This is my first commit of annotateM

annotateM

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+#!/usr/bin/env perl
+###############################################################################
+#
+#    annotateM
+#    
+#    The idea here is to produce a tab-delimited file of all the annotation
+#    pipelines for manual curation afterwards.
+#
+#    Copyright (C) Mohamed Fauzi Haroon
+#
+#    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;
+
+#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 $global_options = checkParams();
+
+######################################################################
+# CODE HERE
+######################################################################
+
+# check that the file exists
+checkFileExists($global_options->{'in'});
+
+# run prokka to generate the ORFs and also prokka annotations
+checkAndRunCommand("prokka", [{
+                                   "--locustag" =>  $global_options->{'locustag'},
+				   "--outdir" => "prokka_annotation",
+				   "--prefix" => $global_options->{'locustag'},
+				   "--kingdom" =>  $global_options->{'kingdom'},
+				   "--cpus" =>  $global_options->{'threads'},
+				   "--keep_names",
+				   $global_options->{'in'},	
+                                   }], DIE_ON_FAILURE);
+
+# identify the ORF called amino acid fasta file for blast-ing
+my $locus = $global_options->{'locustag'};
+
+# blast against img
+if (! -e "./$locus.faaVSimg.blastp")
+{
+print "BLASTing against IMG 4.0 database\n";
+checkAndRunCommand("cat", 
+			[[ 
+			"prokka_annotation/$locus.faa |",	
+			"parallel",
+			"--block"=> "100k", 
+			"--recstart",
+			"'>'",
+			"--pipe",
+			"blastp",
+			-db => "/srv/db/img/4.0/dereplicated/img_dereplicated_species.genes.faa",
+			-outfmt => 6,
+			-max_target_seqs => 1,
+			-query => "-",
+			"> $locus.faaVSimg.blastp",
+			#-num_threads => $global_options->{'threads'},
+			]], DIE_ON_FAILURE);
+}
+
+# blast against uniref				
+if (! -e "./$locus.faaVSuniref90.blastp")
+{
+print "BLASTing against Uniref90 database\n";
+checkAndRunCommand("cat",[[
+			"prokka_annotation/$locus.faa |",
+                        "parallel",
+                        "--block"=> "100k",
+                        "--recstart",
+                        "'>'",
+                        "--pipe",
+			"blastp",
+			-db => "/srv/whitlam/home/users/uqmharoo/Uniref_db/uniref90.fasta",
+			-outfmt => 6,
+                        -max_target_seqs => 1,
+                        -query => "-",
+                        "> $locus.faaVSuniref90.blastp",
+                        #-num_threads => $global_options->{'threads'},
+                        ]], DIE_ON_FAILURE);
+}
+######################################################################
+# 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", "kingdom|k:s", "threads|t: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 $options{'in'} ) { printParamError ("You MUST supply a fasta file"); }
+
+    return \%options;
+}
+
+sub printParamError
+{
+    #-----
+    # What to do if there's something wrong with a parameter
+    #  
+    my ($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 $cmd_str; 
+    logExternalCommand($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
+ Copyright (C) Mohamed Fauzi Haroon
+    
+ This program comes with ABSOLUTELY NO WARRANTY;
+ This is free software, and you are welcome to redistribute it
+ under certain conditions: See the source for more details.
+---------------------------------------------------------------- 
+EOF
+}
+
+__DATA__
+
+=head1 NAME
+
+   annotateM
+
+=head1 COPYRIGHT
+
+   copyright (C) Mohamed Fauzi Haroon
+
+   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
+
+   Insert detailed description here
+
+=head1 SYNOPSIS
+
+    annotateM -i fasta_file 
+
+      -i FASTA_FILE		   	Nucleotide fasta file 
+      -l locustag		   	Name of locus tag
+      -k kingdom (Bacteria/Archaea) 	Kingdom of genome to be annotated
+      -t threads			Number of threads
+      [-help -h]                   	Displays basic usage information
+         
+=cut
+
+