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#!/usr/bin/perl
use lib '/usr/lib/sift/bin';
# This program is licensed to you under the Fred
# Hutchinos Cancer Research Center (FHCRC)
# NONCOMMERICAL LICENSE. A copy of the license may be found at
# http://blocks.fhcrc.org/sift/license.html and should be attached
# to this software
#
# October 11, 2009 created as a script option to SIFT indels
#-------------------------------------------------------------------------
use DBI;
use Tie::IxHash;
use File::Copy;
use Getopt::Std;
$ENV{'SIFT_HOME'} = '/usr/lib/sift';
$SIFT_HOME = $ENV{'SIFT_HOME'};
use vars qw($opt_i $opt_c $opt_d $opt_o);
getopts("i:c:d:o:");
my $usage = "usage:
$0
-i <Query indels filename with complete path>
-c <coding info directory path>
-d <Variation db directory path>
-o <Optional: output file with complete path - default=$SIFT_HOME/tmp>
All values should be in local 0 space based coordinates.
";
$| = 1;
if(!(
defined($opt_i) &&
defined($opt_d) &&
defined($opt_c))){
print STDERR $usage;
die;
}
# Set file permissions to rw-rw----
system("umask 006");
my $bin = "$SIFT_HOME/bin";
my $pid = $$;
my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
require "$bin/SIFT_subroutines.pm";
mkdir $tmp;
chmod 0777, $tmp;
my $coding_info_dir = "$opt_c";
my $Variation_db_dir = "$opt_d";
$snp_classifier = "$bin/Classify_SNPs_Indels.pl";
$reformat_chrfile = "$bin/reformat_chrfile.pl";
$detect_indel = "$bin/detect_indel.pl";
$model_transcript = "$bin/model_transcript.pl";
$small_indels_error_intersect_file = "$tmp/$pid.small_indels_error_intersect.gff";
$small_indels_error_gff = "$SIFT_HOME/db/small_indel_errors_ref.gff";
$repeat_db_file = "$SIFT_HOME/db/repeat_db.gff";
$indelfile_to_gff = "$bin/indelfile_to_gff.pl";
$intersect_locations = "$bin/IntersectLocations.sh";
$detect_repeat = "$bin/detect_repeat.pl";
#get user output options
$all_transcripts = 1;
my $output_options = "";
$chr_file = $opt_i;
## Check for validity of user inputs
my $all_chr_file = $tmp . "/$pid.chrfile";
copy($chr_file, $all_chr_file) or die "File cannot be copied.";
$bin_file = "$coding_info_dir/bins.list";
chmod 0777, $all_chr_file;
#check input validity and reformat chrfile
system("perl $reformat_chrfile $all_chr_file $tmp");
#display wait message
print
"Your job id is $pid and is currently running.\n";
#convert chrfile to gff for intersecting with small indel errors file.
system("perl $indelfile_to_gff $all_chr_file");
$all_chr_gff_file = "$all_chr_file.gff";
#Now intersect gff chrfile with small indels ref file
system("$intersect_locations $all_chr_gff_file gff $small_indels_error_gff gff simple > $small_indels_error_intersect_file");
#create an index %user_small_indels_error_index with key as "chr#startindex" stop index redundant also problem with Intersect script not detecting intersect when start = stop i.e. insertion.
my %user_small_indels_error_index;
if (-e $small_indels_error_intersect_file){
open (SMALL_INDELS,"$small_indels_error_intersect_file");
while (<SMALL_INDELS>){
next if ($_ =~ /^\d+|^Total/i);
chomp;
my @elts = split /\t/, $_;
my $chr = $elts[1];
my $start = $elts[2];
my $key = "$chr\t$start";
$user_small_indels_error_index{"$key"} = 1;
}
}
#Creat binned SNP files for SNP Classifier
system("$bin/map_coords_to_bin_indels.pl $bin_file $all_chr_file $pid $tmp");
#create index of old coords to new coords using pid_old_new_coords_map.txt
open( COORDS_MAP, "$tmp/$pid\_old_new_coords_map.txt" )
|| die("Cannot open old-new coords map file");
while (<COORDS_MAP>) {
chomp;
@elts = split /\t/, $_;
$old_coords = @elts[0];
$new_coords = @elts[1];
@elts2 = split /,/, $new_coords;
$chr = $elts2[0];
$new_start = @elts2[1];
$new_stop = @elts2[2];
$key = "$chr\t$new_start\t$new_stop";
#print "$key *** $old_coords<br>";
$index_old_new_coords{$key} = $old_coords;
}
#Run snp classifier on files in snp_chr_map_file
open( SNP_CHR_MAP_FILE, "$tmp/$pid\_snp_chr_map_file.txt" )
|| die("Cannot open SNP_CHR_MAP_FILE");
while (<SNP_CHR_MAP_FILE>) {
chomp;
@cols = split /\t/, $_;
$chromosome = @cols[0];
$bucket = @cols[1];
$snp_file = "$tmp/@cols[2]";
$coding_info_file = "$coding_info_dir/@cols[3]";
$chr_fasta_file = "$coding_info_dir/@cols[4]";
#print "$snp_classifier -s $snp_file -c $coding_info_file -n $chr_fasta_file -o $tmp/$pid\_snps_classified_chr$chromosome\_bin$bucket<br>";
system(
"$snp_classifier -s $snp_file -c $coding_info_file -n $chr_fasta_file -o $tmp/$pid\_snps_classified_chr$chromosome\_bin$bucket"
);
}
close(SNP_CHR_MAP_FILE);
#Parse denormal files to extract coding info for input coords
open( SNP_CHR_MAP_FILE, "$tmp/$pid\_snp_chr_map_file.txt" )
|| die("Cannot open SNP_CHR_MAP_FILE");
my %coord_result_hash;
my $en_trancript_id_string;
while (<SNP_CHR_MAP_FILE>) {
chomp;
@cols = split /\t/, $_;
$chromosome = @cols[0];
$bucket = @cols[1];
$snp_file = "$tmp/@cols[2]";
$coding_info_file = "$coding_info_dir/chr$chromosome/@cols[3]";
$chr_fasta_file = "$coding_info_dir/chr$chromosome/@cols[4]";
$denormal_file =
"$tmp/$pid\_snps_classified_chr$chromosome\_bin$bucket.denormal";
$normal_file =
"$tmp/$pid\_snps_classified_chr$chromosome\_bin$bucket.normal";
open( DENORMAL, $denormal_file ) || die "(denormal file does not exist)";
while (<DENORMAL>) {
@elts = split /\t/, $_;
$coord = @elts[1];
@coord_elts = split /\:/, $coord;
$allele = $coord_elts[scalar @coord_elts - 1];
$coord = join( ',', @coord_elts );
@coord_elts2 = split( '-', $coord, 2 );
$coord = join( ',', @coord_elts2 );
@elts2 = split /,/, $coord;
$new_start = @elts2[0];
$new_stop = @elts2[1];
$key = "$chromosome\t$new_start\t$new_stop";
$old_coord= $index_old_new_coords{$key};
$coord = $old_coord;
$nu_change = $elts[2];
if ($nu_change =~ /([ATGC]+) ([ATGC]+) ([ATGC]+)/){
$left_flank = uc substr ($1,-5,5);
$deletion = lc $2;
$right_flank = uc substr($3,0,5);
$nu_change_modified = "$left_flank-$deletion-$right_flank";
}
elsif($nu_change =~ /([ATGC]+) - ([ATGC]+)/){
$left_flank = lc substr ($1,-5,5);
$insertion = uc $allele;
$right_flank = lc substr($2,0,5);
$nu_change_modified = "$left_flank-$insertion-$right_flank";
}
$nu_change = $nu_change_modified;
if ( $_ =~ /AA_DELETION | AA_INSERTION | FRAMESHIFT/x ) {
$subst = $&;
$region = "CDS";
if ( $_ =~ /^(\d+).+?ENSG(\d+).+?ENST(\d+).+/) {
$hit_id = $1;
$en_transcript_id = "ENST$3";
$ensg = "ENSG$2";
$result = "$hit_id\t$ensg\t$en_transcript_id\t$subst\t$region";
#append seq (original and modified) to result
$original_seq = "$tmp/$pid\_$en_transcript_id.fa";
$modified_seq = "$tmp/$pid\_$en_transcript_id\_$hit_id.fa";
if (-e $modified_seq && -e $original_seq){
$result.="\t$original_seq\t$modified_seq\t$nu_change";
}
push @{ $coord_result_hash{$coord} }, $result; #hash of arrays: multiple ENSTs per coord
}
}
elsif ( $_ =~ /INTRON|PROMOTOR|DOWNSTREAM|UPSTREAM/ix ) {
$subst = "";
$region = "$&";
if ( $_ =~ /^(\d+).+?ENSG(\d+).+?ENST(\d+).+/) {
$hit_id = $1;
$en_transcript_id = "ENST$3";
$ensg = "ENSG$2";
$result = "$hit_id\t$ensg\t$en_transcript_id\t$subst\t$region\t\t\t$nu_change";
#append seq (original and modified) to result
push @{ $coord_result_hash{$coord} }, $result; #hash of arrays: multiple ENSTs per coord
}
}
elsif ( $_ =~ /CDS/i ) {
$subst = "";
$region = "CDS";
if ( $_ =~ /^(\d+).+?ENSG(\d+).+?ENST(\d+).+/) {
$hit_id = $1;
$en_transcript_id = "ENST$3";
$ensg = "ENSG$2";
$result = "$hit_id\t$ensg\t$en_transcript_id\t$subst\t$region\t\t\t$nu_change";
#append seq (original and modified) to result
push @{ $coord_result_hash{$coord} }, $result; #hash of arrays: multiple ENSTs per coord
}
}
}
close (DENORMAL);
unlink ("$denormal_file");
unlink ("$normal_file");
}
#create original - modified protein files
my $repeat_detect_input_file = "$tmp/$pid\_repeat_detect_input_file.txt";
open (REPEAT_INPUT,">$repeat_detect_input_file");
foreach $coord (keys %coord_result_hash){
my @elts;
my $repeat_input_row = "";
my @indel_result;
my @indel_location_features;
my $chr = (split /,/, $coord)[0];
my $indel_start = (split /,/, $coord)[1];
my $indel_stop = (split /,/, $coord)[2];
@result_set = @{ $coord_result_hash{$coord} };
foreach $result (@result_set){
chomp $result;
@elts = split /\t/,$result;
my $hit_id = $elts[0];
my $ensg = $elts[1];
my $enst = $elts[2];
my $subst = $elts[3];
my $region = $elts[4];
my $original_seq = $elts[5];
my $modified_seq = $elts[6];
@indel_location_features = split /\t/, `$model_transcript $enst $indel_start $indel_stop $Variation_db_dir`;
$indel_start_CDS = $indel_location_features[0];
$indel_stop_CDS = $indel_location_features[1];
$indel_loc_pct = $indel_location_features[2];
$indel_span = $indel_location_features[3];
$num_5UTR = $indel_location_features[4];
$num_exon = $indel_location_features[5];
$num_intron = $indel_location_features[6];
$num_3UTR = $indel_location_features[7];
$tx_length = $indel_location_features[8];
$CDS_length = $indel_location_features[9];
$protein_length = $indel_location_features[10];
$last_exon_length = $indel_location_features[11];
$visual_tx = $indel_location_features[12];
$NMD_protein_region = int(($last_exon_length + 50)/3);
$result.="\t$indel_start_CDS\t$indel_stop_CDS\t$indel_loc_pct\t$indel_span\t$visual_tx";
#print "$last_exon_length $NMD_protein_region $original_length $modified_length<br>";
my $outfile = "";
if (-e $original_seq && -e $modified_seq){
$outfile = "$tmp/$pid\_$enst\_$hit_id\_comparison.fasta";
@indel_result = split /\t/, `$detect_indel $original_seq $modified_seq $outfile`;
$aa_coords_original = $indel_result[0];
$aa_coords_modified = $indel_result[1];
$aa_change_original = $indel_result[2];
$aa_change_modified = $indel_result[3];
$original_length = $indel_result[4];
$modified_length = $indel_result[5];
if ($num_exon < 2) {
$causes_NMD = "N\/A";
}
elsif ($original_length - $modified_length > $NMD_protein_region){
$causes_NMD = "YES";
}
else{
$causes_NMD = "NO";
}
chomp $aa_coords_original,$aa_coords_modified,$aa_change_original,$aa_change_modified;
#print "@indel_result<br>";
$result.="\t$aa_coords_original\t$aa_change_original->$aa_change_modified\t$causes_NMD";
$repeat_input_row = "$chr\t$enst\t$indel_start\t$indel_stop\t".join ("\t", split(/\-/,$aa_coords_original) )."\t$original_seq\t$modified_seq";
print REPEAT_INPUT "$repeat_input_row\n";
}
}
$coord_result_hash{$coord} = [ @result_set ];
}
close (REPEAT_INPUT);
#Run the detect_repeat script on the repeat_input file created in previous loop
my $repeat_detect_output_file = "$tmp/$pid\_repeat_detect_output_file.txt";
system("$detect_repeat $repeat_detect_input_file $repeat_db_file > $repeat_detect_output_file");
my %repeat_index;
if (-e $repeat_detect_output_file){
open (REPEAT_OUTPUT,"$repeat_detect_output_file");
while (<REPEAT_OUTPUT>){
chomp;
my @elts = split /\t/, $_;
my $chr = $elts[0];
my $indel_start = $elts[2];
if ($elts[10] ne "" && $elts[11] ne ""){
my $repeat_change = $elts[10]."-->".$elts[11];
$repeat_index{"$chr\t$indel_start"} = $repeat_change;
}
}
}
## SIFT prediction operations
$exp_option = 1;
#$info = $names{info};
$comments = "$tmp/$pid.comments";
$out = $tmp . "/$$.siftresults";
#build combined classification (no predictions yet for indels) file from %coord_result_hash, hash of arrays. Also get gene infor from Human_supp db
$db_supp = DBI->connect( "dbi:SQLite:dbname=$Variation_db_dir/Human_Supp.sqlite","", "", { RaiseError => 1, AutoCommit => 1 } );
$db_supp->do('PRAGMA synchronous=1');
$sth_db_supp_geneinfo = $db_supp->prepare("select * from GENE_INFO where ENST = ?");
$combined_siftresults_file = "$pid.combined_siftresults";
open (CLASSIFICATION_FILE,">$tmp/$pid.classification_file");
foreach $coord (keys %coord_result_hash) {
my @coord_elts = split /,/, $coord;
#warning if user coordinates intersect with small indel errors
my $chr = $coord_elts[0];
my $coord_start = $coord_elts[1];
my $key_for_small_indels = "$chr\t$coord_start";
if ($user_small_indels_error_index{$key_for_small_indels} == 1){
$small_indel_warning = "Warning: NCBI reference miscall!";
}
else{
$small_indel_warning = "";
}
my $repeat_change = $repeat_index{$key_for_small_indels};
#Populate CLASSIFICATION_FILE with results obtained (multiple results per coord for multiple ENSTs hit)
@result_set = @{ $coord_result_hash{$coord} };
foreach $result (@result_set){
chomp $result;
@elts = split /\t/, $result;
$comparison_file = "";
$hit_id = @elts[0];
$ensg = @elts[1];
$enst = @elts[2];
$subst = @elts[3];
$region = @elts[4];
$original_seq = @elts[5];
$modified_seq = @elts[6];
$nu_change = $elts[7];
$indel_start_CDS = $elts[8];
$indel_stop_CDS = $elts[9];
$indel_loc_pct = $elts[10];
$indel_span = $elts[11];
$visual_tx = $elts[12];
$coords_change = $elts[13];
$aa_change = $elts[14];
$causes_NMD = $elts[15];
$sth_db_supp_geneinfo->execute($enst);
@rows1 = $sth_db_supp_geneinfo->fetchrow_array();
$gene_name = $rows1[3];
$gene_desc = $rows1[4];
$ensfm = $rows1[5];
$fam_desc = $rows1[6];
$gene_status = $rows1[7];
$fam_size = $rows1[8];
$kaks_mouse = $rows1[9];
$kaks_macaque = $rows1[10];
$mim_status = $rows1[11];
unless($original_seq eq ""){
$comparison_file = "$tmp\/$pid\_$enst\_$hit_id\_comparison.fasta";
}
print CLASSIFICATION_FILE "$coord\t$hit_id\t$ensg\t$enst\t$subst\t$coords_change\t$nu_change\t$aa_change\t$region\t$comparison_file\t$indel_span\t$indel_loc_pct\t$visual_tx\t$causes_NMD\t$small_indel_warning\t$repeat_change\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\n";
unlink ("$original_seq");
unlink ("$modified_seq");
}
}
close(CLASSIFICATION_FILE);
#create condensed Classification file (with only one transcript) in case user selects that option.
open( CLASSIFICATION_FILE, "$tmp/$pid.classification_file" )
|| die("Cannot open classification file");
open (CONDENSED_CLASSIFICATION_FILE, ">$tmp/$pid.condensed_classification_file");
my %seen_index;
while (<CLASSIFICATION_FILE>){
chomp;
my @elts = split /\t/, $_;
my $coords = $elts[0];
my $num_elts = num_elts_in_row($_);
if ($seen_index{$coords} ne ""){
my $prev_row = $seen_index{$coords};
my $prev_num_elts = num_elts_in_row($prev_row);
if ($num_elts > $prev_num_elts){
$seen_index{$coords} = $_;
}
}
else{
$seen_index{$coords} = $_;
}
}
foreach my $key (keys %seen_index){
print CONDENSED_CLASSIFICATION_FILE $seen_index{$key},"\n";
}
close (CONDENSED_CLASSIFICATION_FILE);
close (CLASSIFICATION_FILE);
#read from combined file and print table
if ($all_transcripts eq "1"){
open( CLASSIFICATION_FILE, "$tmp/$pid.condensed_classification_file" )|| die("Cannot open classification file");
}
else{
open( CLASSIFICATION_FILE, "$tmp/$pid.classification_file" )|| die("Cannot open classification file");
}
$heading_tsv = get_output_heading_tsv($output_options);
$heading_html = get_output_heading_html($output_options);
open( OUTFILETABLE, ">$tmp/$pid\_predictions.html" );
open( OUTFILETSV, ">$tmp/$pid\_predictions.tsv" );
print OUTFILETSV "$heading_tsv\n";
print OUTFILETABLE '<table border="1" cellspacing="0" cellpadding="4">';
print OUTFILETABLE '<thead>';
print OUTFILETABLE '<tr><th>';
$heading_html =~ s?\t?</th><th>?g;
print OUTFILETABLE "$heading_html</th></tr>\n";
my $warningflag = 0;
while (<CLASSIFICATION_FILE>) {
chomp;
@elts = split /\t/, $_;
$coord = @elts [0];
$hit_id = @elts[1];
$ensg = @elts[2];
$enst = @elts[3];
$subst = @elts[4];
$coords_change = @elts[5];
$nu_change = $elts[6];
$aa_change = @elts[7];
$region = @elts[8];
$comparison_file = @elts[9];
$indel_span = $elts[10];
$indel_loc_pct = $elts[11];
$visual_tx = $elts[12];
$causes_NMD = $elts[13];
$small_indel_warning = $elts[14];
$repeat_change = $elts[15];
$table_row_html = get_output_row_html($output_options,$_);
$table_row_tsv = get_output_row_tsv($output_options,$_);
print OUTFILETSV "$table_row_tsv\n";
print OUTFILETABLE "<tr>\n";
my @fields = split( '\t', $table_row_html );
for $cell (@fields) {
#if small indel error detected, sho warning in coords column
if ($cell =~ /\d+,\d+/){
$cell.="<br><a href=\"\/www\/chr_coords_example_indels.html#miscall\" target=\"_blank\"><font color=red>$small_indel_warning<\/font><\/a>";
print OUTFILETABLE "<td>$cell</td>";
}
#link to original and modfied sequences file
elsif ($cell =~ /comparison/i){
print OUTFILETABLE "<td><a href=\"/sift-bin/catfile.csh?$cell+Alignment+PRE\" target=_blank> $enst change</td>";
}
#color indels red
elsif ($cell =~ /([a-z]|[A-Z])+\*?->([a-z]|[A-Z])+\*?/){
$cell =~ s/[a-z]+/<font color=red>$&<\/font>/g;
print OUTFILETABLE "<td>$cell</td>";
}
#hover text for visual transcript
elsif($cell =~ /\%/ || $cell =~ /\(\d+-\d+\)-\(\d+-\d+\)/ || $cell =~ /CDS|INTRON/){
$hover_cell = "<a title=\'$visual_tx\' class=body_con>$cell</a>";
print OUTFILETABLE "<td>$hover_cell</td>";
}
#color indel(nucleotide) red
elsif ($cell =~ /[atgc]+-[ATGC]+-[atgc]+/){
$cell =~ s/[ATGC]+/<font color=red>$&<\/font>/g;
print OUTFILETABLE "<td>$cell</td>";
}
elsif ($cell =~ /[ATGC]+-[atgc]+-[ATGC]+/){
$cell =~ s/[atgc]+/<font color=red>$&<\/font>/g;
print OUTFILETABLE "<td>$cell</td>";
}
else{
print OUTFILETABLE "<td>$cell</td>";
}
}
print OUTFILETABLE "</tr>\n";
$coord = "";
$ensg = "";
$enst = "";
$subst = "";
$region = "";
$hit_id = "";
$comparison_file = "";
$visual_tx = "";
$indel_loc_pct = "";
$indel_span = "";
}
print OUTFILETABLE "</tr>\n</tbody>\n</table>\n<BR>";
close(FILE);
close(OUTFILETABLE);
close(OUTFILETSV);
sub get_output_heading_tsv{
$oo = @_[0] ;
@elts = split /,/, $oo;
$heading_tsv = "Coordinates\tGene ID\tTranscript ID\tSubstitution Type\tRegion\tAmino acid position change\tIndel Location\tNucleotide change\tAmino acid change\tCauses NMD\tRepeat detected\tTranscript visulization";
@options = ("Gene Name","Gene Desc","Protein Family ID","Protein Family Desc","Transcript Status","Protein Family Size","Ka/Ks (Mouse)","Ka/Ks (Macaque)","OMIM Disease");
return $heading_tsv;
}
sub get_output_heading_html{
$oo = @_[0] ;
@elts = split /,/, $oo;
$heading_html =
"Coordinates\tGene ID\tTranscript ID\tSubstitution Type\tRegion\t<a href=\"\/www\/chr_coords_example_indels.html#Amino_acid_position_change\" target=\"_blank\">Amino acid position change</a>\t<a href=\"\/www\/chr_coords_example_indels.html#Indel_location\" target=\"_blank\">Indel location</a>\t<a href=\"\/www\/chr_coords_example_indels.html#Nucleotide_change\" target=\"_blank\">Nucleotide change</a>\t<a href=\"\/www\/chr_coords_example_indels.html#Amino_acid_change\" target=\"_blank\">Amino acid change</a>\t<a href=\"\/www\/chr_coords_example_indels.html#Protein_sequence_change\" target=\"_blank\">Protein Sequence Change</a>\t<a href=\"\/www\/chr_coords_example_indels.html#NMD\" target=\"_blank\">Causes Nonsense Mediated Decay (NMD)</a>\t<a href=\"\/www\/chr_coords_example_indels.html#repeat\" target=\"_blank\">Repeat detected</a>";
@options = ("Gene Name","Gene Desc","Protein Family ID","Protein Family Desc","Transcript Status","Protein Family Size","Ka/Ks (Mouse)","Ka/Ks (Macaque)","OMIM Disease");
return $heading_html;
}
sub get_output_row_tsv {
$oo = @_[0];
$classification_line = @_[1];
chomp $classification_line;
@elts = split /\t/, $classification_line;
$coord = $elts [0];
$hit_id = $elts[1];
$ensg = $elts[2];
$enst = $elts[3];
$subst = $elts[4];
$coords_change = $elts[5];
$nu_change = $elts[6];
$aa_change = $elts[7];
$region = $elts[8];
$comparison_file = $elts[9];
$indel_span = $elts[10];
$indel_loc_pct = $elts[11];
$visual_tx = $elts[12];
$causes_NMD = $elts[13];
$small_indel_warning = $elts[14];
$repeat_change = $elts[15];
$table_row_tsv = "$coord $small_indel_warning\t$ensg\t$enst\t$subst\t$region\t$coords_change\t$indel_loc_pct\t$nu_change\t$aa_change\t$causes_NMD\t$repeat_change\t$visual_tx";
return $table_row_tsv;
}
sub get_output_row_html {
$oo = @_[0];
$classification_line = @_[1];
chomp $classification_line;
@elts = split /\t/, $classification_line;
$coord = $elts [0];
$hit_id = $elts[1];
$ensg = $elts[2];
$enst = $elts[3];
$subst = $elts[4];
$coords_change = $elts[5];
$nu_change = $elts[6];
$aa_change = $elts[7];
$region = $elts[8];
$comparison_file = $elts[9];
$indel_span = $elts[10];
$indel_loc_pct = $elts[11];
$visual_tx = $elts[12];
$causes_NMD = $elts[13];
$small_indel_warning = $elts[14];
$repeat_change = $elts[15];
$table_row_html ="$coord\t$ensg\t$enst\t$subst\t$region\t$coords_change\t$indel_loc_pct\t$nu_change\t$aa_change\t$comparison_file\t$causes_NMD\t$repeat_change";
return $table_row_html;
}
sub num_elts_in_row{
my $row = @_[0];
my $num_elts;
chomp $row;
my @elts = split /\t/, $row;
foreach my $elt(@elts){
if ($elt ne ""){
$num_elts++;
}
}
return $num_elts;
}
#-------------------------------------------------------------------------
exit(0);
#-------------------------------------------------------------------------
#
# parameter: a string that is the html QUERY_STRING environment
#variable
# returns: an associative array of name/value pairs. The name is the
#key.
sub parse_query {
local ($query_string) = @_;
local ( %ans, @q, $pair );
#print $query_string;
# break up into individual name/value lines
@q = split( /&/, $query_string );
foreach $pair (@q) {
# break the name/value pairs up
# use split rather than regular expressions because the value may
# have
# newlines in it
split( /=/, $pair, 2 );
# change '+' to ' '
$_[1] =~ s/\+/ /g;
# change the escaped characters (has to be after the split on '&'
# and '=')
$_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;
$ans{ $_[0] } = $_[1];
}
return %ans;
}
#-------------------------------------------------------------------------
# parameter: a hex representation of a number (doesn't need to be a
# string)
# returns: the decimal representation of the number
sub hextodec {
unpack( "N", pack( "H8", substr( "0" x 8 . shift, -8 ) ) );
}
#-------------------------------------------------------------------------
# $names = &general_parse($ENV{CONTENT_TYPE}, $QUERY_STRING);
# parameters: CONTENT_TYPE
# QUERY_STRING
# returns: an associative array of name/value pairs. The name is the
# key.
# WARNING: Some of this routine is program-dependent!!!
# CONTENT_TYPE: application/x-www-form-urlencoded
# QUERY_STRING: key1=val1&key2=val2
# CONTENT_TYPE: multipart/form-data; boundary=<boundary>
# QUERY_STRING: <boundary>
# Content-Disposition: form-data; name="key1"
# <blank line>
# val1
# <boundary>
# Content-Disposition: form-data; name="key2"
# <blank line>
# val2
# <boundary>
sub general_parse {
local ( $content_type, $query_string ) = @_;
local ( %ans, @q, $pair, $loc, $boundary, $temp, $temp1 );
if ( $content_type eq "application/x-www-form-urlencoded" ) {
# break up into individual name/value lines
@q = split( /&/, $query_string );
foreach $pair (@q) {
# break the name/value pairs up
# use split rather than regular expressions because the value
# may have
# newlines in it
split( /=/, $pair, 2 );
# change '+' to ' '
$_[1] =~ s/\+/ /g;
# change the escaped characters (must be after the split on '&'
# and '=')
$_[1] =~ s/%(..)/pack("c",&hextodec("$1"))/eg;
$ans{ $_[0] } = $_[1];
} #end of foreach $pair
} #end of if ($content_type)
else {
$loc = index( $content_type, "boundary=" );
if ( $loc > 0 ) {
$temp = substr( $content_type, $loc + 9 );
# Why is this necessary? (boundary= doesn't match actual)
$boundary = "--" . $temp;
# break up into individual name/value lines
@q = split( /$boundary/, $query_string );
foreach $pair (@q) {
# break the name/value pairs up
$loc = index( $pair, "name=" );
$temp = substr( $pair, $loc + 5 );
# $loc = index($temp, "\n\n");
$loc = index( $temp, "\n" );
$temp1 = substr( $temp, $loc + 2 );
# Get rid of stuff after the name; including semicolon if any
$loc_semi = index( $temp, ";" );
$loc_eol = index( $temp, "\n" );
$loc = $loc_eol;
if ( $loc_semi > 0 && $loc_semi < $loc ) {
$loc = $loc_semi;
}
if ( $loc > 0 ) { $temp = substr( $temp, 0, $loc ); }
# Get rid of quotes around the name
$temp =~ s/\"//g;
# Still has a trailing whitespace character ...
$temp =~ s/\s//g;
# Substitute spaces with nothing
# Need to strip leading/ending whitespace off of $temp1,
# but be careful not to strip off internal CRs
# MAC file lines end in just \r, no \n, so makelis won't
# find all
# of the sequences; DOS file lines end in \r\n, UNIX in
#\n.
# Change \r\n to \n and then \r to \n
#######PROGRAM -SPECIFIC!!!!!!!######################
#In my case, I want to keep the newlines in fields which have "file" or
# 'seq"
# and remove newlines everywhere else.
#if ( $temp =~ /file/ || $temp =~ /seq/ || $temp =~ /subst/ ) {
$temp1 =~ s/\r\n/\n/g;
$temp1 =~ s/\r/\n/g;
#}
# for other variables that are NOT files or file-like, remove extra
#whitespace
#else { $temp1 =~ s/\s//g; }
if ( $temp ne "" ) { $ans{$temp} = $temp1; }
} # end of foreach
} #end of if loc > 0
else {
print "Cannot parse\n";
print "content_type=$content_type\n";
print "query_string=$query_string\n";
}
}
return %ans;
#print "</PRE>";
} # end of general_parse
# returns hash for a file, 2nd field is the key and the 3rd field
# is the value 4th field, is the delimiter
sub make_hash {
my ($file) = @_;
my %hash;
open( HASH, $file ) || die "can't open $file";
my $line;
while ( $line = <HASH> ) {
chomp($line);
if ( exists( $hash{$line} ) ) {
$hash{$line}++;
}
else {
$hash{$line} = 1;
}
}
close(HASH);
return (%hash);
}
sub update_IP_logfile {
my ( $queuefile, $IP_address ) = @_;
$lockqueuefile = "$queuefile.lock";
# lockfile will wait until it can lock the file
`./lockfile $lockqueuefile`;
# append the address and command to the queue file
open( FILE, ">>$queuefile" );
print FILE "$IP_address\n";
close(FILE);
chmod( 0664, $queuefile );
# remove the lock file
unlink($lockqueuefile);
}
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