[Bioperl-guts-l] bioperl-live/scripts/searchio fastam9_to_table.PLS, 1.5, 1.6

[Jason Stajich]

Update of /home/repository/bioperl/bioperl-live/scripts/searchio
In directory pub.open-bio.org:/tmp/cvs-serv29148

Modified Files:
	fastam9_to_table.PLS 
Log Message:
deal with TFASTX [f] or [r] fields, properly report querylen as well for these


Index: fastam9_to_table.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/searchio/fastam9_to_table.PLS,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** fastam9_to_table.PLS	4 Mar 2005 15:56:41 -0000	1.5
--- fastam9_to_table.PLS	25 Apr 2005 19:24:22 -0000	1.6
***************
*** 1,4 ****
! #!perl -w
! use strict;
  
  =head1 NAME 
--- 1,3 ----
! #!/usr/bin/perl -w
  
  =head1 NAME 
***************
*** 24,49 ****
  with the standard NCBI -m9 columns.
  
!   queryname
!   hit name
!   percent identity
!   alignment length
!   number mismatches 
!   number gaps
!   query start  (if on rev-strand start > end)
!   query end 
!   hit start (if on rev-strand start > end)
!   hit end 
!   evalue
!   bit score
  
  Additionally 3 more columns are provided
! 
!   fasta score
!   sw-score
!   percent similar
!   query length
!   hit length
!   query gaps
!   hit gaps
  
  =head1 AUTHOR - Jason Stajich
--- 23,47 ----
  with the standard NCBI -m9 columns.
  
!  queryname
!  hit name
!  percent identity
!  alignment length
!  number mismatches 
!  number gaps
!  query start  (if on rev-strand start > end)
!  query end 
!  hit start (if on rev-strand start > end)
!  hit end 
!  evalue
!  bit score
  
  Additionally 3 more columns are provided
!  fasta score
!  sw-score
!  percent similar
!  query length
!  hit length
!  query gaps
!  hit gaps
  
  =head1 AUTHOR - Jason Stajich
***************
*** 53,57 ****
  =cut
  
! 
  use Getopt::Long;
  my $hitsection = 0;
--- 51,55 ----
  =cut
  
! use strict;
  use Getopt::Long;
  my $hitsection = 0;
***************
*** 80,84 ****
  
  my @fields = qw(qname hname percid alen mmcount gapcount 
! 		qstart qend hstart hend evalue score bits score sw-score 
  		percsim qlen hlen qgap hgap);
  print $outfh "#",uc(join("", map{ sprintf("%-10s",$_) } @fields)), "\n" if $header;
--- 78,82 ----
  
  my @fields = qw(qname hname percid alen mmcount gapcount 
! 		qstart qend hstart hend evalue score bits fs sw-score 
  		percsim qlen hlen qgap hgap);
  print $outfh "#",uc(join("", map{ sprintf("%-10s",$_) } @fields)), "\n" if $header;
***************
*** 88,92 ****
      if( /^\s*\d+>>>(\S+).+/ ) {	
  	$data{'qname'} = $1;
! 	if( /\-\s+(\d+)\s+aa\s+$/ ){
  	    $data{'qlen'} = $1;
  	}
--- 86,90 ----
      if( /^\s*\d+>>>(\S+).+/ ) {	
  	$data{'qname'} = $1;
! 	if( /\-\s+(\d+)\s+(aa|nt)\s+$/ ){
  	    $data{'qlen'} = $1;
  	}
***************
*** 99,102 ****
--- 97,101 ----
  	if( s/^(\S+)\s+(.+)\(\s*(\d+)\)\s+// ) {
  	    my ($hit, $desc,$hitlen) = ($1,$2,$3);
+ 	    my ($dir) = ( s/^\[(r|f)\]\s+// );
  	    my @line = split(/\s+/,$_);
  	    $data{'hname'}    = $hit;
***************
*** 112,121 ****
  	    $data{'qstart'}   = shift @line;
  	    $data{'qend'}     = shift @line;
! 	    my $pn0           = shift @line; # pn0
! 	    $data{'qlen'}     = shift @line; # px0
  	    $data{'hstart'}   = shift @line; # an1 
  	    $data{'hend'}     = shift @line; # ax1
! 	    my $pn1           = shift @line; # pn1
! 	    $data{'qlen'}     = shift @line; # px1
  	    # query + hit gaps
  	    $data{'qgap'}     = shift @line;
--- 111,120 ----
  	    $data{'qstart'}   = shift @line;
  	    $data{'qend'}     = shift @line;
! 	    $data{'pn0'}      = shift @line; # pn0
! 	    $data{'px0'}      = shift @line; # px0
  	    $data{'hstart'}   = shift @line; # an1 
  	    $data{'hend'}     = shift @line; # ax1
! 	    $data{'pn1'}      = shift @line; # pn1
! 	    $data{'px1'}      = shift @line; # px1
  	    # query + hit gaps
  	    $data{'qgap'}     = shift @line;