ebd704b803fed9f990e2c8aeda1338a7054f8316
braney
  Wed Feb 22 17:43:49 2012 -0800
more moving things around #6943
diff --git src/utils/omim/parseGeneMap.pl src/utils/omim/parseGeneMap.pl
deleted file mode 100644
index ce63dd1..0000000
--- src/utils/omim/parseGeneMap.pl
+++ /dev/null
@@ -1,221 +0,0 @@
-#!/usr/bin/env perl

-

-#--------------------------------------------------------------------------

-

-use strict;

-use warnings;

-

-

-#--------------------------------------------------------------------------

-#

-# Documentation

-#

-#	./script1.pl --gene-map-file=genemap.txt

-#

-

-

-#--------------------------------------------------------------------------

-#

-# Required packages

-#

-

-

-#--------------------------------------------------------------------------

-#

-# Package Constants

-#

-

-BEGIN {

-

-	# Set the locale to utf8

-	$ENV{'LC_ALL'} = 'en_US.UTF-8';

-	$ENV{'LANGUAGE'} = 'en_US.UTF-8';

-	$ENV{'LANG'} = 'en_US.UTF-8';

-

-}

-

-

-#--------------------------------------------------------------------------

-#

-#	Function:	main()

-#

-#	Purpose:	main

-#

-#	Called by:	

-#

-#	Parameters:	

-#

-#	Global Variables:	

-#

-#	Returns:	void

-#

-

-

-# Gene map file path

-my $geneMapFilePath = './genemap.txt';

-

-

-# Check for command parameters

-for ( my $argc = 0; $argc <= $#ARGV; $argc++ ) {

-

-	my $option = $ARGV[$argc];

-

-	if ( $option =~ /^--gene-map-file=(.*)$/i ) {

-		$geneMapFilePath = $1;

-	}

-	

-	elsif ( $option =~ /^(--help|\-?)$/ ) {

-		printf("Usage:\n");

-		printf("\t[--help|-?] print out this message.\n");

-		printf("\n");

-		printf("\t[--gene-map-file=path] gene map file path, defaults to: '%s'.\n", $geneMapFilePath);

-		printf("\n");

-	}

-	else {

-		printf("Error: Invalid action: '%s', type '%s  --help' for help.\n", $option, $0);

-		exit (0);

-	}

-}

-

-

-# Check the gene map file path

-if ( !defined($geneMapFilePath) ) {

-	die "Undefined gene map file path"

-}

-

-

-

-# Open the gene map file

-open (GENE_MAP_FILE, $geneMapFilePath) || die "Failed to open the gene map file: '$geneMapFilePath'";

-

-

-# Read the gene map file

-while (<GENE_MAP_FILE>) {

- 	

-	# Get the line

- 	my $line = $_;

- 	chomp $line;

- 

-	# Split the fields

- 	my @fields = split(/\|/, $line, 18);

- 	

-	# Get all the data

- 	my $sort = $fields[0];

- 

- 	my $month = $fields[1];

- 	my $day = $fields[2];

- 	my $year = $fields[3];

- 

- 	my $cytoLocation = $fields[4];

- 	my $geneSymbols = $fields[5];

- 	my $confidence = $fields[6];

- 

- 	my $geneName0 = $fields[7];

- 	my $geneName1 = $fields[8];

- 

- 	my $mimNumber = $fields[9];

- 

- 	my $mappingMethod = $fields[10];

- 

- 	my $comments0 = $fields[11];

- 	my $comments1 = $fields[12];

- 

- 	my $phenotypes0 = $fields[13];

- 	my $phenotypes1 = $fields[14];

- 	my $phenotypes2 = $fields[15];

- 

- 	my $mouse = $fields[16];

- 	my $references = $fields[17];

- 

-	# Re-assemble the hacked fields

- 	my $geneName = $geneName0 . ' ' . $geneName1;

- 	my $comments = $comments0 . ' ' . $comments1;

- 	my $phenotypes = $phenotypes0 . ' ' . $phenotypes1 . ' ' . $phenotypes2;

- 

- 	# Clean the reassembled fields

- 	$geneName = _cleanText($geneName);

- 	$comments = _cleanText($comments);

- 	$phenotypes = _cleanText($phenotypes);

- 

-

- 	# Split out the phenotypes

- 	foreach my $phenotype ( split(/;\s*/, $phenotypes) ) {

-

-		my $phenotypeMimNumber = '';

-		my $phenotypeMappingKey = '';

-

-		# Extract the phenotype mim number and remove it

-		if ( $phenotype =~ /(\d{6})/ ) {

-			$phenotypeMimNumber = $1;

-			$phenotype =~ s/\d{6}//;

-		}

-

-		# Extract the phenotype mapping key and remove it

-		if ( $phenotype =~ /(.*)\((\d)\)/ ) {

-			$phenotypeMappingKey = $2;

-			$phenotype = $1

-		}

-	

-		# Strip trailing comma from the phenotype

-		if ( $phenotype =~ /(.*?),\s*$/ ) {

-			$phenotype = $1

-		}

- 	

-		# Final cleaning

- 		$phenotype = _cleanText($phenotype);

- 		

- 		

- 		# Copy the mim number to the phenotype mim number for phenotype mapping key == 2

-#  		if ( $phenotypeMappingKey == 2 ) {

-#  			$phenotypeMimNumber = $mimNumber;

-#  		}

-	

-		

-		# Write out the data

-		printf("%s\t%s\t%s\t%s\n", $mimNumber, $phenotype, $phenotypeMimNumber, $phenotypeMappingKey);

-

- 	}

- 

- }

- 

- 

- # Close the gene map file

- close (GENE_MAP_FILE);

- 

- 

- exit (0);

-

- 

-

-#--------------------------------------------------------------------------

-

- 

-

-sub _cleanText {

-

-	my $text = shift;

-

-

-	# Check the parameter

-	return (undef) if !defined($text);

-	

-

-	# Replace new lines with spaces

-	$text =~ s/[\n\r]/ /g;

-

-	# Deduplicate spaces

-	$text =~ s/\s+/ /g;

-

-	# Trim leading and trailing spaces

-	$text =~ s/^\s+//;

-	$text =~ s/\s+$//;

-

-

-	return ($text);

-

-}

-

-

-#--------------------------------------------------------------------------

-

-