run this script to get the contig id, orf start and end, and also strand

post_annotateM

@@ -0,0 +1,397 @@
+#!/usr/bin/env perl
+###############################################################################
+#
+#    post_annotateM
+#    
+#    The idea here is an automated way of annotating your genome based on 
+#    multiple available databases and to produce a tab-delimited file of 
+#    all the annotations, evalues, scores, descriptions.
+# 
+#    Suggested workflow:
+#	 1) run your genome nucleotide fasta file through annotateM
+#	 2) generate a tab-delimited file
+#	 3) open the file in ms excel or oo calc
+#	 4) manually curate the annotations based on evalues/scores/desc etc	
+#        5) metabolic reconstruction of organism
+#
+#    Copyright (C) Mohamed Fauzi Haroon
+#	 Special appearance from Adam Skarshewski
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+###############################################################################
+
+#pragmas
+use strict;
+use warnings;
+
+#core Perl modules
+use Getopt::Long;
+use Carp;
+use Data::Dumper;
+
+#CPAN modules
+
+#locally-written modules
+
+BEGIN {
+    select(STDERR);
+    $| = 1;
+    select(STDOUT);
+    $| = 1;
+}
+
+# edit here to log all external commands 
+my $global_log_commands = 0;
+
+# ext command failure levels
+use constant {
+    IGNORE_FAILURE => 0,
+    WARN_ON_FAILURE => 1,
+    DIE_ON_FAILURE => 2
+};
+
+# get input params and print copyright
+printAtStart();
+my $global_options = checkParams();
+
+######################################################################
+# CODE HERE
+######################################################################
+
+# check that the final_output.txt file exists
+checkFileExists($global_options->{'in'});
+
+# identify the ORF called amino acid fasta file
+my $locus = $global_options->{'locustag'};
+
+# gff file
+my $gff_file = $global_options->{'gff'};
+
+# to store hash
+my %hashy = ();
+my %orf = ();
+
+# open my final_output.txt file
+open my $final_output, "./final_output.txt", or die "Couldn't open final_output.txt\n";
+while (<$final_output>)
+{
+	#skips first line
+	next if $. < 2;
+	chomp $_;
+        my @columns = split (/\t/, $_);
+        my @baba = @columns[1..$#columns];
+	$hashy{$columns[0]} = join("\t", @baba);
+        #$combined_bighash{$columns[0]}->{'uniref'} = join("\t", @baba);
+#        push @{$combined_bighash{$columns[0]}->{'b-uniref'}}, join("\t", @baba);
+}
+
+close($final_output);
+#print Dumper (\%orf);
+
+# open the prokka annotation gff file
+# sample gff file:
+###gff-version 3
+##sequence-region contig_3875 1 10320
+#contig_3875     Prodigal:2.60   CDS     334     735     .       +       0       ID=test_00001;inference=ab initio prediction:Prodigal:2.60,protein motif:CLUSTERS:PRK10707;locus_tag=test_00001;product=putative NUDIX hydrolase;protein_id=gnl|VBC|test_00001
+#contig_3875     Prodigal:2.60   CDS     930     3221    .       +       0       ID=test_00002;eC_number=1.1.1.40;gene=maeB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P76558;locus_tag=test_00002;product=NADP-dependent malic enzyme;protein_id=gnl|VBC|test_00002
+#contig_3875     Prodigal:2.60   CDS     3229    5175    .       -       0       ID=test_00003;inference=ab initio prediction:Prodigal:2.60;locus_tag=test_00003;product=hypothetical protein;protein_id=gnl|VBC|test_00003
+open my $SUPER_FINAL_OUTPUT, "> ./super_final_output.txt";
+print {$SUPER_FINAL_OUTPUT} "ORF_ID\tcontig_ID\tORF_start_pos\tORF_end_pos\tstrand\timg_evalue\timg_score\timg_gene\timg_organism\timg_reciprocal\tuniref_evalue\tuniref_score\tuniref_gene\tuniref_organism\tuniref_reciprocal\tprokka_gene\tcog_evalues\tcog_scores\tcog_classes\tcog_gene_acronyms\tcog_genes\tpfam_evalues\tpfam_scores\tpfam_genes\ttigrfam_evalues\ttigrfam_scores\ttigrfam_genes\ttigrfam_descriptions\n";
+
+open my $gff, "./$gff_file", or die "Couldn't open $locus.gff\n";
+while (<$gff>)
+{
+	if ($_ =~ /^##/){
+		if ($_ =~ /^##FASTA/){
+			last;
+		}
+		else{	
+			next;
+		}
+	}
+        chomp $_;
+        my @orf_id = ();
+	my @columns = split (/\t/, $_);
+	#my @last_column = split (/\t/, $columns[8]);
+#	$columns[8] =~ /(ID=)/;
+#	print $1;
+	if ($_ =~ /ID=(\w+);/)
+	{	
+	push @orf_id, $1;
+#	print Dumper (\@orf_id);
+	}
+	foreach my $value_in_orf_array (@orf_id)
+	{
+		if (exists $hashy{$value_in_orf_array})
+		{
+	#	print "$value_in_orf_array\t$columns[3]\t$columns[4]";
+		my @print_array = [$value_in_orf_array, $columns[3], $columns[4]];
+	#	unshift @{$hashy{$value_in_orf_array}}, join("\t", @print_array);
+	#	$hashy{$value_in_orf_array} .= "\t" . $value_in_orf_array . "\t$columns[3]\t$columns[4]\t";
+		
+		print {$SUPER_FINAL_OUTPUT} "$value_in_orf_array\t$columns[0]\t$columns[3]\t$columns[4]\t$columns[6]\t$hashy{$value_in_orf_array}\n";
+		}
+	}
+}	
+close($gff);
+close($SUPER_FINAL_OUTPUT);
+
+print "COMPLETED, super_final_output.txt generated! If i was you, i will open super_final_output.txt in excel\n";
+
+######################################################################
+# CUSTOM SUBS
+######################################################################
+
+# who needs custom subs...
+
+######################################################################
+# TEMPLATE SUBS
+
+######################################################################
+# PARAMETERS
+
+sub checkParams {
+    #-----
+    # Do any and all options checking here...
+    #
+    my @standard_options = ( "help|h+", "in|i:s", "locustag|l:s", "gff|g:s");
+    my %options;
+
+    # Add any other command line options, and the code to handle them
+    # 
+    GetOptions( \%options, @standard_options );
+
+    # if no arguments supplied print the usage and exit
+    #
+    exec("pod2usage $0") if (0 == (keys (%options) ));
+
+    # If the -help option is set, print the usage and exit
+    #
+    exec("pod2usage $0") if $options{'help'};
+    
+    # Compulsory items
+    #if(!exists $options{''} ) { printParamError (""); }
+    if(!exists $options{'in'} ) { printParamError ("You MUST supply your final_output.txt from annotateM"); }
+
+    return \%options;
+}
+
+sub printParamError
+{
+    #-----
+    # What to do if there's something wrong with a parameter
+    #  
+    my ($error) = @_;  
+    print "**ERROR: $0 : $error\n"; exec("pod2usage $0");
+}
+
+sub overrideDefault
+{
+    #-----
+    # Set and override default values for parameters
+    #
+    my ($default_value, $option_name) = @_;
+    if(exists $global_options->{$option_name}) 
+    {
+        return $global_options->{$option_name};
+    }
+    return $default_value;
+}
+
+#####################################################################
+# FILE IO
+
+sub openWrite
+{
+    #-----
+    # Open a file for writing
+    #
+    my ($fn) = @_;
+    open my $fh, ">", $fn or croak "**ERROR: could not open file: $fn for writing $!\n";
+    return $fh;
+}
+
+sub openRead
+{   
+    #-----
+    # Open a file for reading
+    #
+    my ($fn) = @_;
+    open my $fh, "<", $fn or croak "**ERROR: could not open file: $fn for reading $!\n";
+    return $fh;
+}
+
+######################################################################
+# EXTERNAL COMMANDS
+#
+# checkAndRunCommand("ls", {
+#                          -a => ""
+#                          }, 
+#                          WARN_ON_FAILURE);
+
+sub checkFileExists {
+    #-----
+    # Does a file exists?
+    #
+    my ($file) = @_;
+    unless(-e $file) {
+        croak "**ERROR: $0 : Cannot find:\n$file\n";
+    }
+}
+
+sub logExternalCommand
+{
+    #-----
+    # Log a command line command to the command line!
+    #
+    if(1 == $global_log_commands) {
+        print $_[0], "\n";
+    }
+}
+
+sub isCommandInPath
+{
+    #-----
+    # Is this command in the path?
+    #
+    my ($cmd, $failure_type) = @_;
+    if (system("which $cmd |> /dev/null")) {
+        handleCommandFailure($cmd, $failure_type);
+    }
+}
+
+sub runExternalCommand
+{
+    #-----
+    # Run a command line command on the command line!
+    #
+    my ($cmd) = @_;
+    logExternalCommand($cmd);
+    system($cmd);
+}
+
+sub checkAndRunCommand
+{
+    #-----
+    # Run external commands more sanelier
+    #
+    my ($cmd, $params, $failure_type) = @_;
+    
+    isCommandInPath($cmd, $failure_type);
+    
+    # join the parameters to the command
+    my $param_str = join " ", map {formatParams($_)} @{$params};
+
+    my $cmd_str = $cmd . " " . $param_str;
+    
+    print "The command currently running:\t$cmd_str\n"; 
+    logExternalCommand($cmd_str);
+
+    # make sure that all went well
+    if (system($cmd_str)) {
+         handleCommandFailure($cmd_str, $failure_type)
+    }
+}
+
+sub formatParams {
+
+    #---------
+    # Handles and formats the different ways of passing parameters to 
+    # checkAndRunCommand
+    #
+    my $ref = shift;
+    
+    if (ref($ref) eq "ARRAY") {
+        return join(" ", @{$ref});
+    } elsif (ref($ref) eq "HASH") {
+       return join(" ", map { $_ . " " . $ref->{$_}} keys %{$ref});
+    }
+    croak 'The elements of the $params argument in checkAndRunCommand can ' .
+        'only contain references to arrays or hashes\n';
+}
+
+
+sub handleCommandFailure {
+    #-----
+    # What to do when all goes bad!
+    #
+    my ($cmd, $failure_type) = @_;
+    if (defined($failure_type)) {
+        if ($failure_type == DIE_ON_FAILURE) {
+            croak "**ERROR: $0 : " . $! . "\n";
+        } elsif ($failure_type == WARN_ON_FAILURE) {
+            carp "**WARNING: $0 : " . $! . "\n";
+        }
+    }
+}
+
+
+######################################################################
+# MISC
+
+sub printAtStart {
+print<<"EOF";
+---------------------------------------------------------------- 
+ 
+ $0
+ post_annotateM - annotate my genome
+ Due to the blast processes against multiple databases, this whole
+ annotation pipeline will usually take awhile. Please be patient!
+ What you get in the end will save you heaps of time.
+ 
+---------------------------------------------------------------- 
+EOF
+}
+
+__DATA__
+
+=head1 NAME
+
+   annotateM
+
+=head1 COPYRIGHT
+
+   Copyright (C) Mohamed Fauzi Haroon
+   Special appearance from Adam Skarshewski
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+=head1 DESCRIPTION
+
+   Want to annotate your genome? annotateM!
+
+=head1 SYNOPSIS
+
+    annotateM -i [finaloutputfromannotatem] -l [locustag] -g [gff]
+
+      -i final_output.txt				final_output.txt file generated from annotateM 
+      -l locustag					Name of locus tag
+      -g locustag.gff					location of gff file in prokka_annotation folder
+      [-help -h]					Displays basic usage information
+         
+=cut
+
+