#!/usr/bin/perl ########################################################### # #SSpro and ACCpro: Protein Secondary Structure/Solvent Accessibility Prediction Programs #configure.pl: to configure the installation of PSpro # #Author: Jianlin cheng #Date: April 8, 2004 #Institute for Genomics and Bioinformatics #School of Information and Computer Science #University of California, Irvine # # Modified: April 15, 2005 #References: #J. Cheng, A. Randall, M. Sweredoski, P. Baldi, SCRATCH: a Protein Structure and Structural Feature Prediction Server, Nucleic Acids Research, Special Issue on Web Servers, in press, 2005. ########################################################## use Cwd 'abs_path'; use File::Basename; #######Customize settings here############################################### #set installation directory of SSpro to your unzipped sspro4 directory #$install_dir = "/scratch/sspro4-bjornw/"; #$install_dir="/local/www/services/ProQ2/apps/sspro4/"; $install_dir=dirname(abs_path($0)); #exit; ##########End of Customizaton################################################ ################Don't Change the code below############## if (! -d $install_dir) { die "can't find installation directory.\n"; } if ( substr($install_dir, length($install_dir) - 1, 1) ne "/" ) { $install_dir .= "/"; } #set the fullpath of nr database $nr_db_dir = "${install_dir}data/nr/"; $nr_db = "nr"; #set the fullpath of big database $big_db_dir = "${install_dir}data/big/"; #set the big database name $big_db = "big_98_X"; #if (! -d $nr_db_dir) #{ # die "can't find nr database directory.\n"; #} #if ( substr($nr_db_dir, length($nr_db_dir) - 1, 1) ne "/" ) #{ # $nr_db_dir .= "/"; #} #if (! -d $big_db_dir) #{ # die "can't find big directory.\n"; #} #if ( substr($big_db_dir, length($big_db_dir) - 1, 1) ne "/" ) #{ # $big_db_dir .= "/"; #} #check if the database are there. $nr_db_f = $nr_db_dir . $nr_db; $big_db_f = $big_db_dir . $big_db; #if (! -f "${big_db_f}.pal") { #if (! -f "${big_db_f}.phr" || ! -f "${big_db_f}.pin" || ! -f "${big_db_f}.psq") #{ # die "can't find the big coil database.\n"; #} #} # #if (! -f "${nr_db_f}.pal") { #if (! -f "${nr_db_f}.phr" || ! -f "${nr_db_f}.pin" || ! -f "${nr_db_f}.psq" || ! -f "${nr_db_f}.pnd" # || ! -f "${nr_db_f}.pni" || ! -f "${nr_db_f}.psd" || ! -f "${nr_db_f}.psi" ) #{ # die "can't find the non-redundant database.\n"; #} #} #check if the installation directory is right #the configuration file must run in the installation directory $cur_dir = `pwd`; chomp $cur_dir; $configure_file = "$cur_dir/configure.pl"; if (! -f $configure_file || $install_dir ne "$cur_dir/") { die "Please check the installation directory setting and run the configure program there.\n"; } $bin_dir = "${install_dir}bin/"; $data_dir = "${install_dir}data/"; $model_dir = "${install_dir}model/"; $script_dir = "${install_dir}script/"; $server_dir = "${install_dir}server/"; $test_dir = "${install_dir}test/"; $blast_dir = "${install_dir}blast2.2.8/"; if ( ! -d $bin_dir || ! -d $data_dir || ! -d $model_dir || ! -d $script_dir || ! -d $server_dir || ! -d $test_dir || ! -d $blast_dir ) { die "some sub directories don't exist. check the installation tar ball.\n"; } $nr_db = ${nr_db_dir} . $nr_db; $big_db = ${big_db_dir} . $big_db; #generate model definition file, server script for sspro $sspro_exe = "${server_dir}predict_seq_ss"; $sspro_sh = "${server_dir}predict_seq_ss.sh"; $sspro_model_dir = "${model_dir}sspro/"; $sspro_model_def = "${model_dir}sspro.model"; $accpro_exe = "${server_dir}predict_seq_sa"; $accpro_sh = "${server_dir}predict_seq_sa.sh"; $accpro_sh_multi = "${server_dir}predict_seq_sa_multi.sh"; $accpro_model_dir = "${model_dir}accpro/"; $accpro_model_def = "${model_dir}accpro.model"; print "generate sspro server script...\n"; open(SERVER_SH, ">$sspro_sh") || die "can't write sspro shell script.\n"; print SERVER_SH "#!/bin/sh\n#predict the secondary stx for one sequence.\n"; print SERVER_SH "if [ \$# -ne 3 ]\n"; print SERVER_SH "then\n\techo \"need three parameters:seq_file, ali_dir, data_format.\"\n\texit 1\nfi\n"; print SERVER_SH "#format: 1:9-line, 2:3-line, all seq must have a title line(1 20 3).\n\n"; print SERVER_SH "$sspro_exe $sspro_model_def \$1 \$2 \$3 \n"; close SERVER_SH; print "generate accpro server script...\n"; open(SERVER_SH, ">$accpro_sh") || die "can't write accpro shell script.\n"; print SERVER_SH "#!/bin/sh\n#predict the solvent acc for one sequence. Don't change this script.\n"; print SERVER_SH "if [ \$# -ne 3 ]\n"; print SERVER_SH "then\n\techo \"need three parameters:seq_file, ali_dir, data_format.\"\n\texit 1\nfi\n"; print SERVER_SH "#format: 1:9-line, 2:3-line, all seq must have a title line(1 20 3).\n\n"; print SERVER_SH "$accpro_exe $accpro_model_def \$1 \$2 \$3 5\n"; close SERVER_SH; print "generate accpro multi-threshold server script...\n"; open(SERVER_SH, ">$accpro_sh_multi") || die "can't write accpro shell script.\n"; print SERVER_SH "#!/bin/sh\n#predict the solvent acc for one sequence.\n"; print SERVER_SH "if [ \$# -ne 4 ]\n"; print SERVER_SH "then\n\techo \"need four parameters:seq_file, ali_dir, data_format, solvent accessibility threshold index(0:0%,1:5%,...,5:25%,....19:95%).\"\n\texit 1\nfi\n"; print SERVER_SH "#format: 1:9-line, 2:3-line, all seq must have a title line(1 20 3).\n\n"; print SERVER_SH "$accpro_exe $accpro_model_def \$1 \$2 \$3 \$4 \n"; close SERVER_SH; print "generate sspro model definition file...\n"; opendir(MODEL_DIR, "$sspro_model_dir") || die "can't open the sspro model dir.\n"; open(MODEL_DEF, ">$sspro_model_def") || die "can't create sspro model def file.\n"; @file_list = readdir(MODEL_DIR); closedir(MODEL_DIR); if (@file_list < 2) { die "can't find sspro model file. check intallation tar ball.\n"; } $model_num = @file_list; $model_num -= 2; print MODEL_DEF "$model_num 3\n"; while (@file_list) { $model_file = shift @file_list; if ($model_file ne "." && $model_file ne ".." && $model_file ne "CVS") { print MODEL_DEF "$sspro_model_dir$model_file\n"; } } close MODEL_DEF; print "generate accpro model definition file...\n"; opendir(MODEL_DIR, "$accpro_model_dir") || die "can't open the accpro model dir.\n"; open(MODEL_DEF, ">$accpro_model_def") || die "can't create sspro model def file.\n"; @file_list = readdir(MODEL_DIR); closedir(MODEL_DIR); if (@file_list < 2) { die "can't find accpro model file. check intallation tar ball.\n"; } $model_num = @file_list; $model_num -= 2; print MODEL_DEF "$model_num 20\n"; while (@file_list) { $model_file = shift @file_list; if ($model_file ne "." && $model_file ne ".." && $model_file ne "CVS") { print MODEL_DEF "$accpro_model_dir$model_file\n"; } } close MODEL_DEF; ############################Generate Shell Script For user############################## #generate script of creating alignment for one sequence open(SHELL, ">${bin_dir}generate_flatblast.sh") || die "can't create genereate_flatblast.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "if [ \$# -ne 2 ]\n"; print SHELL "then\n\techo \"need two parameters:seq_file, output_file.\" \n\texit 1\nfi\n"; print SHELL "${script_dir}generate_flatblast.pl $blast_dir $script_dir $big_db $nr_db \$1 \$2 \n"; close SHELL; #generate script of predicting ss for one sequence open(SHELL, ">${bin_dir}predict_seq_ss.sh") || die "can't create predict_seq_ss.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "if [ \$# -ne 3 ]\n"; print SHELL "then\n\techo \"need three parameters:seq_file(name,seq in compact format), align_dir, output file.\" \n\texit 1\nfi\n"; print SHELL "#assumption: alignment_file = align_dir + name\n"; print SHELL "${script_dir}predict_seq_ss.pl ${server_dir}predict_seq_ss.sh \$1 \$2 \$3 \n"; close SHELL; #generate script of predicting sa for one sequence open(SHELL, ">${bin_dir}predict_seq_sa.sh") || die "can't create predict_seq_ss.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "if [ \$# -ne 3 ]\n"; print SHELL "then\n\techo \"need three parameters:seq_file(name,seq in compact format), align_dir, output file.\" \n\texit 1\nfi\n"; print SHELL "#assumption: alignment_file = align_dir + name\n"; print SHELL "${script_dir}predict_seq_sa.pl ${server_dir}predict_seq_sa.sh \$1 \$2 \$3 \n"; close SHELL; #generate script of predicting sa for one sequence open(SHELL, ">${bin_dir}predict_seq_sa_multi.sh") || die "can't create predict_seq_ss_multi.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "if [ \$# -ne 4 ]\n"; print SHELL "then\n\techo \"need 4 parameters:seq_file(name,seq in compact format), align_dir, output file, solvent acc threshold index(0:0%,1:5%,..., 19:95%).\" \n\texit 1\nfi\n"; print SHELL "#assumption: alignment_file = align_dir + name\n"; print SHELL "${script_dir}predict_seq_sa_multi.pl ${server_dir}predict_seq_sa_multi.sh \$1 \$2 \$3 \$4 \n"; close SHELL; #generate script of predicting ss one single sequence from scratch(generate alignments too) #use homology ss and sa predictor open(SHELL, ">${bin_dir}predict_ssa.sh") || die "can't create predict_ssa.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "#predict ss, sa for a single sequence from scratch.\n"; print SHELL "if [ \$# -ne 2 ]\n"; print SHELL "then\n\techo \"need 2 parameters:seq_file(in fasta format), output_file.\" \n\texit 1\nfi\n"; print SHELL "#output: a file with predicted ss and sa.\n"; print SHELL "${script_dir}predict_ssa.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_ss.sh $script_dir \$1 \$2 \n"; close SHELL; #generate script of predicting ss one single sequence from scratch(generate alignments too) #use ab-initio predictor open(SHELL, ">${bin_dir}predict_ssa_ab.sh") || die "can't create predict_ssa_ab.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "#predict ss for a single sequence from scratch using ab-initio neural network.\n"; print SHELL "if [ \$# -ne 2 ]\n"; print SHELL "then\n\techo \"need 2 parameters:seq_file(in fasta format), output_file.\" \n\texit 1\nfi\n"; print SHELL "#output: a file with predicted ss and sa.\n"; print SHELL "${script_dir}predict_ssa_ab.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_ss.sh $script_dir \$1 \$2 \n"; close SHELL; #generate script of predicting ss and sa one single sequence from scratch(generate alignments too) #use homology ss and sa predictor open(SHELL, ">${bin_dir}predict_ss_sa.sh") || die "can't create predict_ssa.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "#predict ss, sa for a single sequence from scratch.\n"; print SHELL "if [ \$# -ne 2 ]\n"; print SHELL "then\n\techo \"need 2 parameters:seq_file(in fasta format), output_file.\" \n\texit 1\nfi\n"; print SHELL "#output: a file with predicted ss and sa.\n"; print SHELL "${script_dir}predict_ss_sa.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_ss.sh ${server_dir}predict_seq_sa.sh $script_dir \$1 \$2 \n"; close SHELL; #generate script of predicting sa one single sequence from scratch(generate alignments too) #use homology sa predictor open(SHELL, ">${bin_dir}predict_acc.sh") || die "can't create predict_acc.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "#predict sa for a single sequence from scratch.\n"; #print SHELL "if [ \$# -ne 3 ]\n"; #print SHELL "then\n\techo \"need 3 parameters:seq_file(in fasta format), output_file, threshold(0:0%,1:5%,...,5:25%,...19:95%).\" \n\texit 1\nfi\n"; print SHELL "if [ \$# -ne 2 ]\n"; print SHELL "then\n\techo \"need 2 parameters:seq_file(in fasta format), output_file\" \n\texit 1\nfi\n"; print SHELL "#output: a file with predicted ss and sa.\n"; #print SHELL "${script_dir}predict_acc.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_sa.sh $script_dir \$1 \$2 \$3\n"; print SHELL "${script_dir}predict_acc.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_sa.sh $script_dir \$1 \$2 \n"; close SHELL; #generate script of predicting sa one single sequence from scratch(generate alignments too) #use homology sa predictor open(SHELL, ">${bin_dir}predict_acc_multi.sh") || die "can't create predict_acc_multi.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "#predict sa for a single sequence from scratch.\n"; print SHELL "if [ \$# -ne 3 ]\n"; print SHELL "then\n\techo \"need 3 parameters:seq_file(in fasta format), output_file, threshold(0:0%,1:5%,...,5:25%,...19:95%).\" \n\texit 1\nfi\n"; print SHELL "#output: a file with predicted ss and sa.\n"; print SHELL "${script_dir}predict_acc_multi.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_sa.sh $script_dir \$1 \$2 \$3\n"; close SHELL; #generate script of predicting sa one single sequence from scratch(generate alignments too) #use ab-initio sa predictor open(SHELL, ">${bin_dir}predict_acc_ab.sh") || die "can't create predict_acc_ab.sh.\n"; print SHELL "#!/bin/sh\n"; print SHELL "#predict sa for a single sequence from scratch.\n"; #print SHELL "if [ \$# -ne 3 ]\n"; #print SHELL "then\n\techo \"need 3 parameters:seq_file(in fasta format), output_file, threshold(0:0%,1:5%,...,5:25%,...19:95%).\" \n\texit 1\nfi\n"; print SHELL "if [ \$# -ne 2 ]\n"; print SHELL "then\n\techo \"need 2 parameters:seq_file(in fasta format), output_file\" \n\texit 1\nfi\n"; print SHELL "#output: a file with predicted ss and sa.\n"; print SHELL "${script_dir}predict_acc_ab.pl $blast_dir $big_db $nr_db ${server_dir}predict_seq_sa.sh $script_dir \$1 \$2 \n"; close SHELL; `chmod 755 ${bin_dir}*.sh`; `chmod 755 ${server_dir}*`; `chmod 755 ${script_dir}*`;