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pierrepo / PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:
https://pbxplore.readthedocs.org/en/latest/
MIT License
28 stars 17 forks source link

PBxplore from PyPI (v1.0) does not seem to read *.pdb.gz anymore #138

Closed pierrepo closed 7 years ago

pierrepo commented 7 years ago 
wget https://files.rcsb.org/download/3ICH.pdb.gz
PBassign -p 3ICH.pdb.gz -o toto
cat toto.PB.fasta

File toto.PB.fasta is empty.

HubLot commented 7 years ago

same issue with the master version

HubLot commented 7 years ago

Well, in fact, we didn't include .pdb.gz extension in the list of authorized extensions... See in https://github.com/pierrepo/PBxplore/blob/master/pbxplore/structure/PDB.py :

PDB_EXTENSIONS = ('.pdb', '.PDB', '.ent', '.ENT4')
PDBx_EXTENSIONS = ('.cif', '.CIF', '.cif.gz', '.CIF.GZ')

We dont neither have a test for this case (but we do for cif.gz). I'll do a PR to add the correct extensions and a test case ;)