Bio::SFF::Entry - An SFF entry
version 0.007
while(my $entry = $reader->next_entry) { say '>', $entry->name; say $entry->bases; }
This object represents an entry in an SFF file. It contains both processed data (the nucleotides and quality scores) and raw data (e.g. flowgram values).
The name of this sequence
The nucleotides of this sequence
Returns an array containing all flowgram values.
This contains the flow positions for each base in the called sequence (i.e., for each base, the position in the flowgram whose estimate resulted in that base being called). These values are "incremental" values, meaning that the stored position is the offset from the previous flow index in the field. All position values (prior to their incremental encoding) use 1-based indexing, so the first flow is flow 1.
The quality scores for each of the bases in the sequence, where the values use the standard -log10 probability scale.
The first base after the clipping point for quality, using 1-based indexing.
The last base before the clipping point for quality, using 1-based indexing.
Leon Timmermans <leont@cpan.org>
This software is copyright (c) 2011 by Leon Timmermans, Utrecht University.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::SFF, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::SFF
CPAN shell
perl -MCPAN -e shell install Bio::SFF
For more information on module installation, please visit the detailed CPAN module installation guide.