Cython API: compiling but not working

This commit is contained in:
Celine Mercier
2017-03-06 16:07:02 +01:00
parent 778acc48cd
commit 381194194c
19 changed files with 1404 additions and 1531 deletions

View File

@ -2,7 +2,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.files.universalopener cimport uopen
from obitools3.parsers.fasta import fastaIterator
from obitools3.parsers.fastq import fastqIterator
from obitools3.obidms._obidms import OBIDMS
from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
import time
@ -109,22 +109,22 @@ def run(config):
d = OBIDMS(config['obi']['defaultdms'])
# Create view
view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
i = 0
for seq in iseq:
pb(i)
view[i].id = seq['id']
view[i].definition = seq['definition']
view[i].nuc_seq = seq['sequence']
if get_quality :
view[i].quality = seq['quality']
for tag in seq['tags'] :
view[i][tag] = seq['tags'][tag]
i+=1
#print(view.__repr__())
view.close()
# view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
#
# i = 0
# for seq in iseq:
# pb(i)
# view[i].id = seq['id']
# view[i].definition = seq['definition']
# view[i].nuc_seq = seq['sequence']
# if get_quality :
# view[i].quality = seq['quality']
# for tag in seq['tags'] :
# view[i][tag] = seq['tags'][tag]
# i+=1
#
# #print(view.__repr__())
#
# view.close()
d.close()