Hi,
I want to develop an application based on PyGr, and learn to use the
version 0.8.
I first succeeded in merging several FASTA files into pureseq and
seqlen files but I have run
into a problem when trying to create from them a pygr file (I use
eclipse on windows xp and set the environment variable PYGRDATAPATH to
a local disk).
Thanks for your help
Michel
1/ if I run the following program (cf 3/) I get this error message :
Traceback (most recent call last):
File "E:\sosma\projet\python\SYSBIOPY\src\tool\database
\makepygr.py", line 8, in <module>
import Data
File "Z:\prog\python25\lib\site-packages\pygr\Data.py", line 2, in
<module>
from pygr import pygrData,pygrSchema
ImportError: cannot import name pygrData
2/ if I use the console I get this message:
import seqdb
import Data
os.chdir('D:/data/ucsc/genome')
newDB = seqdb.SequenceFileDB('D:/data/ucsc/genome/hg18')
seqLenDict open
newDB.__doc__ = 'homo sapiens genome sequence draft 18'
Data.Bio.Seq.HUMAN.hg18 = newDB
Traceback (most recent call last):
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
905, in update
**mdbArgs)
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
770, in __init__
storage = ShelveMetabase(dbpath, self, **kwargs)
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
488, in __init__
self.db = dbfile.shelve_open(self.dbpath, 'c')
File "Z:\prog\python25\lib\site-packages\pygr\dbfile.py", line 119,
in shelve_open
d = open_index(filename, flag, useHash, mode) # construct Shelf
only if OK
File "Z:\prog\python25\lib\site-packages\pygr\dbfile.py", line 77,
in open_index
return open_bsddb(filename, flag, useHash, mode)
File "Z:\prog\python25\lib\site-packages\pygr\dbfile.py", line 45,
in open_bsddb
return open_anydbm(filename, flag)
File "Z:\prog\python25\lib\site-packages\pygr\dbfile.py", line 21,
in open_anydbm
return anydbm.open(*args, **kwargs)
File "Z:\prog\python25\lib\anydbm.py", line 83, in open
return mod.open(file, flag, mode)
File "Z:\prog\python25\lib\dbhash.py", line 16, in open
return bsddb.hashopen(file, flag, mode)
File "Z:\prog\python25\lib\bsddb\__init__.py", line 310, in hashopen
d.open(file, db.DB_HASH, flags, mode)
DBError: (5, 'Input/output error')
WARNING: error accessing metabase 'D:/pygr/data'. Continuing...
Exception exceptions.AttributeError: "'ShelveMetabase' object has no
attribute 'db'" in <bound method ShelveMetabase.__del__ of
<pygr.metabase.ShelveMetabase object at 0x0122C8B0>> ignored
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
1196, in __setattr__
self._mdb.add_resource(self.getPath(name), obj)
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
724, in add_resource
self.get_writer().saver.add_resource(resID, obj)
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
864, in get_writer
return MetabaseBase.get_writer(self) # proceed as usual
File "Z:\prog\python25\lib\site-packages\pygr\metabase.py", line
721, in get_writer
raise PygrDataReadOnlyError('this metabase is read-only!')
PygrDataReadOnlyError: this metabase is read-only!
3/ my program:
'''
Created on 23 avr. 2009
construct pygr data base
@author: bellis
'''
import os
import seqdb
import Data
def make_blast_db(inputFileDir):
""" generate .seqlen and test.pureseq files.
test.seqlen file is for saving coordinates and identifiers
information
to access your sequences (python shelve file), and test.pureseq
file
is sequence only file without sequence header.
"""
os.chdir(inputFileDir)
fileList=os.listdir(inputFileDir)
for fileName in fileList:
seqdb.BlastDB(fileName)
def make_pygr_db(inputFileDir, speciesName, dbName, shortDescription):
os.chdir(inputFileDir)
newDB = seqdb.SequenceFileDB(inputFileDir+os.sep+dbName)
newDB.__doc__ = shortDescription
eval('Data.Bio.Seq.Genome.%s.%s = newDB',speciesName,dbName)
Data.save()
if __name__=='__main__':
#MERGE FASTA FILES
# INPUTFILE_DIR='D:/data/ucsc/hg18'
# make_blast_db(INPUTFILE_DIR)
#CREATE PYGR RESSOURCE
INPUTFILE_DIR='D:/data/ucsc/genome'
SPECIES='HUMAN'
DB_NAME='hg18'
SHORT_DESCRIPTION='homo sapiens genome sequence draft 18'
make_pygr_db(INPUTFILE_DIR, SPECIES, DB_NAME, SHORT_DESCRIPTION)
#COMMAND USED IN CONSOLE MODE
#import os
#import seqdb
#import Data
#os.chdir('D:/data/ucsc/genome')
#newDB = seqdb.SequenceFileDB('D:/data/ucsc/genome/hg18')
#newDB.__doc__ = 'homo sapiens genome sequence draft 18'
#Data.Bio.Seq.HUMAN.hg18 = newDB
#Data.save()
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