Create WGA_from_mummer.py - handling multi-contig reference??
vehuardo opened this issue · comments
Dear Sir,
I'm a great admirer of your code!
I have particularly enjoyed the tool 'Create WGA_from_mummer.py' which ages better than any wine I have tasted so far. I've been spoiled with closed genome reference sequences in the past, but suddenly I find myself in a situation where my reference exists as multiple contigs (!)
I believe the python code referenced above requires that the reference is in a single contig, but Mummer is able to align genomes existing in multiple contigs. An example of how a *.snps.txt output file from a multi-contig assembly aligned to a multi-contig reference with Mummer is pasted below. Do you think it would be possible to add the ability to handle multi-contig references to 'Create WGA_from_mummer.py' ??
Sincere and utmost regards,
Vegard
[P1] [SUB] [P2] | [BUFF] [DIST] | [FRM] [TAGS]
===================================================================
279 G C 394 | 90 279 | 1 1 FRDV01000001.1 FPLE01000001.1
369 T C 484 | 90 369 | 1 1 FRDV01000001.1 FPLE01000001.1
532 T C 647 | 63 532 | 1 1 FRDV01000001.1 FPLE01000001.1
595 A G 710 | 49 595 | 1 1 FRDV01000001.1 FPLE01000001.1
644 T C 759 | 49 644 | 1 1 FRDV01000001.1 FPLE01000001.1
971 C T 1086 | 146 971 | 1 1 FRDV01000001.1 FPLE01000001.1
1117 A G 1232 | 27 1117 | 1 1 FRDV01000001.1 FPLE01000001.1
1144 G A 1259 | 27 1144 | 1 1 FRDV01000001.1 FPLE01000001.1
1224 G A 1339 | 80 1224 | 1 1 FRDV01000001.1 FPLE01000001.1
........
........
12532 A G 12430 | 82 12430 | 1 1 FRDV01000086.1 FPLE01000067.1
12614 T C 12512 | 72 12512 | 1 1 FRDV01000086.1 FPLE01000067.1
12686 A G 12584 | 72 12584 | 1 1 FRDV01000086.1 FPLE01000067.1
12766 A T 12664 | 12 12664 | 1 1 FRDV01000086.1 FPLE01000067.1
12778 A T 12676 | 12 12676 | 1 1 FRDV01000086.1 FPLE01000067.1