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I want to parse FastA or NCBI -m7 (XML) format, how do I do this?

April 26, 2017fasta format NCBI parse XML

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I want to parse FastA or NCBI -m7 (XML) format, how do I do this?

2 Answers

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It is as simple as parsing text BLAST results – you simply need to specify the format as “fasta” or “blastxml” and the parser will load the appropriate module for you. You can use the exact logic and code for all of these formats as we have generalized the modules for sequence database searching.

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It is as simple as parsing text BLAST results – you simply need to specify the format as fasta or blastxml and the parser will load the appropriate module for you. You can use the exact logic and code for all of these formats as we have generalized the modules for sequence database searching. The page describing Bio::SearchIO provides a table showing how the formats match up to particular modules. Note that, for parsing BLAST XML output, you will need XML::SAX and that XML::SAX::ExpatXS is recommended to speed up parsing.