[BioRuby] Benchmarking FASTA file parsing
Tomoaki NISHIYAMA
tomoakin at kenroku.kanazawa-u.ac.jp
Sun Aug 15 06:19:03 UTC 2010
Hi,
> 1. Adjustment of file position.
> The separator used to read a fasta entry is "\n>", but the ">"
> should be belonging to the next entry. To adjust this, the last
> ">" is stored to @entry_overrun. The Bio::FlatFile wrapper will
> use the content of @entry_overrun in the next time of reading.
I first thought as such, but I could not find the code that actually
use it. Could you specify where it is used?
I could find only several places defining it.
Maybe there was a reformation of Flatfile buffering to use ungets
but not entry_overrun?
#at bioruby/lib/bio/
$ grep entry_overrun * */* */*/* */*/*/*
db/fasta.rb:# attr_reader :entry_overrun
db/fasta.rb:# @entry_overrun = $&
db/fastq.rb: # entry_overrun
db/fastq.rb: attr_reader :entry_overrun
db/fastq.rb: @entry_overrun = sc.rest
db/nbrf.rb: @entry_overrun = $&
db/nbrf.rb: attr_reader :entry_overrun
db/newick.rb: @entry_overrun = $1
db/newick.rb: attr_reader :entry_overrun
appl/blast/format0.rb: @entry_overrun = $1
appl/blast/format0.rb: attr_reader :entry_overrun
appl/blast/rpsblast.rb: @entry_overrun = $1
appl/fasta/format10.rb: @entry_overrun = overruns.join('')
appl/fasta/format10.rb: attr_reader :entry_overrun
appl/spidey/report.rb: @entry_overrun = $1
appl/spidey/report.rb: attr_reader :entry_overrun
--
Tomoaki NISHIYAMA
Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan
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