final kimura calculation missing for LINEs

[hy09]

Hi Toby,
Thanks for adding the re-calculation of Kimura distance in the final gff file. However, I've noticed the values are missing (KIMURA80=nan) for a significant number of LINEs and LTRs. This is due to a discrepancy in repeat IDs. In RepeatMasker's .out file, strings "_3end", "_5end", or "_orf2" are removed after adjusting the positions. Thus the corresponding consensus sequence cannot be found and no error message is produced.

Here is an example line in the final .gff file:

1	Earl_Grey	LINE/L1	3054064	3054829	1592	-	.	TSTART=5335;TEND=6124;ID=L1MB4;SHORTTE=F;KIMURA80=nan

Corresponding repeat IDs in dfam database:

>L1MB4_3end#LINE/L1 @Eutheria [S:45,55]
>L1MB4_5end#LINE/L1 @Eutheria [S:55]

With LTRs, some of the repeatMasker outputs have "-INT" added and that caused the same problem.

Any comments would be appreciated. Thanks!

[TobyBaril]

This is due to using pre-existing libraries in addition to the de novo pipeline. @jamesdgalbraith we should be able to work something out for this I think?