[Bioperl-l] BPlite report->query return only partial name

[Elia Stupka]

>   I have noticed that when using BPlite to parse a
> blast report, the report->query or
> $hsp->query->seqname only return the characters
> between ">" and a blank space in a FASTA file.

This is actually done on purpose, the identifier being considered what
lies between the > sign and the first space, and anything after that being
considered description. It is the only simple way to agree on how to refer
to a particular sequence, because if you take anything after the space
delimiter you could go on taking in the whole line, and would have no easy
way to refer to a particular sequence identifier. However, when you are
parsing the sequence with the bioperl fasta parser, what comes after the
first space will be stored in the ->desc method of the sequence,
i.e. description, if you need to retrieve it.

Elia

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