Start working on fixreference script

fixreference.py

+#!/usr/bin/env python3
+
+
+def get_valid_maps(maps):
+    matchs = []
+    bad_matchs = []
+    with open(maps, 'r') as mps:
+        for line in mps:
+            cols = line.rstrip().split("\t")
+            ref = cols[0]
+            ref_len = int(cols[1])
+            prot = cols[2]
+            prot_len = int(cols[3])
+            start_ref = int(cols[4])
+            end_ref = int(cols[5])
+            start_prot = int(cols[6])
+            end_prot = int(cols[7])
+            ref_seq = cols[8]
+            prot_seq = cols[9]
+            e_value = cols[10]
+            bitscore = cols[11]
+            match_len = int(cols[12])
+            btop = cols[13]
+            ref_frame = int(cols[14])
+            if match_len / prot_len >= 0.98:
+                to_matchs = matchs
+            else:
+                to_matchs = bad_matchs
+            to_matchs.append({
+                "ref": {"id": ref, "len": ref_len, "seq": ref_seq, "start": start_ref, "end": end_ref,
+                        "frame": ref_frame},
+                "prot": {"id": prot, "len": prot_len, "seq": prot_seq, "start": start_prot, "end": end_prot},
+                "e_value": e_value,
+                "bitscore": bitscore,
+                "btop": btop
+            })
+
+            return matchs, bad_matchs
+
+
+def get_gap_sequence(seq, pos_gap):
+    i = 0
+    gap_seq = ""
+    end_seq = False
+    while i < len(seq) and not end_seq:
+        if pos_gap == 0:
+            next_base = seq[i+1]
+            if seq[i] != "-":
+                end_seq = True
+        else:
+            next_base = seq[i]
+            if seq[i+1] != "-":
+                end_seq = True
+        if not end_seq:
+            gap_seq += next_base
+    return gap_seq
+
+
+def parse_btop(btop, rseq, pseq):
+    """
+    Parse btop
+
+    :param btop: btop string
+    :param rseq: reference sequence
+    :param pseq: protein sequence
+    :return: parsed btop
+    """
+    reference = []
+    protein = []
+    i = 0
+    while i < len(btop):
+        char = btop[i]
+        if char.isalpha():
+            pchar = btop[i+1]
+            if pchar.isalpha():
+                reference.append(char)
+                protein.append(btop[i+1])
+                i += 2
+            else:
+                gap_seq = get_gap_sequence(rseq[i:], 1)
+                reference.append(gap_seq)
+                protein.append("-" * len(gap_seq))
+                i += len(gap_seq) + 1
+        elif char.isdigit():
+            j = i+1
+            while btop[i:j].isdigit():
+                j += 1
+            j -= 1
+            m_size = int(btop[i:j])
+            i = j
+        elif char == "-":
+            gap_seq =get_gap_sequence(pseq[i:], 0)
+            protein.append(gap_seq)
+            reference.append("-" * len(gap_seq))
+        elif char == "/":
+            pass  # TODO
+        elif char == "\\":
+            pass  # TODO
+
+    return reference, protein
+
+
+def parse_valid_matches(matches):
+    for match in matches:
+        reference, protein = parse_btop(match["btop"], match["ref"]["seq"], match["prot"]["seq"])
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Fix reference using diamond mapping of reference proteins on"
+                                                 "reference file")
+    parser.add_argument("-r", "--reference", help="Reference fasta file", required=True)
+    parser.add_argument("-d", "--diamond", help="Diamond mapping file", required=True)
+    parser.add_argument("-o", "--output-prefix", help="Output prefix", required=True)