--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RaGOO/lift_over.py	Mon Jul 26 18:22:37 2021 +0000
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+def get_contig_lengths(in_fai):
+    """ Get contig lengths from a fasta index. """
+    lens = dict()
+    with open(in_fai, 'r') as f:
+        for line in f:
+            L1 = line.rstrip().split('\t')
+            lens[L1[0]] = int(L1[1])
+    return lens
+
+
+def get_contig_orderings(in_groupings):
+    """
+    From the orderings files, return the following:
+
+    1. Dictionary associating a reference header with a list of ordered contig headers
+    2. Dictionary associating a contig with an orientation
+    3. Dicitonary associating a contig with its assigned reference header
+    """
+    orderings = dict()
+    orientations = dict()
+    ref_chr = dict()
+
+    # Iterate through the orderings files
+    with open(in_groupings, 'r') as f1:
+        for line1 in f1:
+            header = line1.rstrip().replace('_orderings.txt', '_RaGOO')
+            header = header[header.rfind('/') + 1:]
+
+            # Initialize the list for the orderings
+            orderings[header] = []
+            with open(line1.rstrip(), 'r') as f2:
+                for line2 in f2:
+                    L1 = line2.rstrip().split('\t')
+                    orderings[header].append(L1[0])
+                    orientations[L1[0]] = L1[1]
+                    ref_chr[L1[0]] = header
+    return orderings, orientations, ref_chr
+
+
+def get_reverse_coords(start_coord, end_coord, seq_length):
+    """
+    Returns new genomic coordinates of a region that has undergone reverse complementation.
+    new start coordinate = seqLength - endCoord
+    new end coordinate = seqLength - startCoord
+    """
+    return seq_length - (end_coord - 1), seq_length - (start_coord - 1)
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description='Lift-over gff coordinates to from contigs to RaGOO pseudomolecules.'
+                                                 'Please make sure that you are using the updated gff file and set of contigs if chimera correction was used.'
+                                                 'Also make sure that the gap size (-g) matches that which was used during ordering and orienting.')
+    parser.add_argument("gff", metavar="<genes.gff>", type=str, help="Gff file to be lifted-over")
+    parser.add_argument("orderings", metavar="<orderings.fofn>", type=str, help="List of RaGOO 'orderings' files. 'ls ragoo_output/orderings/* > orderings.fofn'")
+    parser.add_argument("fai", metavar="<contigs.fasta.fai>", type=str, help="Fasta index for contigs.'")
+    parser.add_argument("-g", metavar="100", type=int, default=100, help="Gap size for padding in pseudomolecules (must match what was used for 'ragoo.py'.")
+
+
+    # Get the command line arguments
+    args = parser.parse_args()
+    gff_file = args.gff
+    orderings_file = args.orderings
+    fai_file = args.fai
+    gap_size = args.g
+
+    # Get the contig lengths
+    ctg_lens = get_contig_lengths(fai_file)
+
+    # Get the contig orderings and orientations
+    ctg_orderings, ctg_orientations, ctg_chr = get_contig_orderings(orderings_file)
+
+    #Iterate through the GFF features and update
+    offsets = dict()
+    with open(gff_file) as f:
+        for gff_line in f:
+            if gff_line.startswith("#"):
+                print(gff_line.rstrip())
+            else:
+                gff_fields = gff_line.rstrip().split('\t')
+                gff_header, start, end, strand = gff_fields[0], int(gff_fields[3]), int(gff_fields[4]), gff_fields[6]
+                new_header = ctg_chr[gff_header]
+
+                # Check that this contig header is in our list of headers
+                if gff_header not in ctg_lens.keys():
+                    err_msg = """ %s was not found in the list of orderings files provided.
+                    Please check that you are using the correct files. If chimeric contig correction was
+                    used, please use the corrected gff and fai file. 
+                    """
+                    raise ValueError(err_msg)
+
+                # Check if the contig has been reverse complemented. Update accordingly
+                if ctg_orientations[gff_header] == '-':
+                    start, end = get_reverse_coords(start, end, ctg_lens[gff_header])
+
+                    # Set the opposite strand
+                    if strand == '+':
+                        strand = '-'
+                    else:
+                        strand = '+'
+
+                # Check if the offset for this contig has already been calculated
+                if gff_header in offsets:
+                    offset = offsets[gff_header]
+                else:
+                    ctg_idx = ctg_orderings[new_header].index(gff_header)
+                    offset = 0
+
+                    for ctg in ctg_orderings[new_header][:ctg_idx]:
+                        offset += ctg_lens[ctg]
+                        offset += gap_size
+
+                    # memoize the offset
+                    offsets[gff_header] = offset
+
+                new_start = start + offset
+                new_end = end + offset
+
+                gff_fields[0] = new_header
+                gff_fields[3] = str(new_start)
+                gff_fields[4] = str(new_end)
+                gff_fields[6] = strand
+                print('\t'.join(gff_fields))