def recruit(seqs, reads, k, dir):
dd = DirDistributor(os.path.join(dir, "alignments"))
aligner = Aligner(dd)
params.k = k
relevant_reads = ContigStorage()
disjointigs = seqs
for i in range(2):
sys.stdout.info("Recruiting iteration", i)
als = filter(lambda al: len(al) > k, aligner.localAlign(reads, disjointigs))
print len(als), "alignments"
relevant_reads = alsToReads(als)
l = sum(map(len, seqs.unique()))
disjointigs = constructDisjointigs(relevant_reads, l, dd.nextDir())
print len(disjointigs), "disjointigs"
print disjointigs
disjointigs.writeToFasta(open(os.path.join(dir, "disjointigs.fasta"), "w"))
relevant_reads.writeToFasta(open(os.path.join(dir, "reads.fasta"), "w"))
sys.stdout.info("Aligning repeat sequences to disjointigs")
als = list(aligner.localAlign(seqs, disjointigs))
print "\n".join(map(str, als))
starts = dict()
for dis in disjointigs:
starts[dis.id] = len(dis)
for al in als:
if len(al) > k:
starts[al.seg_to.contig.id] = min(starts[al.seg_to.contig.id], al.seg_to.left)
al = al.rc
starts[al.seg_to.contig.id] = min(starts[al.seg_to.contig.id], al.seg_to.left)
print "Starts:"
for cid, val in starts.items():
print cid, val
contigs = ContigStorage()
cnt = 1
for dis in disjointigs:
if starts[dis.id] > k and starts[dis.id] < len(dis):
print cnt, dis.id, starts[dis.id]
contigs.add(Contig(dis.prefix(starts[dis.id]).Seq(), str(cnt)))
cnt += 1
for dis in disjointigs.unique():
if len(dis) > k and starts[dis.id] == len(dis):
print cnt, dis.id
contigs.add(Contig(dis.seq, str(cnt)))
cnt += 1
contigs.writeToFasta(open(os.path.join(dir, "contigs.fasta"), "w"))
fakeGraph(contigs, open(os.path.join(dir, "graph.gv"), "w"))
import sys
sys.path.append("py")
from common.sequences import ContigStorage
if __name__ == "__main__":
fname = sys.argv[1]
contigs = ContigStorage().loadFromFasta(open(fname, "r"), False)
contigs.writeToFasta(sys.stdout)
