11 Jul
2012
11 Jul
'12
2:46 p.m.
I am trying to compress the Uniprot90 FASTA file database into a binary file using convert() function as provided in examples for the MODELLER. However, my compressed file ends up being even larger than the uncompressed original one. What may be the problem here? Here is the Python code which I a using with MODELLER v9.7.
from modeller import *
log.verbose() env = environ()
sdb = sequence_db(env) sdb.convert(seq_database_file='/gne/research/data/bioinfo/modeller/db/uniprot90', seq_database_format='FASTA', chains_list='ALL', minmax_db_seq_len=[30, 4000], clean_sequences=True, outfile='/gne/research/data/bioinfo/modeller/db/uniprot90_pruned.bin')
Kind regards and thank you, Dimitrije Jevremovic
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Dimitrije Jevremovic
intern at Bioinformatics & Computational Biology Department