--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RaGOO/ragoo_utilities/get_contig_borders.py	Mon Jul 26 18:22:37 2021 +0000
@@ -0,0 +1,41 @@
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description='given and orderings file and a contigs fasta index, print a bed file of contig placements in the pseudomolecules.')
+    parser.add_argument("orderings", metavar="<orderings.txt>", type=str, help="orderings file from RaGOO")
+    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="100", type=int, help="Gap size used for pseudomolecule padding.")
+
+    # Get the command line arguments
+    args = parser.parse_args()
+    orderings_file = args.orderings
+    fai_file = args.fai
+    gap_len = args.gap_len
+
+    # Save the contig orderings
+    ctgs = []
+    with open(orderings_file, 'r') as f:
+        for line in f:
+            ctgs.append(line.rstrip().split('\t')[0])
+
+    # 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])
+
+    # Get contig borders
+    final_bed = []
+    current_pos = 0
+
+    for ctg in ctgs:
+        start = current_pos
+        end = current_pos + ctg_lens[ctg]
+        current_pos += ctg_lens[ctg]
+        current_pos += gap_len
+        pm_header = orderings_file[orderings_file.rfind('/')+1:orderings_file.rfind('_')] + '_RaGOO'
+        final_bed.append('%s\t%r\t%r' % (pm_header, start, end))
+
+    print('\n'.join(final_bed))
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