Output gaps file
"m=i" => \$min, #Minimum number of residues a column must contain to be retained
"f:s" => \$aln_format, #Alignment format (Default = FASTA)
"flat" => \$flat, #use flat to keep coords out of headers
print "processing $input with cutoff $min, will print output to $output\n";
#You're not a bonehead, right?
if(!$input || !$output){ die "You must specific an input and output file!\n" }
#Initialize the framework
my $in_aln = Bio::AlignIO->new(-file => "$input", -format => "$aln_format");
my $out_aln = Bio::AlignIO->new(-file => ">$output", -format => "$aln_format");
open( INGAP, "$ingap" ) || die "can't open input $ingap in$!\n";
open( OUTGAP, ">>$outgap" ) || die "can't open output $outgap in$!\n";
my $aln = $in_aln->next_aln();
my $num_seq = <INGAP>;
my $num_cov_str = <INGAP>;
my @num_cov = split(" ", $num_cov_str);
my $perc_cov_str = <INGAP>;
my @perc_cov = split(" ", $perc_cov_str);
my $size = @perc_cov;
my @Onum_cov = ();
my @Operc_cov = ();
my @remove = ();
close INGAP;
my $i;
#Find the gappy columns
for( $i=0; $i<$size; $i++ ){
if( $num_cov[$i] >= $min ){
#This is a sufficiently filled column, preserve it
push(@Onum_cov, $num_cov[$i]);
push(@Operc_cov, $perc_cov[$i]);
} else {
#Mark this column to be removed
push(@remove, $i+1);
print $aln->length(), "\n";
print "original alignment: $size reduced by: ",scalar(@remove), "\n";
push(@remove, $i+1); #One beyond the end marks the last
#Print the new gaps file
printf OUTGAP $num_seq;
my $format = ("%1.0f " x @Onum_cov)."\n";
printf OUTGAP $format, @Onum_cov;
$format = ("%1.5f " x @Operc_cov)."\n";
printf OUTGAP $format, @Operc_cov;
close OUTGAP;
#Mask character so rows don't get deleted
#Collect together only the good columns
my @aln_slices = ();
my $goodstart = 1;
my $goodend = 1;
my $sum =0;
while ( scalar(@remove) > 0 ){
my $badcol = shift(@remove);
if( $goodstart == $badcol ){
#The next residue is also bad, step forward
} else {
$goodend = $badcol - 1;
if( $goodstart <= $goodend ){
#print "$goodstart - $goodend\n";
my $slice = $aln->slice( $goodstart, $goodend );
push( @aln_slices, $slice );
$goodstart = $badcol+1;
#Print the good rows to file
my $clean_aln = cat(@aln_slices);
print "new alignment: ", $clean_aln->length, "\n";
#UnMask characters so we print something sensible
if( $flat ){