--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff.py	Wed Jun 26 08:01:42 2019 -0400
@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+""" sequence repetitive profile conversion to GFF3 format """
+
+import time
+import configuration
+from operator import itemgetter
+from itertools import groupby
+from tempfile import NamedTemporaryFile
+import os
+
+
+def create_gff(THRESHOLD, THRESHOLD_SEGMENT, OUTPUT_GFF, files_dict, headers):
+    seq_id = None
+    exclude = set(['ALL'])
+    gff_tmp_list = []
+    for repeat in sorted(set(files_dict.keys()).difference(exclude)):
+        gff_tmp = NamedTemporaryFile(delete=False)
+        pos_seq_dict = {}
+        with open(files_dict[repeat][0], "r") as repeat_f, open(
+                files_dict[repeat][2], "r") as quality_f:
+            for line_r, line_q in zip(repeat_f, quality_f):
+                if "chrom" in line_r:
+                    idx_ranges(THRESHOLD_SEGMENT, seq_id, gff_tmp,
+                               configuration.REPEATS_FEATURE, repeat,
+                               pos_seq_dict)
+                    seq_id = line_r.rstrip().split("chrom=")[1]
+                    pos_seq_dict = {}
+                else:
+                    hits = int(line_r.rstrip().split("\t")[1])
+                    if hits >= THRESHOLD:
+                        position = int(line_r.rstrip().split("\t")[0])
+                        pos_seq_dict[position] = line_q.rstrip().split("\t")[1]
+        idx_ranges(THRESHOLD_SEGMENT, seq_id, gff_tmp,
+                   configuration.REPEATS_FEATURE, repeat, pos_seq_dict)
+        gff_tmp_list.append(gff_tmp.name)
+        gff_tmp.close()
+    sort_records(gff_tmp_list, headers, OUTPUT_GFF)
+    for tmp in gff_tmp_list:
+        os.unlink(tmp)
+
+
+def idx_ranges(THRESHOLD_SEGMENT, seq_id, gff_file, feature, repeat,
+               pos_seq_dict):
+    indices = sorted(pos_seq_dict.keys(), key=int)
+    for key, group in groupby(
+            enumerate(indices),
+            lambda index_item: index_item[0] - index_item[1]):
+        group = list(map(itemgetter(1), group))
+        if len(group) > THRESHOLD_SEGMENT:
+            sum_qual = 0
+            for position in group:
+                sum_qual += int(pos_seq_dict[position])
+            qual_per_reg = sum_qual / len(group)
+            # Take boundaries of the group vectors
+            gff_file.write(
+                "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\tName={};Average_PID={}\n".format(
+                    seq_id, configuration.SOURCE_PROFREP, feature, group[
+                        0], group[-1], configuration.GFF_EMPTY,
+                    configuration.GFF_EMPTY, configuration.GFF_EMPTY, repeat,
+                    round(qual_per_reg)).encode("utf-8"))
+
+
+def idx_ranges_N(indices, THRESHOLD_SEGMENT, seq_id, gff_file, feature,
+                 att_name):
+    for key, group in groupby(
+            enumerate(indices),
+            lambda index_item: index_item[0] - index_item[1]):
+        group = list(map(itemgetter(1), group))
+        if len(group) > THRESHOLD_SEGMENT:
+            # Take boundaries of the group vectors
+            gff_file.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\tName={}\n".format(
+                seq_id, configuration.SOURCE_PROFREP, feature, group[0], group[
+                    -1], configuration.GFF_EMPTY, configuration.GFF_EMPTY,
+                configuration.GFF_EMPTY, att_name))
+
+
+def sort_records(gff_tmp_list, headers, OUTPUT_GFF):
+    opened_files = [open(i, "r") for i in gff_tmp_list]
+    files_lines = dict((key, "") for key in opened_files)
+    count_without_line = 0
+    count_seq = 0
+    ####################################################################
+    present_seqs = headers
+    ####################################################################
+    with open(OUTPUT_GFF, "w") as final_gff:
+        final_gff.write("{}\n".format(configuration.HEADER_GFF))
+        while True:
+            for file_name in opened_files:
+                if not files_lines[file_name]:
+                    line = file_name.readline()
+                    if line:
+                        files_lines[file_name] = line
+                    else:
+                        count_without_line += 1
+            if count_without_line == len(opened_files):
+                break
+            count_without_line = 0
+            count = 0
+            lowest_pos = float("inf")
+            for file_key in files_lines.keys():
+                if files_lines[file_key].split("\t")[0] == present_seqs[
+                        count_seq]:
+                    count += 1
+                    start_pos = int(files_lines[file_key].split("\t")[3])
+                    if start_pos < lowest_pos:
+                        lowest_pos = start_pos
+                        record_to_write = files_lines[file_key]
+                        lowest_file_key = file_key
+            if count == 0:
+                count_seq += 1
+            else:
+                final_gff.write(record_to_write)
+                files_lines[lowest_file_key] = ""
+
+
+def main():
+    pass
+
+
+if __name__ == "__main__":
+    main()