def read_input(args):
'''
Handle input to scaffolding from three different files
1. A contig fasta file.
2. A contigs to subsequenc file (made when parsing bam file)
3. A link file that describes all linkings of contigs (made when parsing bam file).
'''
contigs ={}
for accession,sequence in input_.get_contigs(open(args.contigs,'r')):
c = Contig(accession, sequence = sequence)
contigs[c.name] = c
subsequences = {}
for subseq_name, contig, start_pos, end_pos in input_.get_subsequences(open(args.seqs,'r')):
s =SubSequence( subseq_name, contigs[contig], start_pos, end_pos)
subsequences[subseq_name] = s
#print len(subsequences)
G = g()
##
# Initialize nodes
for subseq in subsequences:
G.add_node(subsequences[ subseq ])
##
# Create edges
for (seq1,orientation1, seq2, orientation2, link_count, gap), naive_gap in input_.get_links(open(args.links,'r')):
#TODO: Calculate distance here
#TODO: Add threshold parameter
if link_count >= 5:
if naive_gap < - args.overlap:
naive_gap = 0
G.add_edge((subsequences[ seq1 ] ,orientation1),(subsequences[ seq2 ],orientation2),d=naive_gap,s=score.nr_links(link_count))
G.remove_self_links()
return(G)
s1 = ss('s1',c1,0,3)
s2 = ss('s2',c1,3,6)
s3 = ss('s3',c2,0,3)
s4 = ss('s4',c2,3,6)
print len(s1),len(s2)
# scaf = Scaffold('scaf1')
# # scaf.add_subsequence(s2,False,0)
# scaf.add_subsequence(s1,False,7)
print(s1)
print(s2)
# print(scaf)
G = g()
G.add_node(s1)
G.add_node(s2)
G.add_node(s3)
G.add_node(s4)
G.add_edge((s1,True),(s4,True),d=0,s=score.nr_links(10))
G.add_edge((s2,True),(s3,True),d=0,s=score.nr_links(12))
G.add_edge((s4,False),(s2,False),d=0,s=score.nr_links(7))
# false link!
G.add_edge((s1,True),(s1,False),d=0,s=score.nr_links(5))
# G.add_edge()