Pcdhit
Python interface to cd-hit
Install / Use
/learn @simomarsili/PcdhitREADME
====== pcdhit
Python interface to the cd-hit clustering program. Given a collection of redundant sequence records, (an iterable of (header, sequence) tuples) and a sequence identity threshold, the filter function returns an iterable of non-redundant records::
import pcdhit filtered_records = pcdhit.filter(records, thr=0.9)
In practice, the function dumps the redundant records in a fasta alignment, run cd-hit::
$ cdhit -i <redundant_fasta> -o <non_redundant_fasta> -c <threshold>
via subprocess.Popen and parse the non-redundant records from the cd-hit output file.
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