#!/usr/bin/perl -w

package main;

require 5.004;

use strict;
use Getopt::Std;

########## CONSTANTS  ###############

my $ID_LIMIT = 10000 ;

use vars qw($opt_h $opt_v $opt_d $opt_i $opt_o $opt_g $opt_p) ;
use vars qw($inputFile $outputFile $id $sequenceType) ;
use vars qw($key) ;

use vars qw($numRecords) ;

getopts('i:o:g:p:hvd') ;

$opt_h and die <<"QQ_HELP_QQ" ;

DESCRIPTION

     This program reads a fasta 'Genbank formatted file', retrieves the gi
numbers,
     and writes the numbers to a text file

AVAILABILITY

     Requires perl 5.004 or higher

SYNOPSIS

     makeGIList.pl -h -i [path/fileToRead] -o [path/fileToWrite]

OPTIONS

    -h                          Print help message
    -v                          Verbose mode
    -i	  [path/fileToRead]  	File to process
    -o	  [path/fileToWrite]	Destination
    -g    [gi|gb|both]          Make file with GI or Accession number or
both
    -p	  [n|p]			nucleotide or protein, DEFAULT = 'n'


EXIT STATUS

     0        Fail
     1        Successful completion

QQ_HELP_QQ

if ($opt_d) {
    $opt_v = 'v' ;
    $opt_i = "D:\\datasets\\ncbi\\UniGene\\Ta.seq.uniq" ;
    $opt_o = "D:\\datasets\\ncbi\\UniGene\\gbnumTest.id" ;
}


# Input path parameter
if ($opt_i) {
    $inputFile = $opt_i ;
} else {
    die "an input file with its path is required" ;
}


# output path and filename
if ($opt_o) {
    $outputFile = $opt_o ;
} else {
    die "an ouput file with its path is required" ;
}


# id to fetch, GI, Accession, or both
if ($opt_g) {
    if (($opt_g eq 'gi') or ($opt_g eq 'GI')) {
        $id = 'gi' ;
    } elsif (($opt_g eq 'gb') or ($opt_g eq 'GB')) {
        $id = 'gi' ;
    } elsif (($opt_g eq 'both') or ($opt_g eq 'BOTH')) {
        $id = 'both' ;
    }
} else {
    $opt_g = 'gb' ;
    $id    = $opt_g ;
}


# type of file
if ($opt_p) {
    if (($opt_p eq 'n') or ($opt_p eq 'N')) {
        $sequenceType = 'n';
    } elsif (($opt_p eq 'p') or ($opt_p eq 'P')) {
        $sequenceType = 'p' ;
    }
} else {
    $opt_p = 'p' ;
    $sequenceType = $opt_p ;
}

# Debug mode
# print out variables mapped from input flags

if ($opt_d) {
    print "\$opt_d: $opt_d  DEBUG mode on" ;      # undocumented
    print "\$opt_h: $opt_h\n" ;
    print "\$opt_v: $opt_v\n" ;
    print "\$opt_i: $opt_i ==> \$inputFile:    $inputFile\n" ;
    print "\$opt_o: $opt_o ==> \$outputFile:   $outputFile\n" ;
    print "\$opt_g: $opt_g ==> \$id:           $id\n" ;
    print "\$opt_p: $opt_p\==> \$sequenceType: $sequenceType\n" ;
}

####################  END OF INPUT FLAGS ########################

#################################################################
####################  Main Program ##############################

#open source file
if (open (INPUT, "<$inputFile")) {
    $opt_v and print "opened file $inputFile\n" ;
} else {
    die "Can not open $inputFile: $!.\n" ;
}

#open destination file
if (open (OUTPUT, ">>$outputFile")) {
    $opt_v and print "opened file to write:  $outputFile.\n" ;
} else {
   die "Can not write to $outputFile: $!.\n" ;
}

$opt_v and print "finding $id numbers\n" ;
while (my $line = <INPUT> ) {
    chomp ($line) ;
    if ($key = &getIDnumber($line,$id)) {
        print  OUTPUT "$key\n" ;
    } ;
}

$opt_v and print "done\n" ;
exit;




####################  END of Main Program  #######################
##################################################################


sub getIDnumber {
    my($line, $id) = @_ ;
    my $IDtoReturn = '' ;
    my $IDfromDef = '' ;
    if ($line =~ /^>/) {                # fasta Definition Line
        if (($id eq 'gi') and ($line =~ /\/gi=.*?\s/)) {
            $IDtoReturn= $1 ;
            chomp($IDtoReturn) ;
        } elsif (($id eq 'gb') and ($line =~ /\/gb=.*?\s/)) {
            $IDfromDef = $&;
            $IDtoReturn = substr($IDfromDef, 4) ;
            chomp($IDtoReturn) ;
        }

    } elsif ($line =~ /^$/){        # Blank line
        # do nothing
    } else {                            #sequence
        # do nothing
    }
    return $IDtoReturn
}