initial commit snpExtractor.pl

snpExtract.pl

@@ -0,0 +1,125 @@
+#!/usr/bin/env perl
+
+use strict; use warnings; use diagnostics; use feature qw(say);
+use Getopt::Long; use Pod::Usage;
+
+use FindBin; use lib "$FindBin::RealBin/lib";
+
+use MyIO;
+
+# ==============================================================================
+#
+#   CAPITAN: Andres Breton
+#   FILE: snpExtract.pl
+#   LICENSE:
+#   USAGE: Extract desired SNPs using columns' values as bounds to call true SNPS
+#
+# ==============================================================================
+
+#-------------------------------------------------------------------------------
+# VARIABLES
+my $outFile = "out.txt";
+#-------------------------------------------------------------------------------
+# COMMAND LINE
+my $FILE;
+my @SNP;
+my @DEPTH;
+my $usage = "
+
+ [options]
+
+Options:
+    -snp        SNP percentage (float) lower and upper bound; [90.0 100.0]
+    -depth      Depth of SNP coverage bound; [0 Inf]
+    -help       Shows this message
+
+";
+
+
+# OPTIONS
+GetOptions(
+    'file=s'                => \$FILE,
+    'snp=f{0,100}'          => \@SNP,
+    'depth=i{0,}'           => \@DEPTH,
+    help                    => sub{pod2usage($usage);}
+)or pod2usage(2);
+
+checkCLA(\@SNP, \@DEPTH); #check command line arguments passed
+#-------------------------------------------------------------------------------
+# CALLS
+extractColumns($FILE, $outFile, \@SNP, \@DEPTH);
+
+#-------------------------------------------------------------------------------
+# SUBS
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# $input = argChecks();
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# This function checks for arguments passed in command-line
+# using global variables
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# $output = Dies from errors
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+sub checkCLA {
+    # unless ($FILE) {
+    #     die "You did not provide an input file.", $!, $usage;
+    # }
+    unless (@SNP && @DEPTH) {
+        die "Did not provide snp and/or depth bounds to use as limits.", $!, $usage;
+    }
+    return;
+}
+
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# $input = ();
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# This function takes arguments
+#
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# $return = ();
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+sub extractColumns {
+    my ($file, $outFile, $snp, $depth) = @_;
+    my @snp = @$snp;
+    my $snpMin = $snp[0];
+    my $snpMax = 100.0;
+    $snpMax = $snp[1] if ($snp[1]);
+
+    my @depth = @$depth;
+    my $depthMin = $depth[0];
+    my $depthMax = "inf";
+    $depthMax = $depth[1] if ($depth[1]);
+
+    my $i = 1; my $snpCount = 0;
+    my $FH = getFH("<", $file);
+    while (<$FH>) {
+        next if $. == 1; #skip header
+        my @line = split /\t/; #split line by tab delim
+        my ($snpPer) = $line[10] =~ /(^\d+\.\d+)\s\%/; #get percentage float
+        if ($snpPer <= $snpMax && $snpPer >= $snpMin) { #check SNP % is within bounds
+            my $depth = $line[13];
+            if ($depth <= $depthMax && $depth >= $depthMin) { #check Depth is within bounds
+                say "SNP $i is inside bounds- SNP %: $snpPer \t Depth: $depth";
+                my $outFH = getFH(">", $outFile);
+                say $outFH $_; #write passing SNP to file
+                $snpCount++;
+            } else { #Depth is outside of bounds
+                # say "SNP $i is outside depth bounds- Depth: $depth";
+            }
+        } else { #SNP % is outside of bounds
+            # say "SNP $i is outside SNP % bounds- SNP %: $snpPer";
+        }
+        $i++;
+    }
+    say "-----------------------------------------------------\nTotal number of SNPs: $i";
+    say "Passing: $snpCount\n";
+    return;
+}
+
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# $input = ();
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# This function takes arguments
+#
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# $output =
+#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -