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parseDS_fixattempt.pl
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#!/usr/bin/perl -w
###################################
# DomPred code that
# read-in arguments from Java code
# output results page
# and alot more between
#
# Modification Record
# 23/02/2004 R. Marsden Created.
# 30/04/2004 K. Bryson Added configuration parameters so that the
# script can be used for a 'stand-alone' test-bed.
# 10/05/2004 K. Bryson Fixed output problem for 'Putative domain boundaries' table.
# 10/05/2004 K. Bryson Fixed scale problem on graph
# (normalized smhash values used, not plothash values,
# so biggest_plothash value should no longer be used).
# 14/05/2004 K. Bryson Fixed formatting problem for domain boundaries in the DomSSEA
# results table (re-positioned <TD>..</TD> tags).
# Eliminated output of empty rows when number of hits is less than 10.
# 14/05/2004 K. Bryson Commented out tests on alpha/beta content for the query/match sequences.
# According to Liam these are not needed for DomSSEA output.
# 19/05/2004 K. Bryson Output of DPS multi-domain boundaries in ascending order.
# Output boundary predictions by DomSSEA which are close to
# the N-/C-termini as values in red, rather than '?' symbols.
# Changed the 'flattening' around detected boundaries from +/-20aa to +/-40aa.
# 20/05/2004 K. Bryson Output overall summary of predictions by DPS, even when only 1 domain is predicted.
# This simplifies parsing of the results for the email server and also
# clarifies the overall result produced by DPS for a novice user.
# 28/05/2004 K. Bryson Changed 'flattening' to be +/- 80aa now.
# Fixed bug in output of number of domains
# (Uses $num_peaks now instead of $peaks_detected).
# 04/06/2004 K. Bryson Added configurational parameter for the database used.
# Created a new uniref90_Pfam_A_nofrag database.
# 07/06/2004 K. Bryson After examining the results of some benchmarking,
# put back the old database ! Probably optimally configured for this.
# 07/06/2004 K. Bryson Extended the end-effect flattening to +/-70aa (plus another 10aa possibly ?).
# 15/06/2004 K. Bryson Added '0' to pdb identifiers for SCOP file indexing.
# 17/06/2004 K. Bryson Fixed bug calculating the variance in the z-score section (crashed CASP6 T203 target).
# TEMP FIX - Just take the abs(variance) value --- using the correct value
# 'throws out' all the other calibration and domain prediction becomes unreliable.
# 17/06/2004 K. Bryson Sorted problems with graphing code (flattening smhash, using '-' instead of 0).
# 17/06/2004 K. Bryson Tidied up code by removing completely unused sections of code.
# 17/06/2004 K. Bryson Took out 'helix' and 'strand' profiles from graph since these are distracting from
# the real graph of aligned termini profile and are undocumented in the help file.
# Replaced them with raw output of helix and sheet regions as points, similar to that for coil.
# This is cleaner, less distracting, and provides similar information for domain prediction.
# 18/06/2006 K. Bryson Updated for CASP7 to use the latest uniref90_PfamA databsae.
#
# 06/04/2008 D. Buchan Additionally added an output file for the DOMssea lines that are selected
# Took out that nonsense of wrapping the blast files in <pre> tags so that they are "html"
# (note that .blastdom and blast.bls are identical. blast.bls is then gzipped for passing into the
# rails db).
# Changed the output image to a 16bit png and removed the use of jpegtran. The image is now rotated
# by mogrify in a single rescaling and rotating step. The png is clearer. it might be worth
# playing with the rescaling filter to make the image look nicer.
# Added a couple of output flat files - .boundary for the DPS info
# .domsseatable for the domssea results that will be reported on the webpage
# Removed all code that writes out to any html files. This should be handled by the view in Rails not at the backend.
# PSI-Blast is no longer run within this script, the rails backend now handles this (possible candidate for command line switch though).
# Added too many commandline options to remove any hardcoded paths.
#
##################################
#
# TODO:
# Suppress the calls to gs mogrify and have the java backend run those - annoyingly it does all sorts of stuff about testing
# where the ps and png images are which would also need to be written out.
# Have the input data for the gnuplots output to files and have the java backend run gnuplot
#
##################################
use strict;
###
# Configuration parameters.
###
# Original configuration for web installation.
#
#$OUT_DIR ="/webdata/tmp/NewPredServer/";
#$DOMSSEA_HOME ="/webdata/data/current/dompred/";
#$GNUPLOT_EXEC ="/usr/bin/gnuplot";
#$BLAST_EXEC ="/webdata/binaries/current/blast/bin/blastpgp";
#$JPEGTRAN_EXEC ="/usr/bin/jpegtran";
#$DATABASE_NAME ="uniref90_PfamA"; # ORIGINAL DATABASE.
# $DATABASE_NAME ="nrdb90_Pfam_A_nofrag"; # ORIGINAL DATABASE.
# $DATABASE_NAME ="uniref90_Pfam_A_nofrag";
# Test-bed configuration.
#$OUT_DIR ="/scratch1/NOT_BACKED_UP/ucackxb/projects/Russell/WORK/CASP4_T0087/REPEAT_CASP4_TO087";
#$DOMSSEA_HOME ="/scratch1/NOT_BACKED_UP/ucackxb/projects/Russell/software/others/marsden/DomSSEA";
#$GNUPLOT_EXEC ="/scratch1/NOT_BACKED_UP/ucackxb/projects/Russell/software/others/marsden/gnuplot-3.7.1/gnuplot";
#$BLAST_EXEC ="/scratch1/NOT_BACKED_UP/ucackxb/projects/Russell/BLAST/blastpgp";
#$JPEGTRAN_EXEC ="/scratch1/NOT_BACKED_UP/ucackxb/projects/Russell/JPEGTRAN/jpegtran";
#$DATABASE_NAME ="nrdb90_Pfam_A_nofrag";
# Parameter for the structure DB being used.
my $STRUCTURE_DB = "SCOP";
my $helix_count = 0;
my $extended_count = 0;
my $coil_count = 0;
#GLOBALS BECAUSE REASONS
my %smhash;
my %helixhash;
my %extendedhash;
my %coilhash;
my %howmany;
my $iteration = 0;
my %Zhash;
my %hash;
my %Zseen;
my $total_res = 0;
my $total_seen = 0;
my $v2 = 0;
my $vtot2 = 0;
my $peak_detected = 0;
my $use_cons; #use consensus boundary prediction, never previously set so???
my $cut_DS;
my $cons_stat;
my $consensus_cut;
my $cut_dgs;
my $cut_dil;
my $cut_equal;
my $lib_seq;
my $num_peaks = 0;
my @termini_preds = [];
###
# get name of input sequence
###
my $input_path = $ARGV[0]
or die "Usage parseDS <path/sequence_name>\n"; # path of query sequence
my $do_seq = $ARGV[1]; #1 seqyes seqno (seq dom align)
my $do_database = $ARGV[2]; #2 nonrucl pfama
my $do_evalue = $ARGV[3]; #3 0.001 (evalue)
my $do_its = $ARGV[4]; #4 5 (iterations)
my $do_domssea = $ARGV[5]; #5 IGNORE
my $do_ppred = $ARGV[6]; #6 ppyes ppno
my $do_secprofile = $ARGV[7]; #7 secproyes secprono
my $sequence_name = $ARGV[8]; #8 sequencename
my $DATABASE_NAME = $ARGV[9]
; #9 The blast database of domains that the predictions are based on (uniref90_PfamA)
my $OUT_DIR = $ARGV[10]; #10 the temp directory for all files.
my $DOMSSEA_HOME = $ARGV[11]; #11 The location of the Domssea code
my $GNUPLOT_EXEC = $ARGV[12]; #12 The path to the installation of gnuplot
if ( $sequence_name eq "" ) { $sequence_name = "?"; } #if no given name, call ?
my $sequence_name2 =
substr( $sequence_name, 0, 15 ); #truncate nme to <=15 chars
###
# add below security to front page code, and ask for more data if invalid
###
if ( $do_evalue == 0 ) { $do_evalue = 0.001; } #default e_value of 0.001
$do_evalue =~ s/\s+//; #remove spaces
if ( ( $do_evalue =~ /^\d+\.\d+$/ )
|| ( $do_evalue =~ /^\d+$/ )
|| ( $do_evalue =~ /^\.\d+$/ ) ) #if not an expected number type
{
}
else { $do_evalue = 0.001; } #make default
$do_its =~ s/\s+//; #remove spaces
if ( $do_its =~ /\w+/g ) { $do_its = 5; } #ignore non number chars
if ( $do_its < 1 ) { $do_its = 1; } #make smallest it can be
if ( $do_its > 10 ) { $do_its = 5; } #default iterations
my $input_seq = '';
if ( $input_path =~
/(.*)\/(\S+)\.domssea$/ ) #parse out query name from given path
{
$input_seq = $2;
}
my $target = $input_seq; #for use by difference in length?
my $myps = $input_seq . "myps";
###
# this is the main output file
###
open( BOUNDARYOUT, ">$OUT_DIR/$input_seq.boundary" )
or die "Can't create output boundary file\n";
### eg >/www/htdocs/domout/17_18_59_238.pred
# raw secondary struc output file ACCCCCSCSSDDHHGHHSHSHSHSHAHAHAHAH
### CEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
print("$OUT_DIR/$input_seq.pred\n");
open( SECSTRUC, "$OUT_DIR/$input_seq.pred" )
or die "can't open sec_pred $OUT_DIR $input_seq\n";
my $sec_pred = <SECSTRUC>; #first line
$sec_pred = <SECSTRUC>; #second line
$sec_pred = <SECSTRUC>; #third line
close(SECSTRUC);
my @sec = split( //, $sec_pred );
my $length = scalar(@sec); #can get length of sequence from this
my $ita = 0;
my $aminoacid = '';
# my %coilhash = {};
# my %helixhash = {};
# my %extendedhash = {};
foreach $aminoacid (@sec) #this sets up the coil, helix, beta plot for gnuplot
{
if ( $sec[$ita] =~ /C/ ) { $coilhash{$ita} = 0.1; }
else { $coilhash{$ita} = "-"; }
if ( $sec[$ita] =~ /H/ ) { $helixhash{$ita} = 0.1; }
else { $helixhash{$ita} = "-"; }
if ( $sec[$ita] =~ /E/ ) { $extendedhash{$ita} = 0.1; }
else { $extendedhash{$ita} = "-"; }
$ita++;
}
###
# open alpha beta percentage data and read in
###
open( SECSTRUC, "$DOMSSEA_HOME/2struc_ab_percent" ) or die;
my $line = '';
my %alphahash;
my %betahash;
while ( defined( $line = <SECSTRUC> ) ) {
if ( $line =~ /(\S+)\s+(\d+.\d+)\s+(\d+.\d+)/ ) {
$alphahash{$1} = $2;
$betahash{$1} = $3;
}
}
close(SECSTRUC);
###################################
# Sequence profile code
# will also plot as gnuplot
###################################
#if($do_seq eq "seqyes") #need to sort this
# {
&sequenceX;
# }
###
#run sequence profile algorithm
###
sub sequenceX {
###
#do secondary structure plot
###
###
# calculate percentage of alph and beta residues
###
my $ares = 0;
my $bres = 0;
for ( my $abperc = 0 ; $abperc < ( scalar(@sec) ) ; $abperc++ ) {
if ( $sec[$abperc] =~ /H/ ) { $ares++; }
if ( $sec[$abperc] =~ /E/ ) { $bres++; }
}
my $freq_alpha = $ares / $length;
my $freq_beta = $bres / $length;
&sec_struc;
sub sec_struc {
my %hashb;
my %hasha;
#start with 30 res window from start to end-30
for ( my $secj = 1 ;
$secj <= ( scalar(@sec) - 29 ) ; $secj++ ) #$C - 59....
{
my $counterx = 0;
my $countery = 0;
my $counterz = 0;
for ( my $secl = $secj ; $secl <= ( $secj + 29 ) ; $secl++ ) {
my $element = $sec[ $secl - 1 ];
if ( $element =~ /E/ ) { $counterx++; } #beta
elsif ( $element =~ /H/ ) { $countery++; } #alpha
elsif ( $element =~ /C/ ) { $counterz++; } #coil
elsif ( $element =~ // ) {
$counterz++;
} #nothin due to missin bit
}
$hashb{ $secj + 14 } = sprintf( "%.2f", ( $counterx / 30 ) ); #beta
$hasha{ $secj + 14 } = sprintf( "%.2f", ( $countery / 30 ) ); #alpha
#$hashc{$secj+14} = sprintf("%.2f",($counterz/30));#coil
}
}
#collect test sequence in a cgi way
#run seq against psi blast, num iterations and cutoff params
#filter fragments and output plot.gif
my $num_iterations = $do_its; #number of given itterations
###
# run psiblast
###
#system ("$BLAST_EXEC -i $OUT_DIR/$input_seq -j $num_iterations -a 2 -m 0 -b 1000 -d $DOMSSEA_HOME/$DATABASE_NAME > $OUT_DIR/$input_seq.blastdom");
my $with_eval = 1; #forgot what this is for
my $output_blast =
$input_seq . ".blast"; #thats the name for the blastout html file
my $output_blastsee =
$input_seq . ".blastsee"; #name for the parsed blast output data
my $output_blastPfamA = $input_seq . "PfamA";
open( SEE, ">$OUT_DIR/$output_blastsee.txt" )
or die "Cannot open blastsee_html\n";
&printtoparsed; #start table for parsed blast
open( TEXT, ">$OUT_DIR/$output_blast.bls" )
or die "Cannot open blast_html\n";
#print TEXT "<PRE>\n";
open( PFAMA, ">$OUT_DIR/$output_blastPfamA.html" )
or die "Cannot open blast_html\n";
#print PFAMA "<PRE>\n";
my $interval = 1;
###
# read in blast out and parse it
###
open( INFIL, "$OUT_DIR/$input_seq.blastdom" )
or die "Cannot open $input_seq.blastdom\n";
#my $iteration = 0;
my $curr_it;
my $fragment_seen = 0;
my $initiated = 0;
my $pfamA_hit = 0;
my $colour = "black";
my $score_see = 0;
my $querylist = ();
my $querylistx = ();
my $hitlength;
my $e_value;
#my %howmany = {};
my $name = '';
my %hashC;
my %hashN;
my $pfamA_seen = 0;
my $expecting = 0;
while ( defined( $line = <INFIL> ) ) {
print TEXT "$line";
if ( $line =~ /\((\d+)\s+letters\)/ ) {
$length = $1;
}
if ( $line =~ /Searching/ ) {
#open (SEE, ">$OUT_DIR/$output_blastsee.html") or die "Cannot open blastsee_html\n";
#&printtoparsed;#start table for parsed blast
$iteration++;
$curr_it = $1;
$fragment_seen = 1; #use this to stop previous info being used
}
if ( $line =~ /CONVERGED!/ ) {
#open (SEE, ">$OUT_DIR/$output_blastsee.html") or die "Cannot open blastsee_html\n";
#&printtoparsed;#start table for parsed blast
$curr_it = 0;
$fragment_seen = 1; #use this to stop previouse info being used
}
if ( ( $line =~ /^>(.*)/ )
|| ( $line =~ /Matrix: BLOSUM62/ )
) #next alignment, print out last if seen
{
if ( ( $initiated == 1 )
&& ( $fragment_seen == 0 )
) #ie seen a > and last align wasn't a fragment
{
if ( $pfamA_hit == 1 ) {
#$pfamA_hit=0;
$colour = "blue";
}
for ( my $com = 1 ; $com <= $score_see ; $com++ ) {
# $querylist = "querylist" . $com; #for query ends
# $querylistx = "querylistx" . $com; #for db-hit ends
push $querylist, "querylist" . $com;
push $querylistx, "querylistx" . $com;
$hitlength = shift @$querylist;
$e_value = shift @$querylist;
if ( $e_value <= $do_evalue ) #print out stats
{
$howmany{$iteration}++;
my $name2 =
substr( $name, 0, 35 ); #name of last one seen
if ( length($name2) < 35 ) {
until ( length($name2) == 35 ) {
$name2 = $name2 . " ";
}
}
if ( $e_value == 0.0 ) { $e_value = "1e-200"; }
my $mod_e_value = ( log( 1 / $e_value ) )
; #/log(10); #rm if not want to log eval
#print SEE "<TR>\n";
#print SEE "<TD>$name2</TD>\n";
#print SEE "<TD>$length</TD>\n";
#print SEE "<FONT color = \"$colour\">\n";
print SEE "$name2 ";
print SEE "$length ";
my $startnumber = shift @$querylist;
my $endnumber = pop @$querylist;
my $hitstart = shift @$querylistx;
my $hitend = pop @$querylistx;
#print SEE "<TD>$startnumber</TD>\n";
#print SEE "<TD>$endnumber</TD>\n";
#print SEE "<TD>$hitlength</TD>\n";
#print SEE "<TD>$hitstart</TD>\n";
#print SEE "<TD>$hitend</TD>\n";
#print SEE "<TD>$e_value</TD>\n";
#print SEE "</TR>\n";
print SEE "$startnumber ";
print SEE "$endnumber ";
print SEE "$hitlength ";
print SEE "$hitstart ";
print SEE "$hitend ";
print SEE "$e_value ";
print SEE "\n";
#print SEE "</FONT>";
if ( $pfamA_hit == 1 ) {
#print PFAMA "<FONT color = \"$colour\">\n";
print PFAMA "$name2 ";
print PFAMA "$length ";
print PFAMA "$startnumber ";
print PFAMA "$endnumber ";
print PFAMA "$hitlength ";
print PFAMA "$hitstart ";
print PFAMA "$hitend ";
print PFAMA "$e_value ";
print PFAMA "\n";
#print PFAMA "</FONT>";
}
$pfamA_hit = 0;
$colour = "black";
if ( ( $hitlength - $hitend ) < 10 ) #ie C term
{
$hash{$iteration}{$endnumber}++; #=$mod_e_value;
$hashC{$iteration}{$endnumber}++;
}
if ( $hitstart < 10 ) {
$hash{$iteration}{$startnumber}++; #=$mod_e_value;
$hashN{$iteration}{$startnumber}++;
}
$hash{$iteration}{$startnumber}++;
$hash{$iteration}{$endnumber}++;
$hashN{$iteration}{$startnumber}++;
$hashC{$iteration}{$endnumber}++;
@$querylist = ();
@$querylistx = ();
}
}
$score_see = 0;
}
if ( $line =~ /^>(.*)/ ) #get name of this one
{
$name = $1;
if ( $line =~ /^>(\S+)\s+PF\d+\;/ ) {
$pfamA_hit = 1;
$pfamA_seen = 1;
}
for ( my $com = 1 ; $com <= $score_see ; $com++ ) {
$querylist = "querylist" . $com;
$querylistx = "querylistx" . $com;
@$querylist = ();
@$querylistx = ();
}
$score_see = 0;
}
$initiated = 1;
if ( $line =~ /(FRAGMENT)|(fragment)|(Fragment)/ ) {
$fragment_seen = 1;
next;
}
if ( $line !~ /(FRAGMENT)|(fragment)|(Fragment)/ ) {
$fragment_seen = 0; #reinitialise
}
}
if ( $with_eval == 1 ) {
if ( $line =~ /Length\s+=\s+(\d+)/ ) {
$hitlength = $1;
}
if ( $line =~ /Score\s+=\s+(.*)\s+bits/ ) {
###
#matching more than once to query --> $score_see >1
###
$score_see++;
# $querylist = "querylist" . $score_see;
# $querylistx = "querylistx" . $score_see;
push @$querylist, "querylist" . $score_see;
push @$querylistx, "querylistx" . $score_see;
my $bits = $1;
push @$querylist, $hitlength;
}
if ( $line =~ /Expect\s+=\s+(\d+\.\d+)/ ) {
$expecting++;
$e_value = $1;
push @$querylist, $e_value;
}
if ( $line =~ /Expect\s+=\s+(e\S+)/ ) {
$expecting++;
$e_value = "1" . $1;
push @$querylist, $e_value;
}
if ( $line =~ /Expect\s+=\s+(\d+e\S+)/ ) {
$expecting++;
$e_value = $1;
push @$querylist, $e_value;
}
if ( $line =~ /^Query:\s+(\d+).*\s+(\d+)$/ ) {
my $start = $1;
my $end = $2;
push @$querylist, $start;
push @$querylist, $end;
}
if ( $line =~ /^Sbjct:\s+(\d+).*\s+(\d+)$/ ) {
my $start = $1;
my $end = $2;
push @$querylistx, $start;
push @$querylistx, $end;
}
}
}
#print SEE "</PRE>\n";
close(SEE);
#print TEXT "</PRE>\n";
close(TEXT);
#print PFAMA "</PRE>\n";
close(PFAMA);
###
# blast has been read in and parsed
#
# output / calculate plot data (need to sort)
###
# DON'T NEED THIS AS FAR AS I CAN TELL??
# THIS IS LIKE DONE BEFORE EVERYTHING IS FLATENED,
my $biggest_plothash = 0;
my %plothash = {};
for ( my $i = 1 ; $i <= ( $length - 14 ) ; $i++ ) { #so plot from +45 to -55
for ( my $j = $i ; $j < ( $i + 14 ) ; $j++ ) #or do 36 to 45
{
$plothash{ $i + 7 } +=
$hash{$iteration}{$j}; #get total in window -> middle res
}
$plothash{ $i + 7 } = $plothash{ $i + 7 } / 15; #average smoothing
if ( $plothash{ $i + 7 } > $biggest_plothash ) {
$biggest_plothash = $plothash{ $i + 7 };
}
}
if ( $biggest_plothash == 0 ) { $biggest_plothash = 1; }
###
# analyse psiblast profile
###
### KB (07/06/2004) - Extend this to +/-70aa at boundaries (plus another 10aa possibly ?).
my $bigpoint = 0;
my $seenC = 0;
my $seenN = 0;
#my %smhash = {};
my %smhashN = {};
my %smhashC = {};
for ( my $i = 1 ; $i < 70 ; $i++ ) {
$hash{$iteration}{$i} = 0;
$hashN{$iteration}{$i} = 0;
}
for ( my $i = ( $length - 70 ) ; $i <= $length ; $i++ ) {
$hash{$iteration}{$i} = 0;
$hashC{$iteration}{$i} = 0;
}
#if 'hits' on boundaries rm.... don't want to incorparate into Zscore
for ( my $yi = 70 ; $yi <= 80 ; $yi++ ) #10 or 20?
{
if ( $hashC{$iteration}{$yi} > 0 ) {
$seenC = 1; #have seen a C-term hit here, (so keep)
}
}
if ( $seenC != 1 ) #not = 1 ie not seen any c-term hit
{
for ( my $yi = 70 ; $yi <= 80 ; $yi++ ) #10 or 20?
{
$hash{$iteration}{$yi} = 0;
$hashN{$iteration}{$yi} = 0;
}
}
for ( my $yi = ( $length - 70 ) ; $yi >= ( $length - 80 ) ; $yi-- ) {
if ( $hashN{$iteration}{$yi} > 0 ) {
$seenN = 1; #have seen a N-term hit here, so keep)
}
}
if ( $seenN != 1 ) {
for ( my $yi = ( $length - 70 ) ; $yi >= ( $length - 80 ) ; $yi-- ) {
$hash{$iteration}{$yi} = 0;
$hashC{$iteration}{$yi} = 0;
}
}
###
# smoothing window of 15 residues for N and then C hits
###
for ( my $i = 1 ; $i <= $length - 14 ; $i++ ) { #so plot from +55 to -65
for ( my $j = $i ; $j < ( $i + 15 ) ; $j++ ) {
$smhashN{ $i + 7 } +=
$hashN{$iteration}{$j}; #get total in window -> middle res
}
$smhashN{ $i + 7 } = $smhashN{ $i + 7 } / 15; #average window value
}
for ( my $i = 1 ; $i <= $length - 14 ; $i++ ) { #so plot from +55 to -65
for ( my $j = $i ; $j < ( $i + 15 ) ; $j++ ) {
$smhashC{ $i + 7 } +=
$hashC{$iteration}{$j}; #get total in window -> middle res
}
$smhashC{ $i + 7 } = $smhashC{ $i + 7 } / 15; #average window value
}
###
#check out N and C matching in above smoothed profile
###
for ( my $i = 8 ;
$i <= $length - 7 ; $i++ ) #8 cos thats where 15 window starts
{
if ( ( $smhashN{$i} * $smhashC{$i} ) == 0 ) {
$smhash{$i} = $smhashN{$i} + $smhashC{$i};
}
if ( ( $smhashN{$i} * $smhashC{$i} ) > 0 ) {
my $extra = 0;
if ( $smhashN{$i} > $smhashC{$i} ) { $extra = $smhashC{$i} / 2; }
if ( $smhashC{$i} >= $smhashN{$i} ) { $extra = $smhashN{$i} / 2; }
$smhash{$i} = $smhashN{$i} + $smhashC{$i} + $extra;
}
}
###
# calculate Zscores
###
my $Zscore = 0;
foreach my $x ( sort { $a <=> $b } keys %smhash ) {
$total_res += $smhash{$x};
$total_seen++;
$v2 = ( $smhash{$x} * $smhash{$x} );
$vtot2 += $v2;
if ( $smhash{$x} > $bigpoint ) {
$bigpoint = $smhash{$x};
} #get higherst peak
}
if ( $total_seen == 0 ) { next; } #important, ie no blast profile
my $mean = $total_res / $total_seen;
my $sigx2 = ( ( $total_res * $total_res ) / $total_seen );
# 17/06/2004 KB Fixed bug - division by $total_seen-1,
# rather than $total_res-1;
# TEMP FIX TEMP FIX - Just use abs(variance).
my $variance = ( $vtot2 - $sigx2 ) / ( $total_res - 1 );
my $sd = sqrt abs($variance);
foreach my $e ( sort { $a <=> $b } keys %smhash ) {
if ( ( $smhash{$e} == 0 ) && ( $mean == 0 ) && ( $sd == 0 ) ) {
$Zhash{$e} = 0;
}
else {
$Zscore = ( $smhash{$e} - $mean ) / $sd;
$Zhash{$e} = $Zscore;
}
}
###
# iterate over Zscored profile
###
my $bigZ = 1.5;
my $g = 1.5; #Zscore of 1.5
my $peak = 1;
my $reallybig = 0;
my $Zres = 0;
while ( $peak == 1 ) {
$bigZ = $g;
my $bigZpeak = $g;
$peak = 0;
foreach my $x ( sort { $a <=> $b } keys %smhash ) {
if ( $Zseen{$x} == 1 ) { next; } #so don't see it on next iteration
if ( $bigZpeak < $Zhash{$x} ) #find highest peak first
{
$bigZpeak = $Zhash{$x};
if ( $bigZpeak > $reallybig ) {
$reallybig = $bigZpeak;
}
$peak = 1;
$Zres = $x;
}
}
if ( $peak == 1 ) {
### sort this to store predicted boundaries
$Zseen{$Zres} = 1;
$num_peaks++;
push @termini_preds, $Zres;
# Flatten the smhash/Zhash with +/-80aa around detected boundary.
for ( my $flat = ( $Zres - 80 ) ;
$flat <= ( $Zres + 80 ) ; $flat++ )
{
if ( $flat == $Zres ) { next; }
# 17/06/2004 KB Surely should not flatten smhash,
# otherwise graph shown will have data flattened.
# $smhash{$flat}=0;
$Zhash{$flat} = 0;
}
}
}
$peak_detected = 0;
if ( $num_peaks == 0 ) {
}
if ( $num_peaks > 0 ) {
$peak_detected++;
# $num_peaks=0; # Use $num_peaks.
}
###
# to normalise this plot, divide all points by highest value!#
###
if ( $bigpoint == 0 ) #ie no psiblast hits make all plot 0
{
foreach my $x ( sort { $a <=> $b } keys %smhash ) {
$smhash{$x} = 0;
}
}
if ( $bigpoint > 0 ) {
foreach my $x ( sort { $a <=> $b } keys %smhash ) {
$smhash{$x} = $smhash{$x} / $bigpoint;
}
}
}
###
# output profile plot and secondary structure plot, here use smhash (which is raw data?)
# could also add hashN and hashC and smhash
###
&shownorm();
###
# plot, again with smhash.
# 17/06/2004 KB Rewrote this section.
###
#$helix_count = 0;
#$extended_count = 0;
#$coil_count = 0;
sub shownorm {
open( OUT, ">$OUT_DIR/$input_seq.graph" ) or die "can't create outfile\n";
foreach my $x ( sort { $a <=> $b } keys %smhash ) {
print OUT
"$x $smhash{$x} $helixhash{$x} $extendedhash{$x} $coilhash{$x}\n";
#print "THINGY: ".$helixhash{$x}."\n";
if ( $helixhash{$x} =~ /\d/ ) {
$helix_count++;
}
if ( $extendedhash{$x} =~ /\d/ ) {
$extended_count++;
}
if ( $coilhash{$x} =~ /\d/ ) {
$coil_count++;
}
}
close(OUT);
}
##
# End of shownorm subroutine.
##
if ( $howmany{$iteration} eq "" ) {
$howmany{$iteration} = 0; #eh? should do this sooner?
}
#$howmany{$iteration}=1;
if ( ( $do_secprofile eq "secproyes" )
&& ( $howmany{$iteration} > 0 )
) #$do_secprofile=$ARGV[7]; #7 secproyes secprono
{
&gnuplot1; #plot 2' and psiblast
&pstogif;
}
if ( ( $do_secprofile eq "secprono" ) && ( $howmany{$iteration} > 0 ) ) {
&gnuplot2; #plot only psiblast
&pstogif;
}
if ( ( $do_secprofile eq "secproyes" ) && ( $howmany{$iteration} == 0 ) ) {
print("hi3");
&gnuplot3; #plot only 2'
&pstogif;
}
###
# gnuplot commands
###
#7/4/2009 D.Buchan added some globals that track how many helix, strand or coil residues are to be plotted and if there are none that line is NOT
#added to the gnuplot script
sub gnuplot1 {
### save tmp GNUPLOT file
my $gnufile = "$OUT_DIR/$input_seq.gnu";
open( GNUPLOT, ">$OUT_DIR/$input_seq.gnu" )
or print("Couldn't save gnuplot file: $gnufile\n");
print GNUPLOT ("set terminal postscript color solid \"Times-Roman\" 18\n");
$myps = $input_seq . "myps";
print GNUPLOT ("set output \"$OUT_DIR/$myps.ps\"\n");
#print GNUPLOT ("set yrange [0:]\n");
print GNUPLOT ("set format y \"\"\n");
#print GNUPLOT ("set format y2 \"\"\"\n");
# print GNUPLOT ("set y2range [0:$biggest_plothash]\n");
print GNUPLOT ("set y2range [0:1.2]\n");
print GNUPLOT (
"plot \"$OUT_DIR/$input_seq.graph\" using 1:2 axes x1y2 title 'aligned termini profile' with lines lt 3"
);
# 17/06/2004 KB Changed the alpha-helix, beta-sheet plots into output similar to coil.
if ( $helix_count != 0 ) {
print GNUPLOT (
", \\\n\"$OUT_DIR/$input_seq.graph\" using 1:3 axes x1y2 title 'helix-residues' with points lt 2 pt 5"
);
}
if ( $extended_count != 0 ) {
print GNUPLOT (
", \\\n\"$OUT_DIR/$input_seq.graph\" using 1:4 axes x1y2 title 'strand-residues' with points lt 1 pt 5"
);
}
if ( $coil_count != 0 ) {
print GNUPLOT (
", \\\n\"$OUT_DIR/$input_seq.graph\" using 1:5 axes x1y2 title 'coil-residues' with points lt -1 pt 5"
);
}
print GNUPLOT ("\n");
print GNUPLOT ("exit\n");
close(GNUPLOT);
my $command = "$GNUPLOT_EXEC $OUT_DIR/$input_seq.gnu";
system("$command");
}
sub gnuplot2 {
### save tmp GNUPLOT file
my $gnufile = "$OUT_DIR/$input_seq.gnu";
open( GNUPLOT, ">$OUT_DIR/$input_seq.gnu" )
or print("Couldn't save gnuplot file: $gnufile\n");
print GNUPLOT ("set terminal postscript color solid \"Times-Roman\" 18\n");
$myps = $input_seq . "myps";
print GNUPLOT ("set output \"$OUT_DIR/$myps.ps\"\n");
print GNUPLOT (
"plot \"$OUT_DIR/$input_seq.graph\" using 1:2 title 'aligned termini profile' with lines lt 3\n"
);
print GNUPLOT ("exit\n");
close(GNUPLOT);
my $command = "$GNUPLOT_EXEC $OUT_DIR/$input_seq.gnu";
system("$command");
}
sub gnuplot3 {
### save tmp GNUPLOT file
my $gnufile = "$OUT_DIR/$input_seq.gnu";
open( GNUPLOT, ">$OUT_DIR/$input_seq.gnu" )
or print("Couldn't save gnuplot file: $gnufile\n");
print GNUPLOT ("set terminal postscript color solid \"Times-Roman\" 18\n");
$myps = $input_seq . "myps";
print GNUPLOT ("set output \"$OUT_DIR/$myps.ps\"\n");
#print GNUPLOT ("plot \"$OUT_DIR/$input_seq.graph\" using 1:2 title 'aligned termini profile' with lines lt 3, \\\n");
# 17/06/2004 KB Changed the alpha-helix, beta-sheet plots into output similar to coil.
print GNUPLOT (
"plot \"$OUT_DIR/$input_seq.graph\" using 1:3 axes x1y2 title 'helix-residues' with points lt 2 pt 5, \\\n"
);
print GNUPLOT (
"\"$OUT_DIR/$input_seq.graph\" using 1:4 axes x1y2 title 'strand-residues' with points lt 1 pt 5, \\\n"
);
print GNUPLOT (
"\"$OUT_DIR/$input_seq.graph\" using 1:5 axes x1y2 title 'coil-residues' with points lt -1 pt 5 \n"
);
print GNUPLOT ("exit\n");
close(GNUPLOT);
my $command = "$GNUPLOT_EXEC $OUT_DIR/$input_seq.gnu";
system("$command");
}
###
# make plot correct size / format
###
sub pstogif {
my $myps = $input_seq . "myps";
system(
"gs -q -dNOPAUSE -dBATCH -sDEVICE=png16m -sOutputFile=$OUT_DIR/$myps.png -c save pop -f $OUT_DIR/$myps.ps "
);
my $inputran = $input_seq . "tran";
#system("$JPEGTRAN_EXEC -rot 90 $OUT_DIR/$myps.jpg > $OUT_DIR/$inputran.jpg");
system(
"mogrify -resize 540x700 -rotate 90 -crop 0x0 -quality 100 $OUT_DIR/$myps.png"
);
} #-crop 6%
#http://irl.eecs.umich.edu/jamin/pointers/gnuplot_quick.html
#}
# probably don't need to do this, but will just incase
undef %smhash; #average smoothing
undef %Zhash;
undef %hash;
undef %Zseen;
$total_res = 0;
$total_seen = 0;
$v2 = 0;
$vtot2 = 0;
# Need to sort this out, to make look better / more reliable 0 plot stuff....
#
###
if ( ( $do_secprofile eq "secproyes" )
|| ( $howmany{$iteration} > 0 ) ) #ie can show graph
{
&graphpage;
}
if ( ( $do_secprofile eq "secprono" )
&& ( $howmany{$iteration} == 0 ) ) #ie can't show graph
{
#&graphpage2;
}
###################################
# read in DomSSEA out put
# If peak_detected>0; means
# upreg multi domssea preds.......
#
###################################
my $score = 0;
my $match = 0; #matched db hit
my $num_doms = 0; #global?
my $rest = 0; #ie all the predicted boundaries
my %sec_align; #the 2' structure alignment of this match (could find % a and b)
my $cant = 0;
my $freq_alpha_match = 0;
my $freq_beta_match = 0;
my %numdom_hash;
my $count = 0;
my %cut_hash;
my %score_hash;
my @sorted;
my @score_array = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ); #initialise @score_array
if ( ( $peak_detected > 0 )
) #&&($length>300)) #so saying PsBlast says multi and has to be >300 residues..
{
#&domsseapage; #output domssea bit
open( PAIRS, "$input_path" ) or die "Can't open domlist\n";
my $pair = '';
while (defined($pair = <PAIRS>) ) {
if ( $pair =~ /^(\d+)(\.\d+)?\s+(\S+)\s+(\d+)\s+(.*)\"(.*)\"/
) #open up domssea output file
{
$score = $1 . $2; #get score
if ( $score > 1 ) { next; } #if greater than 1, is wrong...
}
while ( $pair =~
/\s+(\S+)\s+(\d+)\s+(.*)\"(.*)\"/g ) #all the stuff after the score
{
#$target=$1; #global?
$match = $1; #matched db hit
$num_doms = $2; #global?
$rest = $3; #ie all the predicted boundaries
$sec_align{$match} = $4
; #the 2' structure alignment of this match (could find % a and b)
$cant = 0; #
#if(dothis==1) #not intitialised so not doing
# { #this checks boundary cuts that fall in first/last 40 residues
# if($num_doms>1)
# {
# while($rest=~/(\d+)/g)
# {
# if(($1<40)||($1>($length-40)))
# {
# $cant=1;
# }
# }
# }
# }
#if($cant==1){next;}
###
# check out a and b percentage matching...
###
$freq_alpha_match = $alphahash{$match};
$freq_beta_match = $betahash{$match};
# KB - Commented out these tests, not really required for the DomSSEA input.
# if(($freq_alpha<1)&&($freq_beta_match<1)&&($freq_alpha_match>1)) #target no alpha, match no beta......(so unless all coil..)
# {
# next; # completely diff 2' structures !!!!!!!!!!!
# }
# if(($freq_beta<1)&&($freq_alpha_match<1)&&($freq_beta_match>1)) #target no alpha, match no beta......(so unless all coil..)
# {
# next; # completely diff 2' structures !!!!!!!!!!!