Re^2: Read, match string and print

This looks like a standard format - ( examples and more ) - genbank? Is there a parser available from BioPerl or cpan? Sorry if someone has already asked this!!

Just a something something...

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Re^3: Read, match string and print by sophix (Sexton) on Feb 10, 2010 at 14:21 UTC
Hi, I think I stumbled on a GenBank oriented parser (especially, quite useful when you are reading a gene sequence) while reading Perl for Bioinformatics. I`ll check it out, and let you know. Nevertheless, I would like to learn how to use flags to mark the beginning and end of a block to be processed. That is, for the example in this thread, I want the code to make the adequate matchings only when encountered a CDS block (which starts with \sCDS and ends with \sgene) but not a mRNA block. Well, I still did not manage to, though. I understood how it works but could not figure out how to implement. :)	[reply]

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Re^3: Read, match string and print
by sophix (Sexton) on Feb 10, 2010 at 14:21 UTC

Hi, I think I stumbled on a GenBank oriented parser (especially, quite useful when you are reading a gene sequence) while reading Perl for Bioinformatics. I`ll check it out, and let you know. Nevertheless, I would like to learn how to use flags to mark the beginning and end of a block to be processed. That is, for the example in this thread, I want the code to make the adequate matchings only when encountered a CDS block (which starts with \s*CDS and ends with \s*gene) but not a mRNA block. Well, I still did not manage to, though. I understood how it works but could not figure out how to implement. :)

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