# This file contains function definitions for opening the output file and
# writing lines to that file, for the script ab-ind.py

def open_outfile(out_f, in_f):
    try:
        fo = open('ab-ind.txt', 'w')
    except IOError:
        print "%s%s" % ("Error: can\'t open output file ", out_f)
        sys.exit("\nOutput file open error\n\n")
    else:
        print "Opened the output file successfully"

    try:
#        fo.write("##ABySS Insertion-Deletion Identification file\n")
#        fo.write("##Input file: " + in_f + "\n\n")
        fo.write("\n")
    except IOError:
        print "%s%s" % ("Error: can\'t write to output file ", out_f)
        sys.exit("Output file write error\n\n")
    else:
        print "Successful write to output file\n\n"
    return fo


def write_outline(qname, chro, q_start, q_end, s_start, s_end, final_query_string, final_sbjct_string, fo):

# Input Parameters:
# q_start and q_end are strings representing the positional values for the start and end
# of the bases in the contig (query string); whether they are increasing or decreasing
# determines whether the indel is +/-
# s_start and s_end are the same for the sbjct string; except that they are absolute positional
# values where the q values are relative and will always either start or end with value 1

    out_line = ""
    Start_S = ""
    End_S = ""
    s_s = 0
    e_s = 0
    del_len = 0
    q_match = False
    s_match = False
    del_plus = False
    del_minus = False
    ins_plus = False
    ins_minus = False
    s_start_i = int(s_start)
    s_end_i = int(s_end)
    s_minus = False
    if s_start_i > s_end_i:
        s_minus = True
    q_start_i = int(q_start)
    q_end_i = int(q_end)
    q_minus = False
    if q_start_i > q_end_i:
        q_minus = True
    print "%s%s" % ("Concatenated Query string:", final_query_string)

    indel_start_q = final_query_string.find("-")
    if indel_start_q < 0:
        q_match = False
    else:
        q_match = True
        indel_end_q = final_query_string.rfind("-")
        del_len = indel_end_q - indel_start_q + 1

    print "%s%s" % ("Concatenated Sbjct string:", final_sbjct_string)

    indel_start_s = final_sbjct_string.find("-")
    if indel_start_s < 0:
        s_match = False
    else:
        s_match = True
        indel_end_s = final_sbjct_string.rfind("-")
        ins_len = indel_end_s - indel_start_s + 1

    if indel_start_q < 0 and indel_start_s < 0:
        print "%s" % ("No indels this Query\n")
    elif indel_start_q >= 0 and indel_start_s >= 0:
        print "%s" % ("Data error this Query\n")
        out_line = qname.strip() + " has a data error (both INS and DEL are present!\n"
    else:
        out_line = chro + "\t.\t"
        if indel_start_q > 0:
            out_line = out_line + "DEL\t"
            print "%s%i" % ("indel_start_q:", indel_start_q)
            print "%s%i" % ("indel_end_q:", indel_end_q)
            print "%s%s" % ("Length of deletion:", del_len)
            if q_minus:
# Deletion -
                del_minus = True
                print "-Del\n"
            else:
# Deletion +
                del_plus = True
                print "+Del\n"

        else: # indel_start_s must be > 0
            out_line = out_line + "INS\t"
            print "%s%i" % ("indel_start_s:", indel_start_s)
            print "%s%i" % ("indel_end_s:", indel_end_s)
            print "%s%s" % ("Length of insertion:", ins_len)
            if q_minus:
# Insertion -
                print "-Ins\n"
                ins_minus = True
            else:
# Insertion +
                print "+Ins\n"
                ins_plus = True
        if del_plus or del_minus:
            del_segment = final_sbjct_string[indel_start_q:indel_end_q+1].upper()
            del_seg_l = len(del_segment)
            out_line = out_line + "\t" + str(s_start_i + indel_start_q) + "\t" + str(s_start_i + indel_start_q + del_seg_l - 1)
            out_line = out_line + "\t" + "0:" + str(del_seg_l)
            if q_minus:
                out_line = out_line + "\t" + "-"
            else:
                out_line = out_line + "\t" + "+"
            out_line = out_line + "\t" + qname.strip() + ":"
            if q_minus:
                i_val_s = q_start_i - (indel_start_q - 1)
                i_val_e = q_start_i - indel_start_q
                out_line = out_line + str(i_val_s) + "-" + str(i_val_e)
            else:
                i_val_s = q_start_i + indel_start_q - 1
                i_val_e = q_start_i + indel_start_q
                out_line = out_line + str(i_val_s) + "-" + str(i_val_e)

            out_line = out_line + "\t" + "-/" + del_segment + "\n"
        elif ins_plus or ins_minus:
            out_line = out_line + "\t" + str(s_start_i + indel_start_s - 1) + "\t" + str(s_start_i + indel_start_s)

            ins_segment = final_query_string[indel_start_s:indel_end_s+1].upper()
            ins_seg_l = len(ins_segment)
            out_line = out_line + "\t" + str(ins_seg_l) + ":0"
            if q_minus:
                out_line = out_line + "\t" + "-"
            else:
                out_line = out_line + "\t" + "+"
            out_line = out_line + "\t" + qname.strip() + ":"

            if q_minus:
                i_val_s = q_start_i - indel_start_s
                i_val_e = q_start_i - indel_start_s - ins_seg_l + 1
                out_line = out_line + str(i_val_s) + "-" + str(i_val_e)
            else:
                i_val_s = q_start_i + indel_start_s
                i_val_e = q_start_i + indel_start_s + ins_seg_l - 1
                out_line = out_line + str(i_val_s) + "-" + str(i_val_e)

            out_line = out_line + "\t" + ins_segment + "/-" + "\n"
        else:
            out_line = out_line + "\t" + End_S + "\n"
    fo.write(out_line)