def test_midlist_missing( self ):
sffn, sffp = self.sffs.items()[0]
reg = int( sffn.replace( '.sff', '' )[-2:] )
process = demultiplex.demultiplex_sff( sffp, fixtures.MIDPARSE, self.rf[reg].keys() + ['RL99'], self.sfffilecmd, self.tempdir )
stdout, stderr = process.communicate()
read_lst = self.expected_read_list[sffn.replace( '.sff', '.lst' )]
with open( read_lst ) as fh:
result = fh.read() + ' '+fixtures.MIDPREFIX+'RL99: 0 reads found\n'
common.erdiff( result, stdout )
def test_demultiplex_sff( self ):
''' Should match expected output from fixtures '''
for sffn, sffp in self.sffs.items():
reg = int( sffn.replace( '.sff', '' )[-2:] )
read_lst = self.expected_read_list[sffn.replace( '.sff', '.lst' )]
process = demultiplex.demultiplex_sff( sffp, fixtures.MIDPARSE, self.rf[reg].keys(), self.sfffilecmd, self.tempdir )
stdout, stderr = process.communicate()
with open( read_lst ) as fh:
common.erdiff( fh.read(), stdout )
def test_midlist_missingrev( self ):
''' Make sure only midkey list barcodes are extracted '''
sffn, sffp = self.sffs.items()[0]
reg = int( sffn.replace( '.sff', '' )[-2:] )
keys = demultiplex.sort_midlist( self.rf[reg].keys() )[:-2]
process = demultiplex.demultiplex_sff( sffp, fixtures.MIDPARSE, keys, self.sfffilecmd, self.tempdir )
stdout, stderr = process.communicate()
read_lst = self.expected_read_list[sffn.replace( '.sff', '.lst' )]
with open( read_lst ) as fh:
expect = "".join(fh.readlines()[:-2])
common.erdiff( expect, stdout )
def test_midlist_missing(self):
sffn, sffp = self.sffs.items()[0]
reg = int(sffn.replace('.sff', '')[-2:])
process = demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE,
self.rf[reg].keys() + ['RL99'],
self.sfffilecmd, self.tempdir)
stdout, stderr = process.communicate()
read_lst = self.expected_read_list[sffn.replace('.sff', '.lst')]
with open(read_lst) as fh:
result = fh.read(
) + ' ' + fixtures.MIDPREFIX + 'RL99: 0 reads found\n'
common.erdiff(result, stdout)
def test_demultiplex_sff(self):
''' Should match expected output from fixtures '''
for sffn, sffp in self.sffs.items():
reg = int(sffn.replace('.sff', '')[-2:])
read_lst = self.expected_read_list[sffn.replace('.sff', '.lst')]
process = demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE,
self.rf[reg].keys(),
self.sfffilecmd,
self.tempdir)
stdout, stderr = process.communicate()
with open(read_lst) as fh:
common.erdiff(fh.read(), stdout)
def test_midlist_missingrev(self):
''' Make sure only midkey list barcodes are extracted '''
sffn, sffp = self.sffs.items()[0]
reg = int(sffn.replace('.sff', '')[-2:])
keys = demultiplex.sort_midlist(self.rf[reg].keys())[:-2]
process = demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE, keys,
self.sfffilecmd, self.tempdir)
stdout, stderr = process.communicate()
read_lst = self.expected_read_list[sffn.replace('.sff', '.lst')]
with open(read_lst) as fh:
expect = "".join(fh.readlines()[:-2])
common.erdiff(expect, stdout)