decimal2date.pl

#!/usr/bin/perl
# Sam Shepard - 2011
# Converts normal dates into the decimal format.

use Getopt::Long;
GetOptions(
            'delimiter|D:s' => \$delim,
            'field|F:i'     => \$field,
            'ascending|A'   => \$ascending,
            'us-format|U'   => \$usFormat
);

if ( scalar(@ARGV) != 2 ) {
    $message = "\n$0 <input.fasta> <output.fasta> [OPTIONS]\n";
    $message .= "\t-A|--ascending\t\t\t\tAscending date: DD/MM/YYYY. Default is YYYY/MM/DD.\n";
    $message .= "\t-U|--us-format\t\t\t\tUS format date: MM/DD/YYYY. Default is YYYY/MM/DD.\n";
    $message .= "\t-D|--delimiter CHARACTER\t\tSingle character delimiter within FASTA header. Default is '|'.\n";
    $message .= "\t-F|--field POSITIVE_NUMBER\t\tHeader field to use for dates. Default is 1.\n\n";
    die($message);
}

if ( !defined($field) ) {
    $field = 0;
} elsif ( $field == 0 ) {
    die("ERROR: field must be specified.\n");
} elsif ( $field < 0 ) {
    die("ERROR: field must be a positive number.\n");
} else {
    $field -= 1;
}

if ( !defined($delim) ) {
    $delim = '|';
} elsif ( $delim eq '' ) {
    die("ERROR: No delimiter argument detected.\n");
} elsif ( length($delim) > 1 ) {
    die("ERROR: single character delimiter expected instead of '$delim'.\n");
}

open( IN,  '<', $ARGV[0] ) or die("ERROR: Could not open $ARGV[0].\n");
open( OUT, '>', $ARGV[1] ) or die("ERROR: Could not open $ARGV[1].\n");
$/ = ">";
$i = 0;
while ( $record = <IN> ) {
    chomp($record);
    @lines    = split( /\r\n|\n|\r/, $record );
    $header   = shift(@lines);
    $sequence = lc( join( '', @lines ) );
    $length   = length($sequence);

    @values = split( /\Q$delim\E/, $header );
    if ( $length == 0 ) {
        next;
    } elsif ( $header !~ /\Q$delim\E/ && $delim ne '' ) {
        die("ERROR: delimiter '$delim' not found in header:\n\t$header\n");
    } elsif ( $#values < $field && 0 ) {
        $x = $#values + 1;
        $field++;
        die("ERROR: Only $x fields found in header but field $field selected:\n\t$header\n");
    }

    if ( $values[$field] eq '' ) {
        print "WARNING: No date information found. Skipping:\n\t$header\n\n";
        $numberSkipped++;
        next;
    } else {
        $values[$field] = decimalDate( $values[$field] );
    }
    print OUT '>', join( $delim, @values ), "\n", $sequence, "\n";
}

close(IN);
close(OUT);

sub decimalDate($) {

    # Sam Shepard - 6.2011 - decimalDate
    # Converts fasta file with header format: >date_virus
    # To the decimal date format used by beast.
    # Ported from the decimalDate.php by Justin Bahl & Yongmei Liu.
    # Updated to handle empty values found within a database. -SS
    my $date   = $_[0];
    my @days1  = ( 0, 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31 );
    my @days2  = ( 0, 31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31 );
    my $dds    = 0;
    my $ddfrac = 0;
    my $i      = 0;
    my ( $yy, $mm, $dd );

    my @pieces    = split( /\/|-|\./, $date );
    my $numPieces = scalar(@pieces);
    if ( $numPieces == 3 ) {
        if ($ascending) {
            ( $dd, $mm, $yy ) = @pieces;
        } elsif ($usFormat) {
            ( $mm, $dd, $yy ) = @pieces;
        } else {
            ( $yy, $mm, $dd ) = @pieces;
        }

        if ( $dd == 0 ) {
            $dd = 15;
        }
        if ( $mm == 0 ) {
            $mm = 6;
        }
    } elsif ( $numPieces == 2 ) {
        if ( $ascending || $usFormat ) {
            ( $mm, $yy ) = @pieces;
        } else {
            ( $yy, $mm ) = @pieces;
        }
        $dd = 15;
    } else {
        $yy = $pieces[0];
        ( $mm, $dd ) = ( 7, 1 );
    }

    if ( $yy % 4 == 0 ) {
        $dds = 0;
        for ( $i = 1; $i < $mm; $i++ ) {
            $dds = $dds + $days2[$i];
        }
        $dds    = $dds + $dd;
        $ddfrac = $dds / 366.0;
    } else {
        $dds = 0;
        for ( $i = 1; $i < $mm; $i++ ) {
            $dds = $dds + $days1[$i];
        }
        $dds    = $dds + $dd;
        $ddfrac = $dds / 365.0;
    }

    if ( $dd == 31 && $mm == 12 ) {
        $ddfrac = 0.999;
    }

    $ddfrac = sprintf( "%.3f", $ddfrac );
    return sprintf( '%s.%s', $yy, substr( $ddfrac, 2 ) );
}