=head1 SYNOPSIS
- jpred --sequence <fasta file> [--output <output prefix>] [--db <database>] [--psi <psiblast output>] [--pred-nohits] [--verbose] [--debug] [--help] [--man]
+./jpred.pl -in <FILE1> [-outfile <FILE2>] [-logfile <FILE3>] [-output <FILEPREFIX>] [-dbname <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>] [-pred-nohits] [-no-final] [-jabaws] [-verbose] [-debug] [-help] [-man]
=head1 DESCRIPTION
-This is a program which predicts the secondary structure of a sequence given a path to a FASTA sequence.
-It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet.
-
-The program is primarily design for use by the Jpred server, but it can be used directly by any user.
-Some of the output may not be meaningful if used directly - it can be safely ignored.
+This is a program for predicting the secondary structure of a multiple sequence alignment or a protein sequence.
+The input file can be stored in 3 formats: FASTA, MSF, or BLC.
+For the single sequence the program does all the PSI-BLAST searching, preparing PSSM and HMM profiles and
+predicting the secondary structure with Jnet. For the multiple sequence alignment only the HMM profile,
+created from the alignment, is used in Jnet.
=head1 OPTIONS
=over 5
-=item -sequence path to input FASTA file
+=item -in <FILE1>
+
+The path to the sequence file (in FASTA, MSF, or BLC format)
+
+=item -output <FILEPREFIX>
+
+A prefix to the filenames created by Jpred, defaults to the value set by -sequence/-in.
+
+=item -outfile <FILE2>
+
+An output file, by default it is undefined and the -output option is working
-The path to the sequence (in FASTA format) you want to predict.
+=item -logfile <FILE3>
-=item -output file
+Logging file, by default it is undefined and logging switched off
-A prefix to the filenames created by Jpred, defaults to the value set by --sequence.
+=item -dbpath PATH
-=item --db database
+Path to the uniref database used for PSI-BLAST querying. default value: .
-Database to use for PSI-BLAST querying. This only accepts databases from a list which is pre-defined in the code. Crap I know, but that's the way it is at the moment. It's probably best to stick the default for the time being.
+=item -dbname database
-Default: uniref90
+Database to use for PSI-BLAST querying. This only accepts databases from a list which is pre-defined in the code.
+Default value: uniref90
=item -psi path
Path to a PSIBLAST output file.
-=item --pred-nohits
+=item -ncpu NNN
+
+Number of CPU used by jpred.pl. Maximum value is 8
+Default: NNN = 1
+
+=item -pred-nohits
Toggle allowing Jpred to make predictions even when there are no PSI-BLAST hits.
-=item --verbose
+=item -no-final
+
+By default jpred generates a fasts file with sequences found with PSI-BLAST and predicted sequence features
+The option untoggles this step and stops jpred at the concise file generation
+
+=item -jabaws
+
+Redefines some basic variables in order to use the script within JABAWS
+
+=item -verbose
Verbose mode. Print more information while running jpred.
-=item --debug
+=item -debug
Debug mode. Print debugging information while running jpred.
-=item --help
+=item -help
Gives help on the programs usage.
-=item --man
+=item -man
Displays this man page.
Doesn't accept alignments.
-If you find any others please contact me.
+If you find any others please contact authors.
=head1 AUTHORS
use Data::Dumper;
use File::Temp;
-#use UNIVERSAL;
-
# path to Jpred modules
use FindBin qw($Bin);
use lib "$Bin/lib";
# internal jpred modules
use Jpred;
-use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin check_OS);
+use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin $alscript $readseq check_OS setup_env);
use HMMER::Profile;
use HMMER::Profile::Jnet;
use PSIBLAST;
#####################################################################################################
my $infile;
-my $output;
+my $infastafile;
+my $format;
+my $goal = "align";
+my $seqgoal;
+my $outfile;
+my $prefix;
my $psiblast;
-my $ncpu = 1; # number of CPUs for psiblast calculations
-my $predNoHits = 0; # define whether to make predictions when no PSI-BLAST hits are found
-my $db_path = ".";
-my $db_entry = "unknown";
+my $jabaws;
+my $logfile;
+my $ncpu = 1; # number of CPUs for psiblast calculations
+my $predNoHits = 0; # define whether to make predictions when no PSI-BLAST hits are found
+my $db_path = "/homes/www-jpred/databases";
+my $db_entry = "cluster";
+my $nofinal;
my ( $help, $man, $DEBUG, $VERBOSE );
GetOptions(
- "in|sequence=s" => \$infile,
- "out|output=s" => \$output,
- "psi=s" => \$psiblast,
- "dbname=s" => \$db_entry,
- "dbpath=s" => \$db_path,
- "ncpu=s" => \$ncpu,
- "pred-nohits" => \$predNoHits,
- "help" => \$help,
- "man" => \$man,
- "debug" => \$DEBUG,
- "verbose" => \$VERBOSE
+ "in=s" => \$infile,
+ "output=s" => \$prefix,
+ "outfile=s" => \$outfile,
+ "logfile=s" => \$logfile,
+ "psi=s" => \$psiblast,
+ "dbname=s" => \$db_entry,
+ "dbpath=s" => \$db_path,
+ "ncpu=s" => \$ncpu,
+ "pred-nohits" => \$predNoHits,
+ "no-final" => \$nofinal,
+ "jabaws" => \$jabaws,
+
+ "help" => \$help,
+ "man" => \$man,
+ "debug" => \$DEBUG,
+ "verbose" => \$VERBOSE
) or pod2usage(2);
pod2usage(1) if $help;
pod2usage( verbose => 2 ) if $man;
## database used for ported Jpred
ported_db => {
- database => $db_path . "/databases/uniref90.filt",
- unfiltered => $db_path . "/databases/uniref90",
+ database => $db_path . "/uniref90.filt",
+ unfiltered => $db_path . "/uniref90",
},
+
## cluster-specific path for Jpred
cluster => {
- database => "/homes/www-jpred/databases/uniref90.filt",
- unfiltered => "/homes/www-jpred/databases/uniref90",
+ database => $db_path . "/uniref90.filt",
+ unfiltered => $db_path . "/uniref90",
},
## these other DBs are experimental ones used during development.
## check they exist before using them.
+ # generic entry for use with validate_jnet.pl
+ # real db location defined by validate_jnet.pl
swall => {
-
- # generic entry for use with validate_jnet.pl
- # real db location defined by validate_jnet.pl
database => $db_path . "/swall/swall.filt",
unfiltered => $db_path . "/swall/swall",
},
+ # Path to PSIBLAST db
uniprot => {
-
- # Path to PSIBLAST db
database => $db_path . "/3/swall.filt",
unfiltered => $db_path . "/3/swall",
},
+
uniref50 => {
database => $db_path . "/6/swall.filt",
unfiltered => $db_path . "/6/swall",
},
};
-pod2usage(' --sequence argument not provided') unless $infile;
-die "--db $db_entry not recognised" unless exists $database->{$db_entry};
-$output = $infile . ".res" unless $output;
-$ncpu = 1 if ( 1 > $ncpu or 8 < $ncpu );
+my $dpf = $database->{$db_entry}{database}.'.pal';
+my $dpu = $database->{$db_entry}{unfiltered}.'.pal';
+pod2usage("ERROR! Input file should be provided with -sequence/-in") unless $infile;
+pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database") unless exists $database->{$db_entry};
+pod2usage("ERROR! UNIREF filtered database is not available at $dpf Use -dbpath and -dbname for configuring the database") unless -f $dpf;
+pod2usage("ERROR! UNIREF unfiltered database is not available at $dpu Use -dbpath and -dbname for configuring the database") unless -f $dpu;
-for ( [ "input", $infile ], [ "output", $output ], [ "psi", $psiblast ], [ "db", $db_entry ] ) {
+#####################################################################################################
+# lots of preparation steps
+if ( defined $prefix ) {
+ unless ( defined $outfile ) {
+ $outfile = $prefix . ".res.fasta";
+ }
+} else {
+ if ( defined $outfile ) {
+ print "WARNING! file prefix is not defined. Jpred will use $outfile.tmp as the prefix\n";
+ $prefix = $outfile . ".tmp";
+ } else {
+ print "WARNING! file prefix is not defined. Jpred will use $infile.res as the prefix\n";
+ $prefix = $infile . ".res";
+ $outfile = $prefix . ".jnet";
+ }
+}
+
+if ( 1 > $ncpu or 8 < $ncpu ) {
+ print "WARNING! the nuber of CPUs should be between 1 and 8. Jpred will use 1 CPU\n";
+ $ncpu = 1;
+}
+
+$VERBOSE = 1 if $DEBUG;
+
+my $LOG;
+if ( defined $logfile ) {
+ open( $LOG, ">", $logfile ) or die "ERROR! unable to open '$logfile': ${!}\nDied";
+}
+
+for ( [ "input file", $infile ], [ "out file", $outfile ], [ "outprefix", $prefix ], [ "psi", $psiblast ], [ "db name", $db_entry ], [ "db path", $db_path ] ) {
my ( $key, $value ) = @{$_};
defined $value or next;
- errlog( join( ": ", $key, $value ), "\n" );
+ my $par = join( ": ", $key, $value );
+ print "$par\n" if $DEBUG;
+ print $LOG "$par\n" if $LOG;
}
-#####################################################################################################
+if ( defined $jabaws ) {
+ setup_jpred_env($Bin);
+ setup_env($Bin);
+}
my $platform = check_OS();
print "JPRED: checking platiform... $platform\n" if $DEBUG;
+print $LOG "JPRED: checking platiform... $platform\n" if $LOG;
#####################################################################################################
-my $query = FASTA::File->new( read_file => $infile );
-
-my @seqs;
-my $psi = PSIBLAST->new;
-unless ( defined $psiblast && -e $psiblast ) {
- ## potentially a better set of parameters (esp. -b & -v) which avoid PSI-BLAST dying with large number of hits
- # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -F "m S"' # 'soft' filtering of the query sequence
- # args => '-e0.001 -h0.0001 -m6 -b10000 -v10000 -j3' # stricter searching criteria
- # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3'
- my $psi_run = PSIBLAST::Run->new(
- debug => $DEBUG,
- args => "-a" . $ncpu . " -e0.05 -h0.01 -m6 -b10000 -v10000 -j3",
- path => $psiblastbin,
- input => $infile,
- output => "$output.blast",
- matrix => "$output.profile",
- database => $database->{$db_entry}{database},
- );
-
- # For reduced databases, get the size of the orginal and use this as
- # the equivilent DB size
- if ( $db_entry =~ /^sp_red_/ ) {
- ( my $entry = $db_entry ) =~ s/^sp_red_/sp_/;
- $psi_run->args(
- $psi_run->args . " -z " . fasta_seq_length( $database->{$entry}{database} ) # CC sub is below
- );
+# check input file format
+my $nseq = check_FASTA_format($infile);
+if ( 0 < $nseq ) {
+ $format = "fasta";
+ if ( 1 == $nseq ) {
+ # one FASTA record
+ $goal = 'seq';
+ } else {
+ unless ( 0 < check_FASTA_alignment($infile)) {
+ die "\nERROR! jpred requires either FASTA alignment or 1 sequence in the FASTA, MSF, or BLC formats\n";
+ }
}
- print "BLAST matrix: $ENV{BLASTMAT}\n" if $DEBUG;
- print "BLASTDB path: $ENV{BLASTDB}\n" if $DEBUG;
-
- print "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $VERBOSE;
- $psi_run->run or die; # CC sub is from PSIBLAST::Run
-
- $psi->read_file("$output.blast"); # CC PSIBLAST.pm doesn't have a read_file(), but Read.pm does?
- system("gzip -9f $output.blast");
+} elsif ( 0 < check_MSF_format($infile) ) {
+ $format = "msf";
+} elsif ( 0 < check_BLC_format($infile) ) {
+ $format = "blc";
} else {
- if ( $psiblast =~ /.gz$/ ) { $psi->read_gzip_file($psiblast) } # CC PSIBALST.pm doesn't have a read_gzip_file() object, but Read.pm does?
- else { $psi->read_file($psiblast) } # CC ditto above
+ die "ERROR! unknown input file format for multiple sequence alignment (can be FASTA, MSF, or BLC). exit...\n";
}
+$infastafile = $infile . ".fasta" if ( 'msf' eq $format or 'blc' eq $format );
#####################################################################################################
-# Convert the last itteration into a collection of PSISEQ objects
-for ( $psi->get_all ) { # CC sub is from PSIBLAST.pm
- my ( $id, $start, $align ) = @{$_};
- push @seqs,
- PSISEQ->new(
- id => $id,
- start => $start,
- align => [ split( //, $align ) ]
+if ( 'seq' eq $goal ) {
+ my $query = FASTA::File->new( read_file => $infile );
+ my @seqs;
+ my $psi = PSIBLAST->new;
+ unless ( defined $psiblast && -e $psiblast ) {
+ ## potentially a better set of parameters (esp. -b & -v) which avoid PSI-BLAST dying with large number of hits
+ # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -F "m S"' # 'soft' filtering of the query sequence
+ # args => '-e0.001 -h0.0001 -m6 -b10000 -v10000 -j3' # stricter searching criteria
+ # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3'
+ my $psi_run = PSIBLAST::Run->new(
+ debug => $DEBUG,
+ args => "-a" . $ncpu . " -e0.05 -h0.01 -m6 -b10000 -v10000 -j3",
+ path => $psiblastbin,
+ input => $infile,
+ output => "$prefix.blast",
+ matrix => "$prefix.profile",
+ database => $database->{$db_entry}{database},
);
-}
+
+ # For reduced databases, get the size of the orginal and use this as
+ # the equivilent DB size
+ if ( $db_entry =~ /^sp_red_/ ) {
+ ( my $entry = $db_entry ) =~ s/^sp_red_/sp_/;
+ $psi_run->args(
+ $psi_run->args . " -z " . fasta_seq_length( $database->{$entry}{database} ) # CC sub is below
+ );
+ }
+ print "BLAST matrix: $ENV{BLASTMAT}\n" if $DEBUG;
+ print "BLASTDB path: $ENV{BLASTDB}\n" if $DEBUG;
+ print $LOG "BLAST matrix: $ENV{BLASTMAT}\n" if $LOG;
+ print $LOG "BLASTDB path: $ENV{BLASTDB}\n" if $LOG;
+
+ print "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $VERBOSE;
+ print $LOG "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $LOG;
+ $psi_run->run or die; # CC sub is from PSIBLAST::Run
+
+ $psi->read_file("$prefix.blast"); # CC PSIBLAST.pm doesn't have a read_file(), but Read.pm does?
+ system("gzip -9f $prefix.blast");
+ } else {
+ if ( $psiblast =~ /.gz$/ ) { $psi->read_gzip_file($psiblast) } # CC PSIBALST.pm doesn't have a read_gzip_file() object, but Read.pm does?
+ else { $psi->read_file($psiblast) } # CC ditto above
+ }
+
+#####################################################################################################
+ # Convert the last itteration into a collection of PSISEQ objects
+ for ( $psi->get_all ) { # CC sub is from PSIBLAST.pm
+ my ( $id, $start, $align ) = @{$_};
+ push @seqs,
+ PSISEQ->new(
+ id => $id,
+ start => $start,
+ align => [ split( //, $align ) ]
+ );
+ }
#####################################################################################################
-## When there are no PSI-BLAST hits generate an HMM from the query
-## and run Jnet against that only.
-## Accuracy won't be as good, but at least it's a prediction
-if ( @seqs == 0 ) {
- if ( $predNoHits == 0 ) {
- warn "\nJPRED: Warning! no PSI-BLAST hits found and '--pred-nohits' option not set. Exiting...\n";
- print ">>100% complete\n";
- exit;
+ # When there are no PSI-BLAST hits generate an HMM from the query and run Jnet against that only.
+ # Accuracy won't be as good, but at least it's a prediction
+ if ( @seqs == 0 ) {
+ if ( $predNoHits == 0 ) {
+ warn "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n";
+ print ">>100% complete\n";
+ print $LOG "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n" if $LOG;
+ print $LOG ">>100% complete\n" if $LOG;
+ close($LOG) if $LOG;
+ exit;
+ } else {
+ print ">>50% complete\n";
+ warn "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n";
+ print "Running HMMer on query...\n" if $VERBOSE;
+ print $LOG ">>50% complete\n" if $LOG;
+ print $LOG "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n" if $LOG;
+ print $LOG "Running HMMer on query...\n" if $LOG;
+
+ # copy input query to alignment
+ #system("cp $path $prefix.align") == 0 or croak "Error: unable to copy '$path'\n";
+ open( my $ifh, "<", $infile ) or die "JPRED: cannot open file $infile: $!";
+ open( my $ofh, ">", $prefix . ".align" ) or die "JPRED: cannot open file $prefix\.align: $!";
+ while (<$ifh>) { print $ofh, $_ }
+ close $ifh;
+ close $ofh;
+
+ # Temp files required for HMMer
+ my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2;
+ system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $infile");
+ system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out");
+ unlink $hmmbuild_out;
+
+ # Read in the HMMER file
+ my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out );
+
+ # Convert from HMMER::Profile to HMMER::Profile::Jnet
+ my $hmmer_jnet = HMMER::Profile::Jnet->new;
+ $hmmer_jnet->add_line( @{$_} ) for $hmmer->get_line;
+ $hmmer_jnet->write_file("$prefix.hmm");
+ print ">>70% complete\n";
+ print $LOG ">>70% complete\n" if $LOG;
+
+ # Run Jnet for the prediction
+ print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE;
+ print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG;
+ my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) );
+ print ">>90% complete\n";
+ print $LOG ">>90% complete\n" if $LOG;
+ print $jnetlog if $VERBOSE;
+ print $LOG $jnetlog if $LOG;
+ }
} else {
+ psiseq2fasta( "0.fasta.gz", @seqs ) if $DEBUG;
+ print ">>40% complete\n";
+ print $LOG ">>40% complete\n" if $LOG;
+
+ #####################################################################################################
+ # Make PSIBLAST truncated alignments the right length
+ print "Untruncating the PSIBLAST alignments...\n" if $VERBOSE;
+ print $LOG "Untruncating the PSIBLAST alignments...\n" if $LOG;
+ @seqs = extend( $query, @seqs );
+ psiseq2fasta( "1.fasta.gz", @seqs ) if $DEBUG;
+
+ #####################################################################################################
+ # Remove masking from PSIBLAST alignment
+ print "Unmasking the alignments...\n" if $VERBOSE;
+ print $LOG "Unmasking the alignments...\n" if $LOG;
+ my $idx = Index->new( type => "Index::FastaCMD" ) or die "Index type cannot be found.";
+ remove_seq_masks( $idx, $_ ) for @seqs[ 1 .. $#seqs ];
+ psiseq2fasta( "2.fasta.gz", @seqs ) if $DEBUG;
+
+ #####################################################################################################
+ # Convert the sequences to upper case
+ print "Converting sequences to the same case...\n" if $VERBOSE;
+ print $LOG "Converting sequences to the same case...\n" if $LOG;
+ toupper($_) for @seqs; # CC sub is below
+ psiseq2fasta( "${prefix}_backup.fasta.gz", @seqs );
+
+ #####################################################################################################
+ # Remove excessive sequences
+ print "Remove excessive sequences...\n" if $VERBOSE;
+ print $LOG "Remove excessive sequences...\n" if $LOG;
+ @seqs = reduce( $MAX_ALIGN, @seqs );
+ psiseq2fasta( "3.fasta.gz", @seqs ) if $DEBUG;
+
+ #####################################################################################################
+ # Remove sequences that are too long or too short
+ print "Remove sequences which too long or short...\n" if $VERBOSE;
+ print $LOG "Remove sequences which too long or short...\n" if $LOG;
+ @seqs = del_long_seqs( 50, @seqs );
+ psiseq2fasta( "4.fasta.gz", @seqs ) if $DEBUG;
+
+ #####################################################################################################
+ # Remove redundant sequences based upon pairwise identity and OC clustering
+ print "Remove redundant sequences...\n" if $VERBOSE;
+ print $LOG "Remove redundant sequences...\n" if $LOG;
+ @seqs = nonred( $NR_CUT, @seqs );
+ psiseq2fasta( "5.fasta.gz", @seqs ) if $DEBUG;
+
+ #####################################################################################################
+ # Check that we haven't got rid of all of the sequences
+ if ( @seqs < 2 ) {
+ warn "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n";
+ print $LOG "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n" if $LOG;
+ @seqs = fasta2psiseq("${prefix}_backup.fasta.gz");
+ }
+ unlink("${prefix}_backup.fasta.gz") unless $DEBUG;
+
+ # Remove gaps in the query sequence and same positions in the alignment
+ print "Removing gaps in the query sequence...\n" if $VERBOSE;
+ print $LOG "Removing gaps in the query sequence...\n" if $LOG;
+ degap(@seqs);
+ psiseq2fasta( "6.fasta.gz", @seqs ) if $DEBUG;
+
+ # Output the alignment for the prediction
+ print "Outputting cleaned-up PSI_BLAST alignment...\n" if $VERBOSE;
+ print $LOG "Outputting cleaned-up PSI_BLAST alignment...\n" if $LOG;
+ psiseq2fasta( "$prefix.align", @seqs );
+
+ #####################################################################################################
+ # Equivilent to getpssm script
+ print "Output the PSSM matrix from the PSI-BLAST profile...\n";
+ print $LOG "Output the PSSM matrix from the PSI-BLAST profile...\n" if $LOG;
+ my $pssm = PSIBLAST::PSSM->new( read_file => "$prefix.profile" );
+ $pssm->write_file("$prefix.pssm"); # CC write_file() sub is in Write.pm loaded via PSIBLAST::PSSM
print ">>50% complete\n";
- warn "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n";
- print "Running HMMer on query...\n" if $VERBOSE;
-
- # copy input query to alignment
- #system("cp $path $output.align") == 0 or croak "Error: unable to copy '$path'\n";
- open( my $ifh, "<", $infile ) or die "JPRED: cannot open file $infile: $!";
- open( my $ofh, ">", $output . ".align" ) or die "JPRED: cannot open file $output\.align: $!";
- while (<$ifh>) { print $ofh, $_ }
- close $ifh;
- close $ofh;
-
- # Temp files required for HMMer
- my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2;
-
- system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $infile");
- system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out");
-
- # Read in the HMMER file
- my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out );
-
- # Convert from HMMER::Profile to HMMER::Profile::Jnet
- my $hmmer_jnet = HMMER::Profile::Jnet->new;
- $hmmer_jnet->add_line( @{$_} ) for $hmmer->get_line;
- $hmmer_jnet->write_file("$output.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module
+ print $LOG ">>50% complete\n" if $LOG;
+
+ #####################################################################################################
+ # Run HMMER on the sequences
+ print "Running HMMer on sequences found by PSI-BLAST...\n" if $VERBOSE;
+ print $LOG "Running HMMer on sequences found by PSI-BLAST...\n" if $LOG;
+ my $hmmer = hmmer(@seqs); # CC sub is below
+ $hmmer->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module
print ">>70% complete\n";
-
+ print $LOG ">>70% complete\n" if $LOG;
+#####################################################################################################
# Run Jnet for the prediction
- print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE;
- jnet( map { "$output.$_" } qw(hmm jnet) ); # CC sub is below
+ print "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $VERBOSE;
+ print $LOG "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $LOG;
+ my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet pssm) ); # CC sub is below
+ print ">>90% complete\n";
+ print $LOG ">>90% complete\n" if $LOG;
+ print $jnetlog if $VERBOSE;
+ print $LOG $jnetlog if $LOG;
}
} else {
- psiseq2fasta( "0.fasta.gz", @seqs ) if $DEBUG; # CC sub is below
- print ">>40% complete\n";
-
- #####################################################################################################
- # Make PSIBLAST truncated alignments the right length
- print "Untruncating the PSIBLAST alignments...\n" if $VERBOSE;
- @seqs = extend( $query, @seqs ); # CC sub si below
- psiseq2fasta( "1.fasta.gz", @seqs ) if $DEBUG;
-
- #####################################################################################################
- # Remove masking from PSIBLAST alignment
- print "Unmasking the alignments...\n" if $VERBOSE;
- my $idx = Index->new( type => "Index::FastaCMD" ) or die "Index type cannot be found.";
- remove_seq_masks( $idx, $_ ) for @seqs[ 1 .. $#seqs ];
- psiseq2fasta( "2.fasta.gz", @seqs ) if $DEBUG;
-
- #####################################################################################################
- # Convert the sequences to upper case
- print "Converting sequences to the same case...\n" if $VERBOSE;
- toupper($_) for @seqs; # CC sub is below
- psiseq2fasta( "${output}_backup.fasta.gz", @seqs );
-
- #####################################################################################################
- # Remove excessive sequences
- print "Remove excessive sequences...\n" if $VERBOSE;
- @seqs = reduce( $MAX_ALIGN, @seqs );
- psiseq2fasta( "3.fasta.gz", @seqs ) if $DEBUG;
-
- #####################################################################################################
- # Remove sequences that are too long or too short
- print "Remove sequences which too long or short...\n" if $VERBOSE;
- @seqs = del_long_seqs( 50, @seqs );
- psiseq2fasta( "4.fasta.gz", @seqs ) if $DEBUG;
-
- #####################################################################################################
- # Remove redundant sequences based upon pairwise identity and OC clustering
- print "Remove redundant sequences...\n" if $VERBOSE;
- @seqs = nonred( $NR_CUT, @seqs );
- psiseq2fasta( "5.fasta.gz", @seqs ) if $DEBUG;
-
- #####################################################################################################
- # Check that we haven't got rid of all of the sequences
- if ( @seqs < 2 ) {
- warn "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n";
- @seqs = fasta2psiseq("${output}_backup.fasta.gz");
- }
- unlink("${output}_backup.fasta.gz") unless $DEBUG;
-
- # Remove gaps in the query sequence and same positions in the alignment
- print "Removing gaps in the query sequence...\n" if $VERBOSE;
- degap(@seqs);
- psiseq2fasta( "6.fasta.gz", @seqs ) if $DEBUG;
-
- # Output the alignment for the prediction
- print "Outputting cleaned-up PSI_BLAST alignment...\n" if $VERBOSE;
- psiseq2fasta( "$output.align", @seqs );
-
- #####################################################################################################
- # Equivilent to getpssm script
- print "Output the PSSM matrix from the PSI-BLAST profile...\n";
- my $pssm = PSIBLAST::PSSM->new( read_file => "$output.profile" );
- $pssm->write_file("$output.pssm"); # CC write_file() sub is in Write.pm loaded via PSIBLAST::PSSM
- print ">>50% complete\n";
-
- #####################################################################################################
- # Run HMMER on the sequences
- print "Running HMMer on sequences found by PSI-BLAST...\n" if $VERBOSE;
- my $hmmer = hmmer(@seqs); # CC sub is below
- $hmmer->write_file("$output.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module
+ if ( 'fasta' eq $format ) {
+ print "Read FASTA file\n";
+ my $hmmer1 = hmm_for_align($infile);
+ $hmmer1->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module
+ } elsif ( 'msf' eq $format ) {
+ msf2fasta( $infile, $infastafile );
+ my $hmmer2 = hmm_for_align($infastafile);
+ $hmmer2->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module
+ } elsif ( 'blc' eq $format ) {
+ my $tmpfile = File::Temp->new->filename;
+ blc2msf( $infile, $tmpfile );
+ msf2fasta( $infile, $infastafile );
+ my $hmmer3 = hmm_for_align($infastafile);
+ $hmmer3->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module
+ } else {
+ die "ERROR! unknown input format '$format'. exit...\n";
+ }
print ">>70% complete\n";
-
- #####################################################################################################
+ print $LOG ">>70% complete\n" if $LOG;
+#####################################################################################################
# Run Jnet for the prediction
- print "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $VERBOSE;
- jnet( map { "$output.$_" } qw(hmm jnet pssm) ); # CC sub is below
+ print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE;
+ print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG;
+ my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) ); # CC sub is below
+ print ">>90% complete\n";
+ print $LOG ">>90% complete\n" if $LOG;
+ print $jnetlog if $VERBOSE;
+ print $LOG $jnetlog if $LOG;
+}
+
+unless ( defined $nofinal ) {
+ my $aligfile = $prefix . ".align";
+ my $jnetfile = $prefix . ".jnet";
+ my $jnetfastafile = $prefix . ".jnet.fasta";
+ $aligfile = $infile if ( 'fasta' eq $format );
+ $aligfile = $infastafile if ( 'msf' eq $format or 'blc' eq $format );
+ concise2fasta( $jnetfile, $jnetfastafile );
+ open( my $IN1, "<", $aligfile ) or die "ERROR! unable to open '$aligfile': ${!}\nDied";
+ open( my $IN2, "<", $jnetfastafile ) or die "ERROR! unable to open '$jnetfastafile': ${!}\nDied";
+ open( my $OUT, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
+ while (<$IN2>) { print $OUT $_; }
+ while (<$IN1>) { print $OUT $_; }
+ close($IN1);
+ close($IN2);
+ close($OUT);
+ unlink $jnetfastafile;
+ my $seqs = FASTA::File->new( read_file => $outfile );
+ open( my $OUT2, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\n";
+ $seqs->write($OUT2);
+ close($OUT2);
+} else {
+ if ( defined $outfile and $prefix . ".jnet" ne $outfile ) {
+ rename $prefix . ".jnet", $outfile;
+ }
}
print ">>100% complete\n";
print "Jpred Finished\n";
+print $LOG ">>100% complete\n" if $LOG;
+print $LOG "Jpred Finished\n" if $LOG;
+close($LOG) if $LOG;
exit;
#####################################################################################################
# Functions
#####################################################################################################
+sub check_FASTA_format {
+ my $infile = shift;
+
+ open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n";
+ my $check_first_line = 1;
+ my $nseq = 0;
+ local $/ = "\n>";
+ while (<$IN>) {
+ if ($check_first_line) {
+ return 0 unless (/^>/);
+ $check_first_line = 0;
+ }
+ s/^>//g;
+ s/>$//g;
+
+ my ( $id, @seqs ) = split /\n/, $_;
+ return 0 unless ( defined $id or @seqs );
+ my $seq = join( "", @seqs );
+ return 0 unless ( $seq =~ /[a-zA-Z\.-]/ );
+ ++$nseq;
+ }
+ close($IN);
+
+ return $nseq;
+}
+#####################################################################################################
+sub check_FASTA_alignment {
+ my $infile = shift;
+
+ open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n";
+ my $check_first_line = 1;
+ my $nseq = 0;
+ my $seqlen = -1;
+ local $/ = "\n>";
+ while (<$IN>) {
+ if ($check_first_line) {
+ return 0 unless (/^>/);
+ $check_first_line = 0;
+ }
+ s/^>//g;
+ s/>$//g;
+
+ my ( $id, @seqs ) = split /\n/, $_;
+ return 0 unless ( defined $id or @seqs );
+ my $seq = join( "", @seqs );
+ return 0 unless ( $seq =~ /[a-zA-Z\.-]/ );
+ if (-1 == $seqlen) {
+ $seqlen = length ($seq);
+ } else {
+ return 0 if ($seqlen != length ($seq) );
+ }
+ ++$nseq;
+ }
+ close($IN);
+
+ return $nseq;
+}
+#####################################################################################################
+sub check_MSF_format {
+ my $infile = shift;
+ $? = 0;
+ system("$readseq -fMSF -a -p < $infile > /dev/null");
+ return 0 if ($?);
+
+ return 1;
+}
+#####################################################################################################
+sub check_BLC_format {
+ my $infile = shift;
+
+ my ( $tmpfile1, $tmpfile2 ) = map { File::Temp->new->filename } 1 .. 2;
+ open my $fh, ">$tmpfile1" or die "$tmpfile1: $!\n";
+ print $fh "silent_mode\nblock_file $infile\n";
+ print $fh "output_file /dev/null\nmax_nseq 2000\n";
+ print $fh "pir_save $tmpfile2\nsetup\n";
+ close $fh;
+
+ $? = 0;
+ system("$alscript -s -f $tmpfile1");
+ $? = 0;
+ system("$readseq -f8 -a -p < $tmpfile2 > /dev/null");
+ unlink $tmpfile1;
+ unlink $tmpfile2;
+ return 0 if ($?);
+
+ return 1;
+}
+############################################################################################################################################
+# convertor BLC -> MSF
+sub msf2fasta {
+ my $infile = shift;
+ my $outfile = shift;
+
+ my $sequence = "";
+ open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n";
+ while (<$IN>) {
+ $sequence .= $_;
+ }
+ close($IN);
+
+ $sequence =~ s/~/\./g;
+
+ ## check for non-unique sequence names - readseq has problems with these
+ my @lines = split /\n/, $sequence;
+ my %names;
+ foreach my $line (@lines) {
+ if ( $line =~ /Name:\s+(\S+)/ ) {
+ die "ERROR! Alignment has non-unique sequence ids. exit...\n" if ( defined( $names{$1} ) && $names{$1} >= 1 );
+ $names{$1}++;
+ }
+ }
+
+ my $tmpfile1 = File::Temp->new->filename;
+ my $tmpfile2 = File::Temp->new->filename;
+ open my $FILE, ">$tmpfile1" or die "open $tmpfile1 failed: $!";
+ print $FILE $sequence;
+ close $FILE;
+
+ $? = 0;
+ system("$readseq -fMSF -a -p < $tmpfile1 > $tmpfile2");
+ die "Reformatting of $infile failed. exit...\n" if ($?);
+ unlink $tmpfile1;
+
+ $? = 0;
+ system("$readseq -f8 -a -p < $tmpfile2 > $outfile");
+ die "Reformatting of $infile failed. exit...\n" if ($?);
+ unlink $tmpfile2;
+
+ die "Reformatting the input alignment has failed. exit...\n" unless ( -e $outfile );
+}
+
+############################################################################################################################################
+# convertor BLC -> MSF
+sub blc2msf {
+ my ( $in, $out ) = @_;
+
+ my ( $tmp, $tmp_pir ) = map { File::Temp->new->filename } 1 .. 2;
+
+ open my $fh, ">$tmp" or die "$tmp: $!\n";
+ print $fh "silent_mode\nblock_file $infile\n";
+ print $fh "output_file /dev/null\nmax_nseq 2000\n";
+ print $fh "pir_save $tmp_pir\nsetup\n";
+ close $fh;
+
+ $? = 0;
+ system("$alscript -s -f $tmp");
+ die "Reformatting of $infile failed. exit...\n" if ($?);
+ system("$readseq -f=MSF -o=$out -a $tmp_pir");
+
+ unlink $tmp;
+ unlink $tmp_pir;
+}
+
+#####################################################################################################
+
+=begin :private
+
+=head2 fasta2concise ($infile, $outfile)
+
+Convert a file with PSI-BLAST sequences and prediction in the fasta format into concise file
+
+=cut
+
+sub fasta2concise {
+ my $infile = shift;
+ my $outfile = shift;
+
+ open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\nDied";
+ my ( $seq, @seqs, @title );
+ while (<$IN>) {
+ if (s/^>//) {
+ if ($seq) {
+ $seq =~ s/\n|\s//g;
+ $seq =~ s/(.)/$1,/g;
+ push @seqs, $seq;
+ $seq = "";
+ }
+ chomp;
+ push @title, $_;
+ } else {
+ chomp;
+ $seq .= $_;
+ }
+ }
+ $seq =~ s/\n|\s//g;
+ $seq =~ s/(.)/$1,/g;
+ push @seqs, $seq;
+ close($IN);
+
+ if ( @title != @seqs ) {
+ die("non matching number of titles and sequences!\n");
+ }
+
+ open( my $OUT, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
+ foreach ( 0 .. $#title ) {
+ print $OUT "align" . ( $_ + 1 ) . ";$title[$_]:$seqs[$_]\n";
+ }
+ close($OUT);
+}
+
+=begin :private
+
+=head2 concise2fasta ($infile, $outfile)
+
+Convert a file with PSI-BLAST sequences and prediction in the concise format into fasta file
+
+=cut
+
+#####################################################################################################
+sub concise2fasta {
+ my $infile = shift;
+ my $outfile = shift;
+
+ my ( @seqs, %seq, @pred, %pred );
+
+ my @var = (
+ "Lupas_21", "Lupas_14", "Lupas_28", "MULTCOIL", "MULTCOIL_TRIMER", "MULTCOIL_DIMER", "JNETPSSM", "JNETFREQ",
+ "JNETALIGN", "JNETHMM", "JNETSOL5", "JNETSOL25", "JNETSOL0", "jnetpred", "jpred"
+ );
+
+ # parse input concise file
+ open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\nDied";
+ while (<$IN>) {
+ unless (/^\n/) {
+ my ( $id, $seq ) = split( ":", $_ );
+ if ( defined $id and defined $seq ) { # Check we have proper values
+ $seq =~ s/,//g;
+ chomp $seq;
+ if ( $id =~ /;/ ) { # Then it's an alignment
+ @_ = split( ";", $id );
+ push @seqs, $_[1];
+ $seq{ $_[1] } = $seq;
+ }
+ foreach my $v (@var) {
+ if ( $v eq $id ) {
+ push @pred, $v;
+ $pred{$v} = $seq;
+ }
+ }
+ }
+ }
+ }
+ close($IN);
+
+ open( my $OUT, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
+
+ # print out sequences found with PSI-BLAST
+ foreach (@seqs) {
+ $seq{$_} =~ s/(.{72})/$1\n/g;
+ print $OUT ">$_\n$seq{$_}\n";
+ }
+
+ # print out predictions
+ foreach my $p (@pred) {
+ $pred{$p} =~ s/[TCYWXZSI\?_]/-/g;
+ $pred{$p} =~ s/B/E/g;
+ $pred{$p} =~ s/G/H/g;
+
+ if ( $p =~ /SOL/ ) {
+ $pred{$p} =~ s/E/B/g;
+ }
+ $pred{$p} =~ s/(.{72})/$1\n/g;
+ print $OUT ">$p\n$pred{$p}\n";
+ }
+ close($OUT);
+}
=begin :private
=cut
+#################################################################################################################################################
+
+=head2 get_hmm($alignFile, $name)
+
+Adapted from the hmmer() function in Jpred as written by JDB.
+
+Generates an HMMer profile output compatible with Jnet.
+
+Equivilent to gethmm script.
+
+=cut
+
+sub hmm_for_align {
+ my $fastafile = shift;
+
+ # Temp files required
+ print "hmm_for_align: fastafile = $fastafile\n";
+ my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2;
+
+ system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $fastafile");
+ system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out");
+
+ # Read in the HMMER file
+ my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out );
+
+ # Read in the HMMER file
+ my $hmmer_tmp = HMMER::Profile->new( read_file => $hmmconvert_out );
+
+ # Convert from HMMER::Profile to HMMER::Profile::Jnet
+ my $hmmer_jnet = HMMER::Profile::Jnet->new;
+ $hmmer_jnet->add_line( @{$_} ) for $hmmer_tmp->get_line;
+
+ return $hmmer_jnet;
+}
+
#####################################################################################################
sub jnet {
my ( $hmmer, $outfile, $pssm ) = @_;
system("$jnet --concise --hmmer $hmmer > $outfile");
}
check( "jnet", $? ) or exit 1;
+ my $res = "";
+ my $logging = "";
+ open( my $IN, "<", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
+ while (<$IN>) {
+ if (/^jnetpred:|^JNET[A-Z0-9]+:/) {
+ $res .= $_;
+ } else {
+ $logging .= $_;
+ }
+ }
+ close $IN;
+ open( my $OUT, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
+ print $OUT "\n" . $res;
+ close $OUT;
+ return $logging;
}
=head1 psiseq2fasta($path, @PSISEQ)
return @seqs;
}
+#####################################################################################################
+
=head1 extend($FASTA::File, @PSISEQ)
Sometimes PSIBLAST truncates the outputed alignment where it can't matched residues
=cut
-#####################################################################################################
sub extend {
my ( $query, @seqs ) = @_;
return @seqs;
}
+#####################################################################################################
+
=head1 $int = fasta_seq_length($path)
Given the path to a FASTA database, find the number of residues/bases in it. Counts whitespace as a residue.
=cut
-#####################################################################################################
sub fasta_seq_length {
my ($fn) = @_;
open my $fh, $fn or croak "Can't open file $fn: $!\n";
return $length;
}
-
-=head1 log(@messages)
-
-Report messages to STDERR
-
-=cut
-
-#####################################################################################################
-sub errlog { print STDERR @_ }
git://source.jalview.org / jabaws.git / blobdiff