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snpgenie_within_group_processor.pl
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snpgenie_within_group_processor.pl
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#!/usr/bin/env perl
# PREVIOUSLY snpgenie_sw.pl
#########################################################################################
# EXAMPLE CALLS:
#########################################################################################
# snpgenie_within_group_processor.pl <sw_size> <sw_step_size> <num_bootstraps> <procs_per_node>
# snpgenie_within_group_processor.pl --codon_file=within_group_codon_results.txt --sliding_window_size=1 --sliding_window_step=1 --num_bootstraps=10000
#########################################################################################
# PROGRAM: Recalculate sliding window values using a given window and step size for the
# provided CODON results file
# Copyright (C) 2018 Chase W. Nelson
#########################################################################################
## LICENSE
## 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/>.
#########################################################################################
# DATE CREATED: January 21, 2018
# AUTHOR: Chase W. Nelson
# CONTACT1: [email protected]
# CONTACT2: [email protected]
# AFFILIATION1: Sackler Institute for Comparative Genomics, American Museum of Natural
# History, New York, NY 10024, USA
# AFFILIATION2: Special Volunteer, Division of Cancer Epidemiology & Genetics, National
# Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
# AFFILIATION3: BigPlant Consortium, Center for Genomics and Systems Biology, New York
# University, New York, NY 10003, USA
# CITATION1: SNPGenie, https://github.com/chasewnelson/snpgenie
# CITATION2: Nelson CW, Moncla LH, Hughes AL (2015) SNPGenie: estimating evolutionary
# parameters to detect natural selection using pooled next-generation sequencing data.
# Bioinformatics 31(22):3709-11, doi: 10.1093/bioinformatics/btv449.
# CITATION3: Nelson CW, Hughes AL (2015) Within-host nucleotide diversity of virus
# populations: Insights from next-generation sequencing. Infection, Genetics and
# Evolution 30:1-7, doi: 10.1016/j.meegid.2014.11.026
use strict;
#use warnings;
use Data::Dumper;
use Getopt::Long;
use List::Util qw(max);
use Parallel::ForkManager;
#########################################################################################
# INITIALIZE VARIABLES (all optional and/or defaulted)
my $codon_file;
my $sliding_window_size;
my $sliding_window_step;
my $num_bootstraps;
#my $procs_per_node;
# Get user input, if given. If a Boolean argument is passed, its value is 1; else undef
GetOptions( "codon_file=s" => \$codon_file,
"sliding_window_size=i" => \$sliding_window_size,
"sliding_window_step=i" => \$sliding_window_step,
"num_bootstraps=i" => \$num_bootstraps)
# "procs_per_node:i" => \$procs_per_node)
or die "\n### WARNING: Error in command line arguments. SNPGenie for OID terminated.\n\n";
# Get the time
my $time1 = time;
my $local_time1 = localtime;
print "\nSNPGenie sliding windows initiated at local time $local_time1\n\n";
unless(-f "$codon_file") {
die "\n### WARNING: An existing --codon_file option must be provided\n".
"### SNPGenie terminated.\n\n";
}
# Test and/or reset OPTIONS given the user's INPUT and RECORD PARAMETERS
if(! $sliding_window_size) {
$sliding_window_size = 10; # default behavior: 10-mer peptide
print "### SLIDING WINDOW WINDOW SIZE NOT GIVEN. DEFAULT USED: 10 CODONS.\n" .
"### (You sure you don't want to specify?)\n\n";
} elsif($sliding_window_size < 1) {
die "\n### WARNING: The --sliding_window_size option must be an integer ≥1\n".
"### SNPGenie for OID terminated.\n\n";
}
if(! $sliding_window_step) {
$sliding_window_step = 1; # default behavior: one codon
print "### SLIDING WINDOW STEP SIZE NOT GIVEN. DEFAULT USED: JUST 1.\n" .
"### (You sure you don't want to specify?)\n\n";
} elsif($sliding_window_step < 1) {
die "\n### WARNING: The --sliding_window_step option must be an integer ≥1\n".
"### SNPGenie for OID terminated.\n\n";
}
if(! $num_bootstraps) {
$num_bootstraps = 0; # DEFAULT is 1000
print "### BOOTSTRAP VALUE NOT GIVEN. DEFAULT IS NO BOOTSTRAPPING.\n" .
"### (You sure you don't want our statistics, boo?)\n\n";
} elsif($num_bootstraps < 2) {
die "\n### WARNING: The --num_bootstraps option must be an integer ≥2\n".
"### SNPGenie for OID terminated.\n\n";
}
#if(! $procs_per_node) {
# $procs_per_node = 1; # DEFAULT is 1
# print "### PROCS PER NODE VALUE NOT GIVEN. DEFAULT USED: JUST 1.\n" .
# "### (You sure you don't want our parallelization, boo?)\n\n";
#} elsif($procs_per_node < 1) {
# die "\n### WARNING: The --procs_per_node option must be an integer ≥1\n".
# "### SNPGenie for OID terminated.\n\n";
#}
#STDOUT->autoflush(1);
#########################################################################################
# Output file name
my $sw_output_file = 'sw_' . $sliding_window_size . 'codons_results.txt';
#########################################################################################
# PROCESS
# my $family_start_time = time;
print "#########################################################################################";
print "\n##### Performing sliding window using file $codon_file\n";
print "#########################################################################################";
print "\n";
# MAKE SURE WE DON'T OVERWRITE
## if(-f "$OID_USER_DIR/data/$family_id/$between_group_sw_output_file") { # don't re-do if done
## print "Family $family_id already completed for this window size. Moving on to next family.\n";
## #next FAMILY; # this doesn't work because a child process apparently cannot be called
## } els
##################################################################################
# READY THE OUTPUT FILE
open(OUTFILE_SW,">$sw_output_file");
#print OUTFILE_SW "file\twindow\tfirst_codon\tlast_codon\t".
# "num_defined_codons_g1\tnum_defined_codons_g2\tmean_num_defined_codons\tmin_num_defined_codons\t".
# "N_sites\tS_sites\t".
# "N_diffs\tS_diffs\t".
# "dN\tdS\t".
# "dN\-dS\t".
# "dN\/dS\tdN\>total_dS";
print OUTFILE_SW "product\twindow\tfirst_codon\tlast_codon\t".
"N_sites\tS_sites\t".
"N_diffs\tS_diffs\t".
"dN\tdS\t";
if($num_bootstraps > 1) {
print OUTFILE_SW "SE_dN\tSE_dS\t";
}
print OUTFILE_SW "dN_minus_dS\t".
"dN_over_dS\tdN_gt_total_dS";
if($num_bootstraps > 1) {
print OUTFILE_SW "\tSE_dN_minus_dS\tZ_value\tsignificance\n";
} else {
print OUTFILE_SW "\n";
}
close OUTFILE_SW;
##################################################################################
# STORE WITHIN-GROUP CODON DATA
# Get header names
my @header_names_arr = &get_header_names($codon_file,$codon_file);
#print "@header_names_arr";
my %header_indices;
# Determine the index of each column
for (my $i=0; $i<scalar(@header_names_arr); $i++) {
my $curr_header = $header_names_arr[$i];
$header_indices{$curr_header} = $i;
}
# Make sure we got all the expected headers
#my @required_headers = qw/analysis family partition group_1 group_2 codon variability num_defined_codons_g1 num_defined_codons_g2 comparisons N_sites S_sites N_diffs S_diffs/;
my @required_headers = qw /product codon variability comparisons N_sites S_sites N_diffs S_diffs/;
foreach(@required_headers) {
unless(exists $header_indices{$_}) {
die "### DIE: the header name $_ is not present in the codon results file.\n\n";
}
}
# STORE ALL PRODUCT CODON DATA
my %product_codon_data_hh;
# STORE overall partition values
my %product_sums;
# my $between_product_N_sites_sum = 0;
#my $product_S_sites_sum = 0;
# my $between_product_N_diffs_sum = 0;
#my $product_S_diffs_sum = 0;
open(IN_CODON_FILE, "$codon_file") or die "\nCould not open the file $codon_file - $!\n\n";
my $line = 0;
while(<IN_CODON_FILE>) { # record
if($line == 0) {
$line++;
} else {
chomp;
my @line_arr = split(/\t/,$_,-1);
# Store data here
my $product = $line_arr[$header_indices{'product'}];
my $codon = $line_arr[$header_indices{'codon'}];
$codon =~ s/codon_//; # in case it's the old format
$codon =~ s/\s//g; # in case it's the old format
$product_codon_data_hh{$product}->{$codon}->{variability} = $line_arr[$header_indices{'variability'}];
# $product_codon_data_hh{$product}->{$codon}->{num_defined_codons_g1} = $line_arr[$header_indices{'num_defined_codons_g1'}];
# $product_codon_data_hh{$product}->{$codon}->{num_defined_codons_g2} = $line_arr[$header_indices{'num_defined_codons_g2'}];
$product_codon_data_hh{$product}->{$codon}->{comparisons} = $line_arr[$header_indices{'comparisons'}];
$product_codon_data_hh{$product}->{$codon}->{N_sites} = $line_arr[$header_indices{'N_sites'}];
$product_codon_data_hh{$product}->{$codon}->{S_sites} = $line_arr[$header_indices{'S_sites'}];
$product_codon_data_hh{$product}->{$codon}->{N_diffs} = $line_arr[$header_indices{'N_diffs'}];
$product_codon_data_hh{$product}->{$codon}->{S_diffs} = $line_arr[$header_indices{'S_diffs'}];
# print "\n\nVariability: " . $product_codon_data_hh{$product}->{$codon}->{variability} . "\n\n";
# print "\n\nN_diffs: " . $product_codon_data_hh{$product}->{$codon}->{N_diffs} . "\n\n";
# print "\nSTORING:\nanalysis: $analysis\nfamily: $family\npartition: $partition\ncodon: $codon\nNsites: ".
# $line_arr[$header_indices{'N_sites'}] . "\n\n";
# Sum partition values here
$product_sums{$product}->{N_sites} += $line_arr[$header_indices{'N_sites'}];
$product_sums{$product}->{S_sites} += $line_arr[$header_indices{'S_sites'}];
$product_sums{$product}->{N_diffs} += $line_arr[$header_indices{'N_diffs'}];
$product_sums{$product}->{S_diffs} += $line_arr[$header_indices{'S_diffs'}];
}
}
close IN_CODON_FILE;
#my $product_dS;
#if($product_S_sites_sum > 0) {
# $product_dS = $product_S_diffs_sum / $product_S_sites_sum;
#} else {
# $product_dS = '*';
#}
##################################################################################
# LOOP THROUGH EACH ANALYSIS, FAMILY, AND PARTITION FOR SLIDING WINDOW ANALYSIS
PRODUCT: foreach my $this_product (sort {$a <=> $b} keys %product_codon_data_hh) {
my $product_dS = '*';
if($product_sums{$this_product}->{S_sites} > 0) {
$product_dS = $product_sums{$this_product}->{S_diffs} / $product_sums{$this_product}->{S_sites};
}
# print "\nTEST RETRIEVAL:\nanalysis: $this_analysis\nfamily: $this_family\npartition: $this_product\n\n";
#############################################################
# SLIDING WINDOW WITH BOOTSTRAPS
# Generate and store sliding window and bootstrap analyses
my %sliding_window_results_hh; # Will store first_codon->N_diffs_window/S_diffs_window/...
# my $sw_file_name = "partition$partition_id\_sw_" . $sliding_window_size . "codons\_results.txt";
#
# if (-e "$sw_file_name") {
# die "\n\n### WARNING:\n## The file $sw_file_name already exists.\n## Please ".
# "rename or move this file so a new one ".
# "can be created.\n\n";
# }
my @codons = keys (%{$product_codon_data_hh{$this_product}});
my @sorted_codons = sort {$a <=> $b} (@codons);
my $num_sorted_codons = scalar @sorted_codons;
# print "\n\ncodons: @sorted_codons\n\n";
if($sliding_window_size > $num_sorted_codons) {
warn "\n\n### WARNING:\n## For partition $this_product\,\n## there are ".
"not enough codons to perform a sliding window of $sliding_window_size.".
"\n### Product skipped.\n\n";
next PRODUCT;
}
# FOR EACH WINDOW
my $window_num = 0;
my $first_print = 0;
# print "\nProcessing sliding windows...\n";
# CODON_INDEX must begin one before the smallest actual codon number... don't assume it's 1
for (my $codon_index = 0; $codon_index <= ($num_sorted_codons - $sliding_window_size); $codon_index += $sliding_window_step) {
$window_num++;
my $first_codon = $codon_index + $sorted_codons[0];
my $last_codon = $first_codon + $sliding_window_size - 1;
# print "#### PROCESSING WINDOW $window_num\, codons $first_codon\-$last_codon\... \n";
if ($last_codon <= ($num_sorted_codons + $sorted_codons[0])) { # as long as we're in range
my $window_N_diffs;
my $window_S_diffs;
my $window_N_sites;
my $window_S_sites;
for (my $i = $first_codon; $i <= $last_codon; $i++) {
# print "\n\nTo codon $i, we add: " . $product_codon_data_hh{$this_product}->{$i}->{N_diffs} . "\n\n";
# print "\nTEST RETRIEVAL:\nanalysis: $this_analysis\nfamily: $this_family\npartition: $this_product\n\n";
$window_N_diffs += $product_codon_data_hh{$this_product}->{$i}->{N_diffs};
$window_S_diffs += $product_codon_data_hh{$this_product}->{$i}->{S_diffs};
$window_N_sites += $product_codon_data_hh{$this_product}->{$i}->{N_sites};
$window_S_sites += $product_codon_data_hh{$this_product}->{$i}->{S_sites};
}
my $window_dN;
if ($window_N_sites > 0) {
$window_dN = ($window_N_diffs / $window_N_sites);
} else {
$window_dN = '*';
}
my $window_dS;
if ($window_S_sites > 0) {
$window_dS = ($window_S_diffs / $window_S_sites);
} else {
$window_dS = '*';
}
my $window_w;
if ($window_dS > 0 && $window_dS ne '*') {
$window_w = ($window_dN / $window_dS);
} else {
$window_w = '*';
}
my $window_dN_minus_dS;
if($window_dN >= 0 && $window_dS >= 0) {
$window_dN_minus_dS = $window_dN - $window_dS;
}
# print "\n\n";
#################################################################################
# BOOTSTRAP the WINDOW
my $SE_dN_minus_dS = 0;
my $window_boot_Z = 'NA';
my $SE_dN;
my $SE_dS;
if($num_bootstraps > 1) {
# MAKE BOOTSTRAP FILE
#print "num_codons_in_product: $num_codons_in_product\n";
my @sim_N_sites_arr;
my @sim_S_sites_arr;
my @sim_N_diffs_arr;
my @sim_S_diffs_arr;
for(my $bootstrap_num = 1; $bootstrap_num <= $num_bootstraps; $bootstrap_num++) {
srand();
# New bootstrap run, of $num_bootstraps
#if($this_family == 460) {
# print "\nPartition $this_product \| BOOTSTRAP REPLICATE $bootstrap_num\n";
#}
my $sim_N_sites_sum = 0;
my $sim_S_sites_sum = 0;
my $sim_N_diffs_sum = 0;
my $sim_S_diffs_sum = 0;
# METHOD
# (1) loop through $num_codons_in_product
# (2) for each, select a random codon position's results: Nd, Sd, Ns, Ss.
# where are the aforementioned stored? As before:
# $product_codon_data_hh{$this_product}->{$codon_num}->{N_diffs}, etc.
# SAMPLE codon sites, up to the actual number of codons in window
for(my $window_codon_index = 0; $window_codon_index < $sliding_window_size; $window_codon_index++) {
# Choose a random codon between this window $first_codon and $last_codon
my $random_codon_num = int(rand($last_codon - $first_codon + 1)) + $first_codon;
my $sampled_N_diffs = $product_codon_data_hh{$this_product}->{$random_codon_num}->{N_diffs};
my $sampled_S_diffs = $product_codon_data_hh{$this_product}->{$random_codon_num}->{S_diffs};
my $sampled_N_sites = $product_codon_data_hh{$this_product}->{$random_codon_num}->{N_sites};
my $sampled_S_sites = $product_codon_data_hh{$this_product}->{$random_codon_num}->{S_sites};
$sim_N_diffs_sum += $sampled_N_diffs;
$sim_S_diffs_sum += $sampled_S_diffs;
$sim_N_sites_sum += $sampled_N_sites;
$sim_S_sites_sum += $sampled_S_sites;
} # finished compiling all sampled codons (cols in alignment)
push(@sim_N_diffs_arr,$sim_N_diffs_sum);
push(@sim_S_diffs_arr,$sim_S_diffs_sum);
push(@sim_N_sites_arr,$sim_N_sites_sum);
push(@sim_S_sites_arr,$sim_S_sites_sum);
#print $random_sum . "\n";
} # end last bootstrap
# Recall we have $window_dN_minus_dS above
# CALCULATE BOOTSTRAP STANDARD ERROR HERE; NEI & KUMAR (2000) METHOD
my @sim_dN_minus_dS;
my @sim_dN;
my @sim_dS;
for(my $sim_num = 0; $sim_num < scalar(@sim_N_sites_arr); $sim_num++) {
my $this_round_dN = '*';
if($sim_N_sites_arr[$sim_num] > 0) {
$this_round_dN = $sim_N_diffs_arr[$sim_num] / $sim_N_sites_arr[$sim_num];
}
my $this_round_dS = '*';
if($sim_S_sites_arr[$sim_num] > 0) {
$this_round_dS = $sim_S_diffs_arr[$sim_num] / $sim_S_sites_arr[$sim_num];
}
my $this_round_dN_minus_dS = '*';
if($this_round_dN >= 0 && $this_round_dS >= 0) {
$this_round_dN_minus_dS = $this_round_dN - $this_round_dS;
}
push(@sim_dN_minus_dS,$this_round_dN_minus_dS);
push(@sim_dN, $this_round_dN);
push(@sim_dS, $this_round_dS);
}
$SE_dN_minus_dS = &standard_deviation(@sim_dN_minus_dS);
$SE_dN = &standard_deviation(@sim_dN);
$SE_dS = &standard_deviation(@sim_dS);
if($SE_dN_minus_dS > 0) {
$window_boot_Z = $window_dN_minus_dS / $SE_dN_minus_dS;
}
} # END BOOTSTRAPS for WINDOW
my $partition_between_group_dS = '*';
if($product_sums{$this_product}->{S_sites} > 0) {
$partition_between_group_dS = $product_sums{$this_product}->{S_diffs} /
$product_sums{$this_product}->{S_sites};
}
my $window_dN_exceeds_product_dS = '';
if($window_dN > $product_dS) {
$window_dN_exceeds_product_dS = '*';
}
# my $min_defined_codons_in_window = 1000; # or something big
# my $window_num_defined_codons_g1 = 0;
# for(my $j = $first_codon; $j <= $last_codon; $j++) {
# $window_num_defined_codons_g1 += $product_codon_data_hh{$this_product}->{$j}->{'num_defined_codons_g1'};
#
# if($product_codon_data_hh{$this_product}->{$j}->{'num_defined_codons_g1'} < $min_defined_codons_in_window) {
# $min_defined_codons_in_window = $product_codon_data_hh{$this_product}->{$j}->{'num_defined_codons_g1'};
# }
# }
# my $window_num_defined_codons_g2 = 0;
# for(my $j = $first_codon; $j <= $last_codon; $j++) {
# $window_num_defined_codons_g2 += $product_codon_data_hh{$this_product}->{$j}->{'num_defined_codons_g2'};
#
# if($product_codon_data_hh{$this_product}->{$j}->{'num_defined_codons_g2'} < $min_defined_codons_in_window) {
# $min_defined_codons_in_window = $product_codon_data_hh{$this_product}->{$j}->{'num_defined_codons_g2'};
# }
# }
# if($min_defined_codons_in_window==0 || $min_defined_codons_in_window eq '' || ! defined($min_defined_codons_in_window)) {
# $min_defined_codons_in_window = 0;
# }
# my $window_mean_num_defined_codons = ($window_num_defined_codons_g1 + $window_num_defined_codons_g2)/2;
# my $out_line_sw = "$this_analysis\t$this_family\t$this_product\t$group_name_i\t$group_name_j\t".
# "$window_num\t$first_codon\t$last_codon\t" .
# "$window_num_defined_codons_g1\t$window_num_defined_codons_g2\t$window_mean_num_defined_codons\t$min_defined_codons_in_window\t".
# "$window_N_sites\t$window_S_sites\t$window_N_diffs\t$window_S_diffs\t".
# "$window_dN\t$window_dS\t$window_dN_minus_dS\t$window_w\t$window_dN_exceeds_product_dS";
my $out_line_sw = "$this_product\t".
"$window_num\t$first_codon\t$last_codon\t" .
"$window_N_sites\t$window_S_sites\t$window_N_diffs\t$window_S_diffs\t".
"$window_dN\t$window_dS\t";
if($num_bootstraps > 1) {
$out_line_sw .= "$SE_dN\t$SE_dS\t";
}
$out_line_sw .= "$window_dN_minus_dS\t$window_w\t$window_dN_exceeds_product_dS";
if($num_bootstraps > 1) {
my $significance = '';
if($SE_dN_minus_dS > 0) {
if(abs($window_boot_Z) > 2.81) {
$significance = '***';
} elsif(abs($window_boot_Z) > 1.96) {
$significance = '**';
} elsif(abs($window_boot_Z) > 1.64) {
$significance = '*';
}
}
$out_line_sw .= "\t$SE_dN_minus_dS\t$window_boot_Z\t$significance\n"; #####
} else {
$out_line_sw .= "\n";
}
open(OUTFILE_SW,">>$sw_output_file");
print OUTFILE_SW "$out_line_sw";
close OUTFILE_SW;
}
}
} # done looping products
print "\n\n";
#########################################################################################
# END PROGRAM and print a completion message to screen
&end_the_program;
exit;
#########################################################################################
#########################################################################################
#################################### ####################################
#################################### SUBROUTINES ####################################
#################################### ####################################
#########################################################################################
#########################################################################################
#########################################################################################
sub mean {
my @values = @_;
my $length = @values;
my $sum;
foreach (@values) {
$sum += $_;
}
return($sum / $length);
}
#########################################################################################
sub standard_deviation {
my @values = @_;
my $length = @values;
my $mean_of_values = &mean(@values);
my $sum_squared_deviations;
foreach (@values) {
$sum_squared_deviations += ($_ - $mean_of_values)**2;
}
my $variance = ($sum_squared_deviations) / ($length - 1);
return(sqrt($variance));
}
#########################################################################################
sub get_header_names {
# Originally assumed that we've received a tempfile ending in "_snpg9temp.txt"
# However, we're now calling it at least once before creating the tempfile to
# see what kind of processing (e.g., Geneious to CLC) is needed prior to tempfile
# creation. Must include capability to get headers for .CSV file
my ($curr_snp_report_filename,$filename) = @_;
#print "\n$curr_snp_report_filename\n";
#my $newline_char = &detect_newline_char($curr_snp_report_filename);
#my $old_newline = $/;
#$/ = $newline_char;
my $seen_tab_delimited = 0;
my $seen_comma_delimited = 0;
my $seen_vcf_tab_delimited = 0;
my @line_arr;
my $line = 0;
open (CURRINFILE, $curr_snp_report_filename);
#seek(CURRINFILE,0,0);
while (<CURRINFILE>) {
#print "$_";
if($line == 0) {
chomp;
# CHOMP for 3 operating systems
if($_ =~ /\r\n$/) {
$_ =~ s/\r\n//;
} elsif($_ =~ /\r$/) {
$_ =~ s/\r//;
} elsif($_ =~ /\n$/) {
$_ =~ s/\n//;
}
if($_ =~/\t\w+\t/) { # it's TAB-delimited
@line_arr = split(/\t/,$_);
#print "TAB!!!!!";
last;
} elsif($_ =~/,\w+,/) { # it's COMMA-delimited
@line_arr = split(/,/,$_);
#print "COMMA!!!!!";
last;
}
$line++;
} elsif($line > 0 && $_ =~ /^##/) {
$line++;
} elsif($line > 0 && ($_ =~ /^#CHROM/)) {
chomp;
# CHOMP for 3 operating systems
if($_ =~ /\r\n$/) {
$_ =~ s/\r\n//;
} elsif($_ =~ /\r$/) {
$_ =~ s/\r//;
} elsif($_ =~ /\n$/) {
$_ =~ s/\n//;
}
if($_ =~/\t/) { # it's TAB-delimited
@line_arr = split(/\t/,$_);
#print "TAB!!!!!";
last;
} elsif($_ =~/,/) { # it's COMMA-delimited
@line_arr = split(/,/,$_);
#print "COMMA!!!!!";
last;
} else {
chdir('SNPGenie_Results');
open(ERROR_FILE,">>SNPGenie\_LOG\.txt");
# FILE | PRODUCT | SITE | CODON | WARNING
# No change OR error should occur if the file does not, in fact, end
# with this SUFFIX
my $file_nm = $curr_snp_report_filename;
#$file_nm =~ s/_snpg9temp.txt/.txt/;
$file_nm =~ s/_\w\w\w\w.txt/.txt/;
print ERROR_FILE "$filename\tN/A\tN/A\t".
"File not TAB(\\t)- or COMMA-delimited, or there is only one column. SNPGenie terminated.\n";
close ERROR_FILE;
chdir('..');
#unlink $curr_snp_report_filename;
die "\n\n## WARNING: The SNP Report $filename is ".
"not TAB(\\t)- or COMMA-delimited, or there is only one column. SNPgenie ".
"terminated\n\n";
}
} else {
chdir('SNPGenie_Results');
open(ERROR_FILE,">>SNPGenie\_LOG\.txt");
# FILE | PRODUCT | SITE | CODON | WARNING
# No change OR error should occur if the file does not, in fact, end
# with this SUFFIX
my $file_nm = $curr_snp_report_filename;
#$file_nm =~ s/_snpg9temp.txt/.txt/;
$file_nm =~ s/_\w\w\w\w.txt/.txt/;
print ERROR_FILE "$filename\tN/A\tN/A\t".
"File not TAB(\\t)- or COMMA-delimited, or there is only one column. SNPGenie terminated.\n";
close ERROR_FILE;
chdir('..');
#unlink $curr_snp_report_filename;
die "\n\n## WARNING: The SNP Report $filename is ".
"not TAB(\\t)- or COMMA-delimited, or there is only one column. SNPgenie ".
"terminated\n\n";
}
}
seek(CURRINFILE,0,0);
close CURRINFILE;
#$/ = $old_newline;
return @line_arr;
}
#########################################################################################
# End the program by notifying the screen at command line
sub end_the_program {
my $time2 = time;
my $local_time2 = localtime;
my $time_diff = ($time2 - $time1);
my $time_diff_rounded = sprintf("%.2f",$time_diff);
my $mins_elapsed = ($time_diff / 60);
my $whole_mins_elapsed = int($mins_elapsed);
my $whole_mins_in_secs = ($whole_mins_elapsed * 60);
my $secs_remaining = ($time_diff - $whole_mins_in_secs);
my $secs_remaining_rounded = sprintf("%.2f",$secs_remaining);
print "SNPGenie completed at local time $local_time2. The process took $time_diff_rounded secs, i.e., ".
"$whole_mins_elapsed mins and $secs_remaining_rounded secs\n";
print "\n################################################################################".
"\n## SNPGenie sliding window completed successfully. ##".
"\n## Please find results in the working directory in $sw_output_file ##\n".
"################################################################################".
"\n\n\n";
}