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226 10 Transforming with Traditional Programming Languages following file that was produced by BioProspector (Liu et al. 2001). ...

10.1 Text Transformations 227 while (<>) { chomp; if (/Motif #1:/) { print "The first motif has been found!\n"; } } Progra ...

228 10 Transforming with Traditional Programming Languages while (<>) { chomp; if (/Motif #[0-9]+:/) { print "A motif has ...

10.1 Text Transformations 229 while (<>) { chomp; if (/Motif #([0-9]+):/) { print "The motif $1 has been found!\n"; } } Pr ...

230 10 Transforming with Traditional Programming Languages When a pattern matches, Perl extracts the text that matches the whol ...

10.1 Text Transformations 231 can be hashes as well as arrays. Furthermore, data structures in general can mix arrays, hashes, a ...

232 10 Transforming with Traditional Programming Languages while (<>) { chomp; if (/^MATRIX ([0-9]+)$/) { $label = $1; } e ...

10.1 Text Transformations 233 Given the label for a motif, one can obtain the motif by using the label as the key:$motifs{$label ...

234 10 Transforming with Traditional Programming Languages A 0.222 C 0.407 T 0.074 G 0.296 Summary One can represent complex da ...

10.2 Transforming XML 235 rather more liketissuesthan organs or organisms, because all of the entities that make up the collecti ...

236 10 Transforming with Traditional Programming Languages Once bioinformatics data have been represented in an XML format, it c ...

10.2 Transforming XML 237 use XML::Parser; $p = new XML::Parser(Handlers => { Start => \&start }); $p->parsefile($A ...

238 10 Transforming with Traditional Programming Languages procedure to the parser as a parameter. Without this Perl would simpl ...

10.2 Transforming XML 239 the name of the parameter and the value of the parameter. The=>symbols are suggestive of this way o ...

240 10 Transforming with Traditional Programming Languages use XML::Parser; $p = new XML::Parser(Handlers => { Start => \& ...

10.2 Transforming XML 241 299-308 Massachusetts General Hospital, Boston, Massachusetts 02114-2617, USA. [email protected] ...

242 10 Transforming with Traditional Programming Languages use XML::Parser; $p = new XML::Parser(Handlers => { Start => \& ...

10.2 Transforming XML 243 Descriptor: Antineoplastic Agents, Hormonal Descriptor: Antineoplastic Combined Chemotherapy Protocols ...

244 10 Transforming with Traditional Programming Languages use XML::DOM; $p = new XML::DOM::Parser; $doc = $p->parsefile($ARG ...

10.2 Transforming XML 245 For DOM lists one uses theitemmethod. DOM uses the single word “node” for anything that can occur in a ...