pb_assembly/FALCON/falcon_kit/mains/contig_annotate.py

from falcon_kit.fc_asm_graph import AsmGraph
import sys


def main(argv=sys.argv):
    G_asm = AsmGraph("sg_edges_list", "utg_data", "ctg_paths")

    p_ctg_coor_map = {}
    for fn in ("p_ctg_tiling_path", "a_ctg_tiling_path"):
        f = open(fn)
        for row in f:
            row = row.strip().split()
            ctg_id, v, w, edge_rid, b, e = row[:6]
            if ctg_id not in p_ctg_coor_map:
                coor = 0   # the p_ctg_tiling_path should be sorted by contig the order of the edges in the tiling path
                p_ctg_coor_map[ctg_id] = {}
                p_ctg_coor_map[ctg_id][v] = 0
                coor += abs(int(b) - int(e))
                p_ctg_coor_map[ctg_id][w] = coor
                G_asm.node_to_ctg[w]
                print(ctg_id, v, 0, " ".join(list(G_asm.node_to_ctg[v])))
                print(ctg_id, w, coor, " ".join(list(G_asm.node_to_ctg[w])))
                continue
            else:
                coor += abs(int(b) - int(e))
                p_ctg_coor_map[ctg_id][w] = coor
                print(ctg_id, w, coor, " ".join(list(G_asm.node_to_ctg[w])))
        f.close()


if __name__ == "__main__":
    main(sys.argv)