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obi export: view type is now checked and progress bar functioning

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Celine Mercier
2016-11-08 11:17:20 +01:00
parent 2d2fe5279d
commit 4bc19c3e49
1 changed files with 8 additions and 4 deletions
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12
python/obitools3/commands/export.pyx
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@ -1,5 +1,5 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.obidms._obidms import OBIDMS # TODO cimport doesn't work from obitools3.obidms._obidms import OBIDMS, OBIView_NUC_SEQS # TODO cimport doesn't work
from obitools3.utils cimport bytes2str from obitools3.utils cimport bytes2str
import time import time
@ -38,7 +38,7 @@ def addOptions(parser):
metavar='<FORMAT>', metavar='<FORMAT>',
default="fasta", default="fasta",
type=str, type=str,
help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.") help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.") # TODO export in csv
def run(config): def run(config):
@ -56,12 +56,16 @@ def run(config):
# Open input view # Open input view
iview = d.open_view(config['obi']['inputview']) iview = d.open_view(config['obi']['inputview'])
# 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) :
raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
# Initialize the progress bar # Initialize the progress bar
#pb = ProgressBar(len(iview), config, seconde=5) pb = ProgressBar(len(iview), config, seconde=5)
i=0 i=0
for seq in iview : for seq in iview :
#pb(i) pb(i)
toprint = ">"+seq.get_id()+" " toprint = ">"+seq.get_id()+" "