update pipeline for new dfe with h-s relationship

[chriscrsmith]

For issue #106

Changed one block of code in ts2fs.py, to deal with lists of mutation types within a DFE.

Tested by running sims with Mixed_K23 DFE (and also the Kim DFE), and running the dfe.snake pipeline. Example output below:

[chriscs@talapas-ln1 analysis2]$ cat results/inference/OutOfAfrica_3G09/dadi/Gamma_H17/ensembl_havana_104_exons/1845187043/pop1/pop1.dadi.neu.fs
41 unfolded
4603 1058 315 206 156 128 94 88 79 69 60 45 50 46 39 33 29 51 35 32 35 39 33 35 23 35 32 26 42 30 38 39 26 48 35 39 21 29 33 41 214
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

[chriscs@talapas-ln1 analysis2]$ cat results/inference/OutOfAfrica_3G09/dadi/Gamma_H17/ensembl_havana_104_exons/1845187043/pop1/pop1.dadi.nonneu.fs
41 unfolded
5235 1456 333 186 127 122 83 75 63 52 40 41 39 49 26 38 29 42 30 20 22 29 29 30 22 21 18 13 19 10 22 20 14 21 26 29 20 19 19 41 2168
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

[chriscs@talapas-ln1 analysis2]$ cat results/inference/OutOfAfrica_3G09/dadi/Mixed_K23/ensembl_havana_104_exons/1675701734/pop0/pop0.dadi.neu.fs
41 unfolded
2778 1871 897 550 356 254 235 178 173 151 123 120 88 87 73 90 63 65 62 40 57 43 37 23 29 49 46 29 32 39 35 41 22 37 42 29 23 34 34 35 9
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

[chriscs@talapas-ln1 analysis2]$ cat results/inference/OutOfAfrica_3G09/dadi/Mixed_K23/ensembl_havana_104_exons/1675701734/pop0/pop0.dadi.nonneu.fs
41 unfolded
4320 2623 1018 562 402 274 229 160 154 116 116 83 97 59 80 55 66 61 35 48 33 41 34 18 36 29 36 24 18 39 26 25 26 19 25 22 18 19 16 28 2216
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

[petrelharp]

LGTM, but someone actually working on this code base should merge this? (@lntran26? @mufernando?)

[lntran26]

I'll test this out to make sure it works before merging

[lntran26]

@chriscrsmith I ran the full pipeline workflow and found that we also need to change workflows/stairway.py line 76 to make this compatible with the n_t part of the pipeline. The exact same change you did for ts2fs.py here would work. Once you add this change I think we can merge.

[chriscrsmith]

Thanks @lntran26 . How does this look?

[petrelharp]

Waiting on @chriscrsmith or @lntran26 to test this again to merge (unless that's been done)?

[lntran26]

I've done the testing already and think it's ready to merge!