Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

[jabaws.git] / binaries / src / jpred / jpred.pl

diff --git a/binaries/src/jpred/jpred.pl b/binaries/src/jpred/jpred.pl
index 99d7fdc..bd23814 100755 (executable)
--- a/binaries/src/jpred/jpred.pl
+++ b/binaries/src/jpred/jpred.pl
@@ -6,14 +6,15 @@ jpred - Secondary structure prediction program
 
 =head1 SYNOPSIS
 
-./jpred.pl -in <FILE1> [-outfile <FILE2>] [-logfile <FILE3>] [-output <FILEPREFIX>] [-dbname <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>] [-seq] [-pred-nohits] [-no-final] [-jabaws] [-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 for predicting the secondary structure of a multiple sequence alignment (by default) or a protein sequence 
-(with the -seq option). 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.
+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
 
@@ -23,10 +24,6 @@ secondary structure with Jnet. For the multiple sequence alignment only the HMM
 
 The path to the sequence file (in FASTA, MSF, or BLC format)
 
-=item -seq
-
-The input file is a FASTA file with one sequence only.
-
 =item -output <FILEPREFIX>
 
 A prefix to the filenames created by Jpred, defaults to the value set by -sequence/-in.
@@ -211,7 +208,6 @@ GetOptions(
   "ncpu=s"      => \$ncpu,
   "pred-nohits" => \$predNoHits,
   "no-final"    => \$nofinal,
-  "seq"         => \$seqgoal,
   "jabaws"      => \$jabaws,
 
   "help"    => \$help,
@@ -222,8 +218,6 @@ GetOptions(
 pod2usage(1) if $help;
 pod2usage( verbose => 2 ) if $man;
 
-$goal = "seq" if ( defined $seqgoal );
-
 #####################################################################################################
 # Key to database information and information for accessing them
 my $database = {
@@ -327,25 +321,23 @@ print $LOG "JPRED: checking platiform... $platform\n" if $LOG;
 
 #####################################################################################################
 # check input file format
-if ( 'seq' eq $goal ) {
-  $format = "seq";
-  if ( 1 != check_FASTA_format($infile) ) {
-    die "\nERROR! jpred requires 1 sequence in the FASTA file if the option -seq used. exit\n";
-  }
-} else {
-  my $nseq = check_FASTA_format($infile);
-  if ( 0 < $nseq ) {
-    $format = "fasta";
-    if ( 1 == $nseq ) {
-      die "\nERROR! jpred requires alignment with more than 1 sequence\n       if you provide only one sequence use the -seq option.\n";
-    }
-  } elsif ( 0 < check_MSF_format($infile) ) {
-    $format = "msf";
-  } elsif ( 0 < check_BLC_format($infile) ) {
-    $format = "blc";
+my $nseq = check_FASTA_format($infile);
+if ( 0 < $nseq ) {
+  $format = "fasta";
+  if ( 1 == $nseq ) {
+    # one FASTA record
+    $goal = 'seq';
   } else {
-    die "ERROR! unknown input file format for multiple sequence alignment (can be FASTA, MSF, or BLC). exit...\n";
+    unless ( 0 < check_FASTA_alignment($infile)) {
+      die "\nERROR! jpred requires either FASTA alignment or 1 sequence in the FASTA, MSF, or BLC formats\n";
+    }
   }
+} elsif ( 0 < check_MSF_format($infile) ) {
+  $format = "msf";
+} elsif ( 0 < check_BLC_format($infile) ) {
+  $format = "blc";
+} else {
+  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 );
 
@@ -645,6 +637,38 @@ sub check_FASTA_format {
   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;