Use pyfastx instead of biopython

genotoul-bioinfo / dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

http://dgenies.toulouse.inrae.fr

GNU General Public License v3.0

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Open pbordron opened 1 year ago

pbordron commented 1 year ago

Pyfastx is faster than Biopython.

Warning

pyfastx is 1-offset based (i.e. sequence start index is 1), biopython is 0-offset
sequence end is included in interval with pyfastx [start, end], whereas end in not included with biopython [start, end[
pyfastx create an index (sqlite file), biopython not

pbordron commented 1 year ago

Can be studied when working on job script part of #67