def constructe_aln_graph_from_fasta(read_fasta_fn,
backbone_fasta_fn,
max_num_reads = None,
remove_in_del = False,
ref_group = None,
min_length = None):
import os
os.system("blasr %s %s -m 5 -nproc 8 -out %s" % (read_fasta_fn, backbone_fasta_fn, read_fasta_fn+".aln_unsorted"))
os.system("cat %s | sort > %s" % (read_fasta_fn+".aln_unsorted", read_fasta_fn+".aln" ))
aln_hit_iterator = simple_align_hit_iterator(read_fasta_fn+".aln", ref_group = ref_group)
alns = get_aln_array(aln_hit_iterator,
max_num_reads = max_num_reads,
remove_in_del = remove_in_del,
min_length = min_length)
backboneSeq = open(backbone_fasta_fn).read()
backboneSeq = "".join(backboneSeq.split()[1:])
g = AlnGraph(backboneSeq)
i = 0
for aln in alns:
rId = aln[2]
rId = rId.split("/")[0]
aln = aln[0:2]
g.add_alignment( aln, "%s" % rId)
return g
def constructe_aln_graph_from_cmph5(cmpH5_fn,
backbone_fasta_fn,
max_num_reads = None,
remove_in_del = False,
ref_group = None,
min_length = None):
from pbcore.io import cmph5
from pbcore.io.cmph5 import CmpH5
cmpType = CmpH5.SFCmpH5
cmph5f = cmph5.factory.create( cmpH5_fn, "r", cmpType=cmpType )
aln_hit_iterator = None
if ref_group != None:
aln_hit_iterator = cmph5f["/%s" % ref_group].alnHitIterator()
else:
aln_hit_iterator = cmph5f.alnHitIterator()
alns = get_aln_array(aln_hit_iterator,
max_num_reads = max_num_reads,
remove_in_del = remove_in_del,
min_length = min_length)
backboneSeq = open(backbone_fasta_fn).read()
backboneSeq = "".join(backboneSeq.split()[1:])
g = AlnGraph(backboneSeq)
i = 0
for aln in alns:
rId = aln[2]
aln = aln[0:2]
g.add_alignment( aln, "%s" % rId)
cmph5.factory.close(cmph5f)
return g