function for nucmer

lib/phame/nucmer.pm

@@ -0,0 +1,136 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FileHandle;
+use File::Basename;
+use Cwd;
+
+package nucmer;
+
+sub run_nucmer {
+
+    # Runs nucmer, returns delta file, moves it to nucmer folder
+    my ($args) = @_;
+
+    my $prefix            = $args->{prefix};
+    my $ref_fasta         = $args->{ref_fasta};
+    my $full_genome_fasta = $args->{full_genome_fasta};
+    my $opt               = $args->{options};
+
+    if ( !-e "nucmer" ) {
+        mkdir "nucmer";
+    }
+    my $delta_file =
+      File::Spec->catpath( $args->{outdir}, "nucmer",
+        $args->{prefix} . '.delta' );
+    if ( -e $delta_file ) {
+        print
+"nucmer complete for $args->{ref_fasta} and $args->{full_genome_fasta}.\n";
+    }
+    else {
+        print "Running nucmer on $prefix\n";
+        my $nc1 =
+          "nucmer $opt -p $prefix $ref_fasta $full_genome_fasta  2>/dev/null";
+        print "[RUNNING:] $nc1\n";
+        if ( system($nc1) ) {
+            die "Error running nc1 $nc1.\n";
+        }
+        `mv $args->{prefix}.delta nucmer/`;
+    }
+}
+
+sub run_delta_filter_snp {
+
+    # Runs delta filter, and writes the output in .snpfilter
+    my ($args) = @_;
+
+    my $outdir   = $args->{outdir};
+    my $identity = $args->{identity};
+    my $prefix   = $args->{prefix};
+
+    my $snpfilter_file =
+      File::Spec->catpath( $outdir, "nucmer", $prefix . '.snpfilter' );
+    my $delta_file =
+      File::Spec->catpath( $outdir, "nucmer", $prefix . '.delta' );
+    if ( -e $snpfilter_file ) {
+        print "nucmer already complete for $prefix.\n";
+    }
+    else {
+        my $filter_command1 =
+          "delta-filter -1 $identity $delta_file > $snpfilter_file";
+
+        if ( system($filter_command1) ) {
+            die "Error running filter_command1 $filter_command1.\n";
+        }
+    }
+}
+
+sub run_delta_filter_gap {
+
+    # Runs delta filter, and writes the output in .gapfilter
+    my ($args) = @_;
+
+    my $out_dir  = $args->{outdir};
+    my $identity = $args->{identity};
+    my $prefix   = $args->{prefix};
+
+    my $gapfilter_file =
+      File::Spec->catpath( $out_dir, "nucmer", $prefix . '.gapfilter' );
+    my $delta_file =
+      File::Spec->catpath( $out_dir, "nucmer", $prefix . '.delta' );
+    if ( -e $gapfilter_file ) {
+        print "nucmer already complete for $prefix.\n";
+    }
+    else {
+        my $filter_command1 =
+          "delta-filter $identity $delta_file > $gapfilter_file";
+
+        if ( system($filter_command1) ) {
+            die "Error running filter_command1 $filter_command1.\n";
+        }
+    }
+}
+
+sub run_show_snps {
+    my ($args) = @_;
+
+    my $outdir = $args->{outdir};
+    my $prefix = $args->{prefix};
+
+    my $snpfilter_file =
+      File::Spec->catpath( $outdir, "nucmer", $prefix . '.snpfilter' );
+    my $snp_file = File::Spec->catpath( $outdir, "nucmer", $prefix . '.snps' );
+    if ( -e $snp_file ) {
+        print "nucmer already complete for $prefix.\n";
+    }
+    else {
+        my $snp_command1 = "show-snps -CT $snpfilter_file > $snp_file";
+        if ( system($snp_command1) ) {
+            die "Error running snp_command1 $snp_command1.\n";
+        }
+    }
+}
+
+sub run_show_coords {
+    my ($args) = @_;
+    my $outdir = $args->{outdir};
+    my $prefix = $args->{prefix};
+
+    my $gfilt_file =
+      File::Spec->catpath( $outdir, "nucmer", $prefix . '.gapfilter' );
+
+    my $coord_file =
+      File::Spec->catpath( $outdir, "nucmer", $prefix . '.coords' );
+    if ( -e $gfilt_file ) {
+        print "nucmer already complete for $prefix.\n";
+    }
+    else {
+        my $coords_command1 = "show-coords -clTr $gfilt_file > $coord_file";
+        if ( system($coords_command1) ) {
+            die "Error running coords_command1 $coords_command1.\n";
+        }
+    }
+}
+
+1;