obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Added view type property to OBIView cython class and updated obi export

Browse Source 
to use it
This commit is contained in:
Celine Mercier
2016-11-08 17:49:59 +01:00
parent 51b23915ca
commit 359578814b
2 changed files with 12 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
python/obitools3/commands/export.pyx
View File

@ -1,5 +1,5 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.obidms._obidms import OBIDMS, OBIView_NUC_SEQS # TODO cimport doesn't work
from obitools3.obidms._obidms import OBIDMS # TODO cimport doesn't work
from obitools3.utils cimport bytes2str
import time
@ -56,8 +56,10 @@ def run(config):
# Open input view
iview = d.open_view(config['obi']['inputview'])
print(iview.type)
# TODO check that the view has the type NUC_SEQS
if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (isinstance(iview, OBIView_NUC_SEQS) == False) :
if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (iview.type != "NUC_SEQS_VIEW") : # TODO find a way to import those macros
raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
# Initialize the progress bar