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lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm  view on Meta::CPAN

    # parse out organelle, common name, abbreviated name if present;
    # this should catch everything, but falls back to
    # entire GBSeq_taxonomy element just in case
    if ($get->('source') =~ m{^
		              (mitochondrion|chloroplast|plastid)?
		              \s*(.*?)
		              \s*(?: \( (.*?) \) )?\.?
		              $}xms ) { 
        ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional
    } else {
        $abbr_name = $get->('source'); # nothing caught; this is a backup!
    }

    # Convert data in classification lines into classification array.
    my @class = split(/; /, $get->('taxonomy'));

    # do we have a genus?
    my $possible_genus =  quotemeta($class[-1])
       . ($class[-2] ? "|" . quotemeta($class[-2]) : '');
    if ($sci_name =~ /^($possible_genus)/) {
	$genus = $1;

lib/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm  view on Meta::CPAN

    # parse out organelle, common name, abbreviated name if present;
    # this should catch everything, but falls back to
    # entire GBSeq_taxonomy element just in case
#     if ($get->('source') =~ m{^
# 		              (mitochondrion|chloroplast|plastid)?
# 		              \s*(.*?)
# 		              \s*(?: \( (.*?) \) )?\.?
# 		              $}xms ) { 
#         ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional
#     } else {
#         $abbr_name = $get->('source'); # nothing caught; this is a backup!
#     }

#     # Convert data in classification lines into classification array.
    my @class = split(/; /, $get->('Lineage'));

    # do we have a genus?
    my $possible_genus =  quotemeta($class[-1])
       . ($class[-2] ? "|" . quotemeta($class[-2]) : '');
    if ($sci_name =~ /^($possible_genus)/) {
	$genus = $1;