#!/usr/bin/python
##!/opt/python/bin/python

import sys
import ab_out

# process a blast file for indels and generate an output file from it
# default data file: "/projects/stsi2/acarson/indels/Abyss/indels/BLAT/indels.blast"

#in_file = "indels-test.blast"
in_file = "indels.blast"
#out_file = "ab-ind-test.txt"
out_file = "ab-ind.txt"
q_group_count = 0
q_group = []
try:
    fi = open(in_file)
except IOError:
    print "%s%s" % ("Error: can\'t open input file ", in_file)
    sys.exit("\nInput file open error\n\n")
l = fi.readline()

fo = ab_out.open_outfile(out_file, in_file)

# collect all the lines up to the next "BLASTN" in a list named q_group
# process that group, then collect the lines for the next group
while len(l) > 0:
# collect all the lines from a query group
# the group ends with the string 'Database:' indented by 2 spaces
    while not l.startswith('  Database:') and len(l) > 0:
        q_group.append(l)
        l = fi.readline()

# at this point we have a complete query group
    q_group_count = q_group_count + 1
    print "%s%s" % ("Query group #:", q_group_count)
    next_contig = False
    qname = ""
    score_set = False
    ident_set = False
    strand_set = False
    query_in_progress = False
    sbjct_in_progress = False
    q_line = ""
    s_line = ""
    segm= ""
    q_start = 0
    q_end = 0
    s_start = 0
    s_end = 0
    qry = []
    sbj = []
    final_sbjct_string = ""
    final_query_string = ""
    out_line = ""
# there are three conditions where we will end processing and write this out
# (in addition to the query_in_progress being True):
# 1. "Score = "
# 2. ">"
# 3. "  Database "
# This condition must be checked before the others because we want to output
# as soon as we have the query data collected
    for line in q_group:
#        print "%s%s" % ("line:", line)
        if line.strip() == "":
            continue
        if query_in_progress and (line.lstrip().startswith("Score = ") or
                line.lstrip().startswith(">") or line.lstrip().startswith("Database: ")):
            ab_out.write_outline(qname, chr, q_start, q_end, s_start, s_end, final_query_string, final_sbjct_string, fo)

            next_contig = True
            query_in_progress = False
            sbjct_in_progress = False
            print
            break
        if line.lstrip().startswith("Query: ") and not query_in_progress:
# start a new query line with current line
# set initial start and end values
# set query in progress
            qry = line.split(":")
            segm = qry[1]
            q_line = segm.split()
            q_start = q_line[0]
            q_end = q_line[2]
            final_query_string = q_line[1]
            query_in_progress = True
            continue
        if line.lstrip().startswith("Sbjct: ") and not sbjct_in_progress:
# start a new sbjct line with current line
# set initial start and end values
# set query in progress
            sbj = line.split(":")
            segm = sbj[1]
            s_line = segm.split()
            s_start = s_line[0]
            s_end = s_line[2]
            final_sbjct_string = s_line[1]
            sbjct_in_progress = True
            continue
        if line.lstrip().startswith("Query: ") and query_in_progress:
# append to current query line
            qry = line.split(":")
            segm = qry[1]
            q_line = segm.split()
            final_query_string = final_query_string + q_line[1]
# update end value
            q_end = q_line[2]
            continue
        if line.lstrip().startswith("Sbjct: ") and sbjct_in_progress:
# append to current sbjct line
            sbj = line.split(":")
            segm = sbj[1]
            s_line = segm.split()
            final_sbjct_string = final_sbjct_string + s_line[1]
# update end value
            s_end = s_line[2]
            continue
        elif line.startswith("Query="):
            qvars = line.split("=")
            qname = qvars[1]
            print "%s%s" % ("Contig name:", qname.rstrip())
            continue
        elif line.lstrip().startswith("Length = "):
            leng = line.split("=")
            seq_len = leng[1]
#            print "%s%s" % ("Sequence length:", seq_len.rstrip())
            continue
        elif line.startswith(">"):
            chrs = line.split(">")
            chr = chrs[1].rstrip()
#            print "%s%s" % ("Best chromosome hit: ", chr)
            continue
        elif line.lstrip().startswith("Identities = ") and not ident_set:
            ids = line.split("=")
            idents = ids[1]
#            print "%s%s" % ("Identities:", idents.rstrip())
            ident_set = True
            continue
        elif line.lstrip().startswith("Score = ") and not score_set:
            score_tokens = line.split(",")
            scr = score_tokens[0]
            score = scr.split('=')
#            print "%s%s" % ("Score: ", score[1].strip())
            expct = score_tokens[1]
            expect = expct.split('=')
#            print "%s%s" % ("Expect: ", expect[1].strip())
            score_set = True
            continue
        elif line.lstrip().startswith("Strand = ") and not strand_set:
            strnd = line.split("=")
            strand = strnd[1]
#            print "%s%s" % ("Strand:", strand.rstrip())
            strand_set = True
            continue
        else: continue
        if next_contig: break
# If next_contig is true, we are done processing the query; this value will be
# set after the last line is processed for this group, which will be after the
# last set of Sbjct and Query data lines have been collected for the best hit.
# We have to cleanup here for the case when there is only a single query
# since this case is not handled inside the main loop
    if query_in_progress:
        ab_out.write_outline(qname, chr, q_start, q_end, s_start, s_end, final_query_string, final_sbjct_string, fo)

# after processing and outputting the group, begin collecting the next one
    l = fi.readline()
    q_group = []

sys.exit("Processing complete\n\n")
"""
try:
    fo = open('ab-ind.txt', 'w')
except IOError:
    print "%s%s" % ("Error: can\'t open output file ", out_file)
    sys.exit("Output file open error")
else:
    print "Opened the output file successfully"

try:
    fo.write("##ABySS Insertion-Deletion Identification file\n")
    fo.write("##Input file: " + in_file + "\n\n")
except IOError:
    print "%s%s" % ("Error: can\'t write to output file ", out_file)
    sys.exit("Output file write error")
else:
    print "Wrote content in the output file successfully"
"""