--- /dev/null
+#!/usr/bin/perl
+
+#####################################################################
+# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp)
+#
+# Ver. Date Changelog
+#####################################################################
+# 1.0 07.26.13 Initial release
+# 2.0 09.03.13 Added extensive warnings and error messages
+# 3.0 10.28.13 Fix for retrieving large files. Added STDERR logs
+# 3.1 11.08.13 Added LWP failsafe. Made hat3 not a required output
+# 3.2 12.08.14 Removed 5-char restriction for own structure files
+#
+#####################################################################
+
+use strict;
+use Getopt::Long;
+use File::Path qw(make_path remove_tree);
+use LWP::Simple;
+use LWP::UserAgent;
+
+# to prevent error 'Header line too long (limit is 8192)' [v3.1]
+use LWP::Protocol::http;
+push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
+
+
+
+my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft";
+
+my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE );
+
+GetOptions
+(
+ 'd=s' => \$WORKDIR,
+ 'p=s' => \$PDBLIST,
+ 'o=s' => \$OWNLIST,
+ 'h=s' => \$HAT3FILE,
+ 'i=s' => \$INSTRFILE,
+);
+
+print STDERR "[MAFFTash-premafft]\n";
+
+# set temp directory
+my $TMP = "/tmp/mapremafft$$";
+make_path($TMP) unless -d $TMP;
+
+
+
+######
+# validation
+&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST);
+&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR;
+
+$HAT3FILE = "hat3" unless defined $HAT3FILE;
+$INSTRFILE = "instr" unless defined $INSTRFILE;
+chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g;
+
+
+######
+# prepare inputs
+print STDERR "Preparing inputs for service request...\n";
+
+my @files = ();
+push(@files, "strweight" => "0.5");
+push(@files, "premafft" => "1");
+
+
+# pdb entries
+if ( defined $PDBLIST )
+{
+ print STDERR "PDB List defined!\n";
+ &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST;
+ my $listfile = "$TMP/pdblist.inp";
+
+
+ open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!");
+ open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!");
+
+ while(<INPF>)
+ {
+ chomp;
+ if ( /^(\w{5})$/ )
+ {
+ print OUTF ">PDBID\n$1\n";
+ }
+ }
+
+ close OUTF;
+ close INPF;
+
+ push(@files, "inputfile" => ["$listfile"]);
+}
+
+
+
+# upload own structures
+my %ownids = ();
+
+if ( defined $OWNLIST )
+{
+ print STDERR "OWN List defined!\n";
+ &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST;
+
+
+ open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!");
+
+ while(<OWNINPF>)
+ {
+ chomp;
+
+ if ( /^(\S+)$/ )
+ {
+ my $fileref = "$WORKDIR/$1.pdb";
+
+ unless (-e $fileref)
+ {
+ close OWNINPF;
+ &bail("Error: File $fileref does not exists!");
+ }
+
+ push(@files, "inputownfile[]" => ["$fileref"]);
+ $ownids{$1} = 1;
+ }
+ }
+
+ close OWNINPF;
+}
+
+
+
+######
+# start rest service
+print STDERR "Sending service request...\n";
+
+my $browser = LWP::UserAgent->new;
+$browser->timeout(0);
+
+
+# post: running a mafftash job
+my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' );
+&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success);
+
+
+# get response from post request
+my ($status, $mafftashid) = &parseResponse($postResponse->content);
+
+
+
+my $MAXTRIES = 3;
+my $STIMER = 4;
+my $longtimer = 0;
+
+print STDERR "Request sent! Waiting for response...[$mafftashid]\n";
+
+
+# wait for results until it becomes available
+while(1)
+{
+ $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER;
+ sleep $longtimer;
+
+
+ # get: get results for mafftash job
+ my $getResponse = $browser->get("$BASEURL/$mafftashid");
+
+ if ( $getResponse->is_success )
+ {
+
+ # get response from get request
+ ($status, $mafftashid) = &parseResponse($getResponse->content);
+ next unless ( $status eq "done" );
+
+
+ # if job is finished and ready
+ print STDERR "Results found!\n";
+ my $csfile = "$TMP/checksum.tar.gz";
+ my $try1 = 1;
+
+
+ while(1)
+ {
+ print STDERR "Fetching Results... [Trial $try1]\n";
+
+ if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile )
+ {
+ # get response from get request
+ my $checklist = &extractchecksum($csfile);
+ &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
+
+
+ foreach my $id ( keys %$checklist )
+ {
+ my $checkfile = "$TMP/$id";
+ my $checkid = $checklist->{$id};
+ my $try2 = 1;
+
+ while(1)
+ {
+ unlink $checkfile if -e $checkfile;
+
+ if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
+ {
+ my $hashid = &getchecksum($checkfile);
+ #print STDERR "[hashid]$hashid [checkid]$checkid\n";
+
+ if ($hashid ne "" && $hashid ne $checkid )
+ {
+ unlink $checkfile if -e $checkfile;
+ &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
+ $try2++;
+ sleep $STIMER;
+ }
+ else
+ {
+ last;
+ }
+ }
+ else
+ {
+ &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
+ $try2++;
+ sleep $STIMER;
+ }
+ }
+ }
+
+ last;
+ }
+ else
+ {
+ &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
+ $try1++;
+ sleep $STIMER;
+ }
+ }
+
+ last;
+
+ }
+ else
+ {
+ &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content)));
+ }
+
+}
+
+
+# make sure outputs were generated
+# decompress
+print STDERR "Assembling final results...\n";
+
+&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/");
+&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr";
+&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3";
+
+# sometimes no hat3 file is generated [v3.1]
+#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE;
+&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE;
+
+
+# warn if some ownids were ommitted
+if ( scalar keys(%ownids) > 0 )
+{
+ my %instrids = ();
+
+ open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!");
+
+ while(<INSTRF>)
+ {
+ chomp;
+
+ if ( /^>\d+_(\S+)$/ )
+ {
+ $instrids{$1} = 1;
+ }
+ }
+
+ close INSTRF;
+
+ foreach my $id ( keys %ownids )
+ {
+ warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id};
+ }
+
+}
+
+
+
+&cleanup();
+
+
+
+####################
+####################
+
+
+
+sub parseResponse
+{
+ my $response = shift;
+
+ #"status":"wait","mafftashid":"Ma8211432R"
+
+ my $status = "";
+ my $mafftashid = "";
+
+ if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
+ {
+ $mafftashid = $1;
+ $status = $2;
+ }
+
+ return ($status, $mafftashid);
+
+}
+
+
+sub extractchecksum
+{
+ my $infile = shift;
+ my %dataset = ();
+
+ open CSUM, "tar -zxf $infile -O|" or return \%dataset;
+
+ while(<CSUM>)
+ {
+ chomp;
+ if ( /^(\S+)\s+(\S+)$/ )
+ {
+ $dataset{$2} = $1;
+ }
+
+ }
+
+ close CSUM;
+
+ return \%dataset;
+
+}
+
+
+sub parseError
+{
+ my $response = shift;
+
+ #"error":"Invalid number of inputs found."
+ my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : "";
+ return $errorstr;
+}
+
+
+sub getchecksum
+{
+ my $infile = shift;
+
+ # md5 binary check
+ my $MD5BIN = "";
+
+ if ( -x "/usr/bin/md5sum" )
+ {
+ $MD5BIN = "/usr/bin/md5sum";
+ }
+ elsif ( -x "/sbin/md5" )
+ {
+ $MD5BIN = "/sbin/md5 -q";
+ }
+
+ return "" if $MD5BIN eq "";
+
+
+ my $checksum = "";
+ open MD5EXE, "$MD5BIN $infile|" or return "";
+
+ while(<MD5EXE>)
+ {
+ if (/^(\S+)\s+(\S+)$/)
+ {
+ $checksum = $1;
+ last;
+ }
+ elsif (/^(\S+)$/)
+ {
+ $checksum = $1;
+ last;
+ }
+ }
+
+ close MD5EXE;
+
+ return $checksum;
+
+}
+
+
+sub backticks
+{
+ my $command = shift;
+
+ `$command`;
+ return ($? == -1) ? 0 : 1;
+}
+
+
+sub bail
+{
+ my $str = shift;
+ print STDERR "$str\n" if defined $str;
+
+ &cleanup();
+ exit(1);
+}
+
+
+sub cleanup
+{
+ return if ($TMP eq "" || !-d $TMP);
+
+ opendir(MAINDIR, $TMP);
+ my @files = readdir(MAINDIR);
+ closedir(MAINDIR);
+
+ foreach my $file (@files)
+ {
+ unlink "$TMP/$file" if -e "$TMP/$file";
+ }
+
+ remove_tree($TMP);
+
+}
+
+
+sub help
+{
+ my $str = shift;
+
+ print <<'HELPME';
+
+USAGE
+ ./mafftash_premafft.pl -p [FILE]
+ ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY]
+ ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY]
+
+
+PARAMETERS
+ -p [FILE]
+ FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format
+
+ -o [FILE] -d [DIRECTORY]
+ FILE contains a list of IDs from your own structure/pdb files (one entry per line)
+ for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY
+
+ -h [HATFILE]
+ save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory
+
+ -i [INSTRFILE]
+ save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory
+
+HELPME
+
+ &bail($str);
+}
+
+
+
git://source.jalview.org / jabaws.git / blobdiff