--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RaGOO/make_agp.py	Mon Jul 26 18:22:37 2021 +0000
@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+import sys
+import argparse
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Produce an AGP v2.0 file describing the ordering and orienting performed by RaGOO.')
+    parser.add_argument("orderings", metavar="<orderings.fofn>", type=str, help="file of orderings files ($ls ragoo_output/orderings/* > orderings.fofn)")
+    parser.add_argument("fai", metavar="<contigs.fasta.fai>", type=str, help="index file for contigs ($samtools faidx contigs.fasta)")
+    parser.add_argument("gap_len", metavar="gap_size", type=int, help="Gap size used for pseudomolecule padding.")
+
+    # Get the command line arguments
+    args = parser.parse_args()
+    orderings_fofn = args.orderings
+    fai_file = args.fai
+    gap_len = args.gap_len
+
+    # Save the contig orderings
+    orderings = dict()
+    with open(orderings_fofn, 'r') as f1:
+        for line1 in f1:
+            chrom = line1[line1.rfind("/")+1:line1.rfind("_orderings.txt")] + "_RaGOO"
+            orderings[chrom] = []
+            with open(line1.rstrip(), 'r') as f2:
+                for line2 in f2:
+                    L1 = line2.rstrip().split('\t')
+                    # Append (ctg_header, orientation)
+                    orderings[chrom].append((L1[0], L1[1]))
+
+    # Get contig lengths
+    ctg_lens = dict()
+    with open(fai_file, 'r') as f:
+        for line in f:
+            L1 = line.split('\t')
+            ctg_lens[L1[0]] = int(L1[1])
+
+    # Write the final AGP file
+    current_pos = 1
+    idx = 1
+    chrom_idx = 1
+    out_buff = []
+
+    sys.stdout.write("## AGP-version 2.0\n")
+    sys.stdout.write("## AGP constructed by RaGOO\n")
+    for chrom in orderings:
+        if orderings[chrom]:
+            for ctg, strand in orderings[chrom]:
+                start = current_pos
+                end = current_pos + ctg_lens[ctg] - 1
+                line_buff = list()
+
+                # Write the line for the contig
+                line_buff.append(chrom)
+                line_buff.append(str(start))
+                line_buff.append(str(end))
+                line_buff.append(str(idx))
+                line_buff.append("W")
+                line_buff.append(ctg)
+                line_buff.append("1")
+                line_buff.append(str(end - start + 1))
+                line_buff.append(strand)
+                out_buff.append("\t".join(line_buff))
+
+                # Write the line for the gap
+                idx += 1
+                current_pos += ctg_lens[ctg]
+                start = current_pos
+                end = current_pos + gap_len - 1
+                line_buff = list()
+
+                line_buff.append(chrom)
+                line_buff.append(str(start))
+                line_buff.append(str(end))
+                line_buff.append(str(idx))
+                line_buff.append("N")
+                line_buff.append(str(gap_len))
+                line_buff.append("scaffold")
+                line_buff.append("yes")
+                line_buff.append("align_genus")
+                out_buff.append("\t".join(line_buff))
+
+                idx += 1
+                current_pos += gap_len
+
+            # Pop the last gap since we don't end with padding
+            out_buff.pop()
+            idx =1
+            chrom_idx += 1
+            current_pos = 1
+
+    sys.stdout.write("\n".join(out_buff) + "\n")
\ No newline at end of file