[Bioperl-guts-l] bioperl-live/Bio/Tools/Run RemoteBlast.pm, 1.21, 1.22

Brian Osborne bosborne at pub.open-bio.org
Mon Apr 25 21:47:41 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Run
In directory pub.open-bio.org:/tmp/cvs-serv30182/Bio/Tools/Run

Modified Files:
	RemoteBlast.pm 
Log Message:
Add POD, move to scripts/


Index: RemoteBlast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Run/RemoteBlast.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** RemoteBlast.pm	17 Nov 2004 23:54:50 -0000	1.21
--- RemoteBlast.pm	26 Apr 2005 01:47:39 -0000	1.22
***************
*** 196,200 ****
     '(Pairwise|(Flat)?QueryAnchored(NoIdentities)?|Tabular)',
  	 # Pairwise, QueryAnchored, QueryAnchoredNoIdentities, 
!   	 # FlatQueryAnchored, FlatQueryAnchoredNoIdentities, Tabular 
  	 'DESCRIPTIONS'	=> '\d+',			# Positive integer
  	 'ENTREZ_LINKS_NEW_WINDOW' => '(yes|no)',	# yes, no
--- 196,200 ----
     '(Pairwise|(Flat)?QueryAnchored(NoIdentities)?|Tabular)',
  	 # Pairwise, QueryAnchored, QueryAnchoredNoIdentities, 
!   	 # FlatQueryAnchored, FlatQueryAnchoredNoIdentities, Tabular
  	 'DESCRIPTIONS'	=> '\d+',			# Positive integer
  	 'ENTREZ_LINKS_NEW_WINDOW' => '(yes|no)',	# yes, no
***************
*** 563,567 ****
  				$blastobj = new Bio::Tools::BPlite(-file => $tempfile);
  	    	} else {
! 				$blastobj = new Bio::SearchIO( -file     => $tempfile,
  														 -format => 'blast');
  			}
--- 563,567 ----
  				$blastobj = new Bio::Tools::BPlite(-file => $tempfile);
  	    	} else {
! 				$blastobj = new Bio::SearchIO( -file => $tempfile,
  														 -format => 'blast');
  			}
***************
*** 571,575 ****
  	    	return $blastobj;
  		} elsif( $size < 500 ) { # search had a problem
! 			open(ERR, "<$tempfile") or $self->throw("cannot open file $tempfile"); 
  			$self->warn(join("", <ERR>));
  			close ERR;
--- 571,576 ----
  	    	return $blastobj;
  		} elsif( $size < 500 ) { # search had a problem
! 			open(ERR, "<$tempfile")
! 			  or $self->throw("cannot open file $tempfile");
  			$self->warn(join("", <ERR>));
  			close ERR;
***************
*** 622,657 ****
  
  sub _load_input {
!     my ($self, $input) = @_;
  
!     if( ! defined $input ) {
  		$self->throw("Calling remote blast with no input");
-     }
-     my @seqs;
-     if( ! ref $input ) {
- 	if( -e $input ) {
- 	    my $seqio = new Bio::SeqIO(-format => 'fasta', -file => $input);
- 	    while( my $seq = $seqio->next_seq ) {
- 		push @seqs, $seq;
- 	    }
- 	} else {
- 	    $self->throw("Input $input was not a valid filename");
- 	}	
-     } elsif( ref($input) =~ /ARRAY/i ) {
- 	foreach ( @$input ) {
- 	    if( ref($_) && $_->isa('Bio::PrimarySeqI') ) {
- 		push @seqs, $_;
- 	    } else {
- 		$self->warn("Trying to add a " . ref($_) .
- 			    " but expected a Bio::PrimarySeqI");
- 	    }
  	}
! 	if( ! @seqs) {
! 	    $self->throw("Did not pass in valid input -- no sequence objects found");
  	}
!     } elsif( $input->isa('Bio::PrimarySeqI') ) {
! 	push @seqs, $input;
!     }
!     return @seqs;
  }
  1;
  __END__
--- 623,661 ----
  
  sub _load_input {
! 	my ($self, $input) = @_;
  
! 	if( ! defined $input ) {
  		$self->throw("Calling remote blast with no input");
  	}
! 	my @seqs;
! 	if( ! ref $input ) {
! 		if( -e $input ) {
! 			my $seqio = new Bio::SeqIO(-format => 'fasta',
! 												-file => $input);
! 			while( my $seq = $seqio->next_seq ) {
! 				push @seqs, $seq;
! 			}
! 		} else {
! 			$self->throw("Input $input was not a valid filename");
! 		}
! 	} elsif( ref($input) =~ /ARRAY/i ) {
! 		foreach ( @$input ) {
! 			if( ref($_) && $_->isa('Bio::PrimarySeqI') ) {
! 				push @seqs, $_;
! 			} else {
! 				$self->warn("Trying to add a " . ref($_) .
! 								" but expected a Bio::PrimarySeqI");
! 			}
! 		}
! 		if( ! @seqs) {
! 			$self->throw("Did not pass in valid input -- no sequence objects found");
! 		}
! 	} elsif( $input->isa('Bio::PrimarySeqI') ) {
! 		push @seqs, $input;
  	}
! 	return @seqs;
  }
+ 
  1;
+ 
  __END__



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