BioPerl

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Bio/SeqFeature/Tools/Unflattener.pm  view on Meta::CPAN

   #
   # for example, the CDS feature may have a resolver tag of /derives_from
   # which is a 'foreign key' into the /label tag of the mRNA feature
   #
   # this kind of tag-based resolution is possible for a certain subset
   # of genbank records
   #
   # if no resolver tag is specified, we revert to the normal
   # resolver_method
   if ($resolver_tag) {
       my $backup_resolver_method = $resolver_method;
       # closure: $resolver_tag is remembered by this sub
       my $sub = 
	 sub {
	     my ($self, $sf, @possible_container_sfs) = @_;
	     my @container_sfs = ();
	     if ($sf->has_tag($resolver_tag)) {
		 my ($resolver_tagval) = $sf->get_tag_values($resolver_tag);
		 # if a feature has a resolver_tag (e.g. /derives_from)
		 # this specifies the /product, /symbol or /label for the
		 # parent feature

Bio/SeqFeature/Tools/Unflattener.pm  view on Meta::CPAN

			       if (grep {$_ eq $resolver_tagval} @vals) {
				   $match = 1;
				   last;
			       }
			   }   
		       }
		       $match;
		   } @possible_container_sfs;
	     } 
	     else {
		 return $backup_resolver_method->($sf, @possible_container_sfs);
	     }
	     return map {$_=>0} @container_sfs;
	 };
       $resolver_method = $sub;
   }
   else {
       # CONDITION: $resolver_tag is NOT set
       $self->throw("assertion error") if $resolver_tag;
   }
   # we have now set $resolver_method to a subroutine for

Bio/SeqIO/Handler/GenericRichSeqHandler.pm  view on Meta::CPAN

                                   $data->{ORGANISM} || '');
    my ($organelle,$abbr_name, $common);    
    my @class = reverse split m{\s*;\s*}, $class;
    # have to treat swiss different from everything else...
    if ($sl =~ m{^(mitochondrion|chloroplast|plastid)?   # GenBank format
                \s*(.*?)
                \s*(?: \( (.*?) \) )?\.?$ 
         }xmso ){ 
        ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional
    } else {
        $abbr_name = $sl;	# nothing caught; this is a backup!
    }
    # there is no 'abbreviated name' for EMBL
    $sci_name = $abbr_name if $seqformat ne 'genbank';
    $organelle ||= '';
    $common ||= '';
    $sci_name || return;
    unshift @class, $sci_name;
    # no genus/species parsing here; moving to Bio::Taxon-based taxonomy
    my $make = Bio::Species->new();
    $make->scientific_name($sci_name);

Bio/SeqIO/genbank.pm  view on Meta::CPAN

    # entire SOURCE line just in case
    if ($sl =~ m{^(mitochondrion|chloroplast|plastid)?
                  \s*(.*?)
                  \s*(?: \( (.*?) \) )?\.?
                  $
                 }xms
        ) {
        ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional
    }
    else {
        $abbr_name = $sl; # nothing caught; this is a backup!
    }

    # Convert data in classification lines into classification array.
    # only split on ';' or '.' so that classification that is 2 or more words will
    # still get matched, use map() to remove trailing/leading/intervening spaces
    my @class = map { $_ =~ s/^\s+//;
                      $_ =~ s/\s+$//;
                      $_ =~ s/\s{2,}/ /g;
                      $_; }
                split /(?<!subgen)[;\.]+/, $class_lines;

ide/bioperl-mode/site-lisp/bioperl-mode.el  view on Meta::CPAN

		  (and mod (not (string-match "^\*" mod))))
	  (setq done t)
	(let (
	      ;; local vars here
	      )
	  (setq name-list (bioperl-module-names nmspc nil t))
	  (setq mod (completing-read 
		     (concat prompt-prefix nmspc " Module: ")
		     name-list nil (not no-retry)
		     (if mod (replace-regexp-in-string "^\*" "" mod) nil)))
	  ;; allow a backup into namespace completion
	  (if (or no-retry (not (string-equal mod "")))
	      (setq done t)
	    ;; retry setup
	    ;; try again, backing up
	    (setq done nil)
	    (let ( (splt (bioperl-split-name nmspc nil)) )
	      (if (elt splt 1)
		  (progn
		    (setq nmspc (elt splt 0))
		    ;; kludge : "pretend" mod is not found using the "*"

ide/bioperl-mode/site-lisp/bioperl-mode.el  view on Meta::CPAN

	(setq name-list (bioperl-method-names (concat nmspc "::" mod) t pthn))
	(let (
	      ;; local vars here...
	      )
	  (setq mth (completing-read
		     (concat prompt-prefix "Method in " nmspc "::" mod ": ")
		     name-list nil (not no-retry)))
	  (if (or no-retry (not (string-equal mth "")))
	      (setq done t)
	    ;; retry setup
	    ;; allow a backup into module completion
	    (setq done nil)
	    (let ( 
		  (splt (bioperl-split-name (concat nmspc "::" mod) nil pthn))
		  )
	      (setq nmspc (elt splt 0))
	      ;; kludge : "pretend" mod is not found using the "*"
	      (setq mod (concat "*" (elt splt 1))))))
	))
    ;; return values
    (if get-method