def __init__(self, namesToReferences):
from ssw import ssw_wrap
self.namesToAligners = {}
for name, ref in namesToReferences.iteritems():
self.namesToAligners[name] = ssw_wrap.Aligner(
ref, report_cigar=True, report_secondary=True)
def check_swalign():
try:
from ssw import ssw_wrap
aligner = ssw_wrap.Aligner("AGTCGT",
report_cigar=True,
report_secondary=True)
aligner.align("AGTC")
except OSError:
return False
return True
def __init__(self, namesToReferences, tryExact=False):
from ssw import ssw_wrap
self.tryExact = tryExact
self.namesToAligners = {}
self.namesToRefs = {}
for name, ref in namesToReferences.items():
self.namesToAligners[name] = ssw_wrap.Aligner(
ref, report_cigar=True, report_secondary=True)
self.namesToRefs[name] = ref
def align(ref, seq):
aligner = ssw_wrap.Aligner(ref, report_cigar=True, report_secondary=True)
result = remap.alignBothStrands(seq, aligner)
print result
def __init__(self, names_to_contigs):
self.names_to_aligners = collections.OrderedDict()
for name, contig in names_to_contigs.items():
self.names_to_aligners[name] = ssw_wrap.Aligner(
contig, report_cigar=True, report_secondary=True)