MHCflurry 1.0.0: support for percentile ranks, cross validation, faster predictions, and other improvements

[timodonnell]

• First cut of supporting quantiles ("percent ranks") per allele. Closes #87.
• Some refactoring of amino_acid.py

[coveralls]

Coverage increased (+3.3%) to 72.718% when pulling 868caf01d508c99ad4a918b4664c07c8f4d243e6 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.8%) to 72.278% when pulling 868caf01d508c99ad4a918b4664c07c8f4d243e6 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.5%) to 71.988% when pulling e4c21bcba014600c072bb1bc9e0d6313fb205d2c on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.5%) to 71.96% when pulling 2b2ce0ce10a048f653a05a85106d908fb3fc6996 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.123% when pulling ac3f874fa90dc032bf592b2f364a5564c9cd8373 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.123% when pulling ac3f874fa90dc032bf592b2f364a5564c9cd8373 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.123% when pulling ec543a8a8388b5356419b24ce3d77acaefb07896 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.123% when pulling ec543a8a8388b5356419b24ce3d77acaefb07896 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.123% when pulling ec543a8a8388b5356419b24ce3d77acaefb07896 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.123% when pulling 700535fa58a6854280f15f75fdf0df8f49764bf6 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.102% when pulling 55e3cfc12f49b5526a6abdbe2b38e9d9abe495f8 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+4.8%) to 74.191% when pulling 78cdb2651e41c42667610636caac663c6f180410 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+4.8%) to 74.191% when pulling 78cdb2651e41c42667610636caac663c6f180410 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+4.8%) to 74.191% when pulling 78cdb2651e41c42667610636caac663c6f180410 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.184% when pulling 78cdb2651e41c42667610636caac663c6f180410 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.184% when pulling 78cdb2651e41c42667610636caac663c6f180410 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.7%) to 72.157% when pulling 419853382a008de3d498664ebedc82c526351419 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.8%) to 72.239% when pulling cbb649d692b684ba2f847a226449c7c9a9ddbe46 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.0%) to 72.39% when pulling 38adfb4d8f310f7f3399e4149271b1a8bc7aef82 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.6%) to 73.029% when pulling ffcb693f624232798536cd135f02f36ef1da915a on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.6%) to 73.029% when pulling ffcb693f624232798536cd135f02f36ef1da915a on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.6%) to 73.029% when pulling ffcb693f624232798536cd135f02f36ef1da915a on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.0%) to 72.39% when pulling ffcb693f624232798536cd135f02f36ef1da915a on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.0%) to 72.39% when pulling ef9a61a968531cc8d36ad695eed4936acef3f7ea on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.6%) to 71.043% when pulling 5b4dfbd205e4c26c6f39c983cd1125038e5bc7d6 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.6%) to 71.043% when pulling c0fbebe1b4b95c0988fdbe874d1f48706a743040 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.7%) to 71.123% when pulling b1dbb362f947bf21006fda46188cd4de055f0c95 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.6%) to 71.019% when pulling e062613c0c34c2860b0364c99b072c5ab50ccbaf on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.07%) to 71.506% when pulling 7d323a86386d682e43afafc52887161316c35b8c on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.8%) to 71.284% when pulling bdee83303432495c30bd5c3b8387bab6e5f303b2 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.8%) to 71.284% when pulling bdee83303432495c30bd5c3b8387bab6e5f303b2 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.8%) to 71.284% when pulling d65f774059bc3388db6afda3e5db868a62799e89 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.8%) to 71.284% when pulling d65f774059bc3388db6afda3e5db868a62799e89 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.8%) to 71.284% when pulling d65f774059bc3388db6afda3e5db868a62799e89 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+2.0%) to 71.389% when pulling 873a60a5f83973165680f8577a5c76ee3a260a0a on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.9%) to 71.298% when pulling 1f38fa819734f5676b0cd7a448a77477e0531373 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[timodonnell]

Thanks for the code review @iskandr , updated to address comments

[coveralls]

Coverage increased (+1.6%) to 71.038% when pulling 4e68da437496ddf8e6158103e7bd44698bbcd291 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.7%) to 71.091% when pulling b2b032c76a5a8999be8ffd6626865fbca9d916e9 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.7%) to 71.117% when pulling 6f6070b23a0e152a947f6b2909d80f87214bd9db on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+1.6%) to 71.012% when pulling 3f8bcde12e0a3b7da59363f237a757e15661a775 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.6%) to 73.055% when pulling 8cd37f0801455d4a759a654616648d12f6800863 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.099% when pulling 5a7a65f8ecb44e15fed3f3833f2643e937389a57 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.099% when pulling 19b6a156f849e5d97797d76e5d89a6c6d2e091a7 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.099% when pulling 9644ae148c84fd8d5821a9f65846086fa2fd6abc on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.099% when pulling 2aa3ed5dcad77b80549a25a6193c5601ae6ae2fa on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.099% when pulling 2aa3ed5dcad77b80549a25a6193c5601ae6ae2fa on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.099% when pulling d6d0fc9a76ee6d86e31732336c934e1553f96dea on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.7%) to 73.143% when pulling d52134fed62c8dddc3461c3e0b666197ba48ba50 on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.

[coveralls]

Coverage increased (+3.5%) to 72.978% when pulling a837de1a74af5478f2b7fd36f8771e8f781b2dde on percentile-ranks into bbcfc2ba17c2450023411dd14e3f1c418a577af1 on master.