Mercurial > repos > abims-sbr > pogs
changeset 4:b7bd93fc0ac9 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 8a27e74e95c5639292ca09c7e1680acd1088dcdd-dirty
| author | abims-sbr |
|---|---|
| date | Mon, 29 May 2017 07:45:07 -0400 |
| parents | 1c1798e15bb1 |
| children | dad7053ba20e |
| files | 02_backup_list_LOCUS POGs.xml scripts/S02_get_locus_orthologs_part2_v2.py test-data/outputfilter.zip test-data/outputpairwise.zip |
| diffstat | 5 files changed, 27061 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
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+S'>Pf7571_1/1_1.000_266' +p9215 +aS'>Pg3483_1/1_1.000_243' +p9216 +aa(lp9217 +S'>Pf263_1/1_1.000_244' +p9218 +aS'>Pg4026_1/1_1.000_186' +p9219 +aa(lp9220 +S'>Pf5677_1/1_1.000_213' +p9221 +aS'>Pg6624_1/1_1.000_161' +p9222 +aa(lp9223 +S'>Pf4760_1/1_1.000_240' +p9224 +aS'>Pg2876_1/1_1.000_217' +p9225 +aS'>Te6448_1/1_1.000_249' +p9226 +aa(lp9227 +S'>Pf4094_1/1_1.000_240' +p9228 +aS'>Pg7417_1/1_1.000_234' +p9229 +aa(lp9230 +S'>Pf190_1/1_1.000_461' +p9231 +aS'>Pg5667_1/1_1.000_630' +p9232 +aa(lp9233 +S'>Pf6045_1/1_1.000_489' +p9234 +aS'>Pg7476_1/1_1.000_222' +p9235 +aa(lp9236 +S'>Pf3936_1/1_1.000_201' +p9237 +ag7120 +aS'>Pg398_1/1_1.000_357' +p9238 +ag6092 +ag7123 +ag7124 +aS'>Th7730_1/1_1.000_464' +p9239 +aa(lp9240 +S'>Am4983_1/1_1.000_348' +p9241 +aS'>Pu769_1/1_1.000_216' +p9242 +aa(lp9243 +S'>Am7826_1/1_1.000_675' +p9244 +aS'>Pu6719_1/1_1.000_465' +p9245 +aa(lp9246 +S'>Am4865_1/1_1.000_261' +p9247 +aS'>Pu935_1/1_1.000_235' +p9248 +aa(lp9249 +S'>Ac4506_1/1_1.000_256' +p9250 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+aS'>Ph1477_1/1_1.000_211' +p10863 +aa(lp10864 +S'>Am3321_1/1_1.000_1287' +p10865 +aS'>Ph6121_1/1_1.000_162' +p10866 +aS'>Te6299_1/1_1.000_224' +p10867 +aa(lp10868 +S'>Am7571_1/1_1.000_226' +p10869 +aS'>Ph2530_1/1_1.000_1083' +p10870 +aa(lp10871 +S'>Am4406_1/1_1.000_314' +p10872 +aS'>Ph1523_1/1_1.000_1086' +p10873 +aa(lp10874 +S'>Am3370_1/1_1.000_204' +p10875 +aS'>Ph7246_1/1_1.000_246' +p10876 +aS'>Te6940_1/1_1.000_223' +p10877 +aa(lp10878 +S'>Am6859_1/1_1.000_259' +p10879 +aS'>Ph4305_1/1_1.000_270' +p10880 +aa(lp10881 +S'>Am5885_1/1_1.000_262' +p10882 +aS'>Ph2395_1/1_1.000_329' +p10883 +aa(lp10884 +S'>Am1672_1/1_1.000_831' +p10885 +aS'>Ph2308_1/1_1.000_202' +p10886 +aa(lp10887 +S'>Am432_1/1_1.000_214' +p10888 +aS'>Ph4045_1/1_1.000_330' +p10889 +aS'>Te6166_1/1_1.000_263' +p10890 +aa(lp10891 +S'>Am6903_1/1_1.000_258' +p10892 +aS'>Pg7191_1/1_1.000_1050' +p10893 +aS'>Ph434_1/1_1.000_386' +p10894 +aa(lp10895 +S'>Am5178_1/1_1.000_693' +p10896 +aS'>Ph4404_1/1_1.000_232' +p10897 +aa(lp10898 +S'>Am982_1/1_1.000_335' +p10899 +aS'>Ph1168_1/1_1.000_383' +p10900 +aS'>Te6349_1/1_1.000_340' +p10901 +aS'>Th5955_1/1_1.000_1070' +p10902 +aa(lp10903 +S'>Am5525_1/1_1.000_288' +p10904 +aS'>Ph66_1/1_1.000_443' +p10905 +aa(lp10906 +S'>Am18_1/1_1.000_223' +p10907 +aS'>Ph339_1/1_1.000_495' +p10908 +aa(lp10909 +S'>Am7299_1/1_1.000_517' +p10910 +aS'>Ph4694_1/1_1.000_540' +p10911 +aa(lp10912 +S'>Am2162_1/1_1.000_1158' +p10913 +aS'>Ph2812_1/1_1.000_267' +p10914 +aa(lp10915 +S'>Am5160_1/1_1.000_263' +p10916 +aS'>Ph6848_1/1_1.000_588' +p10917 +aS'>Th182_1/1_1.000_513' +p10918 +aa(lp10919 +S'>Am3954_1/1_1.000_543' +p10920 +aS'>Ph4187_1/1_1.000_161' +p10921 +aa(lp10922 +S'>Pg7831_1/1_1.000_278' +p10923 +aS'>Pu7247_1/1_1.000_453' +p10924 +aa(lp10925 +S'>Pg8267_1/1_1.000_846' +p10926 +aS'>Pu1720_1/1_1.000_840' +p10927 +aS'>Th5298_1/1_1.000_690' +p10928 +aa(lp10929 +S'>Pg2161_1/1_1.000_304' +p10930 +aS'>Pu2341_1/1_1.000_804' +p10931 +aa(lp10932 +S'>Pg3818_1/1_1.000_440' +p10933 +aS'>Pu4656_1/1_1.000_767' +p10934 +aa(lp10935 +S'>Ap1819_1/1_1.000_321' +p10936 +aS'>Pg6827_1/1_1.000_381' +p10937 +aS'>Pu5902_1/1_1.000_470' +p10938 +aa(lp10939 +S'>Pg260_1/1_1.000_195' +p10940 +aS'>Pu7920_1/1_1.000_227' +p10941 +aa(lp10942 +S'>Pg6332_1/1_1.000_318' +p10943 +aS'>Pu1481_1/1_1.000_228' +p10944 +aa(lp10945 +S'>Pg7576_1/1_1.000_524' +p10946 +aS'>Pu6775_1/1_1.000_808' +p10947 +aa(lp10948 +S'>Ap3262_1/1_1.000_237' +p10949 +ag7691 +aS'>Pg7704_1/1_1.000_240' +p10950 +ag7694 +ag7695 +aS'>Pu6106_1/1_1.000_277' +p10951 +aS'>Th4122_1/1_1.000_375' +p10952 +aa(lp10953 +S'>Pg1791_1/1_1.000_150' +p10954 +aS'>Pu4015_1/1_1.000_144' +p10955 +aa(lp10956 +S'>Pg2031_1/1_1.000_1207' +p10957 +aS'>Ph1246_1/1_1.000_492' +p10958 +aS'>Pu612_1/1_1.000_391' +p10959 +aa(lp10960 +S'>Ap4081_1/1_1.000_461' +p10961 +aS'>Pg6972_1/1_1.000_522' +p10962 +aS'>Pu4584_1/1_1.000_200' +p10963 +aa(lp10964 +S'>Pg1733_1/1_1.000_368' +p10965 +aS'>Pu5410_1/1_1.000_233' +p10966 +aa(lp10967 +S'>Pg1242_1/1_1.000_309' +p10968 +aS'>Pu358_1/1_1.000_606' +p10969 +aa(lp10970 +S'>Pg1145_1/1_1.000_250' +p10971 +aS'>Pu2146_1/1_1.000_728' +p10972 +aa(lp10973 +S'>Pg4099_1/1_1.000_159' +p10974 +aS'>Pu5147_1/1_1.000_175' +p10975 +aa(lp10976 +S'>Pg155_1/1_1.000_690' +p10977 +aS'>Pu7447_1/1_1.000_240' +p10978 +aa(lp10979 +S'>Pg4066_1/1_1.000_390' +p10980 +aS'>Pu443_1/1_1.000_572' +p10981 +aa(lp10982 +S'>Pg4470_1/1_1.000_298' +p10983 +aS'>Pg4732_1/1_1.000_634' +p10984 +aS'>Pu372_1/1_1.000_391' +p10985 +ag7054 +aS'>Th5688_1/1_1.000_256' +p10986 +aS'>Th663_1/1_1.000_215' +p10987 +aa(lp10988 +S'>Pg415_1/1_1.000_443' +p10989 +aS'>Ph6173_1/1_1.000_832' +p10990 +aS'>Pu4285_1/1_1.000_233' +p10991 +aa(lp10992 +S'>Pg3879_1/1_1.000_180' +p10993 +aS'>Pu6563_1/1_1.000_198' +p10994 +aa(lp10995 +S'>Ap6502_1/1_1.000_366' +p10996 +aS'>Pg7977_1/1_1.000_330' +p10997 +aS'>Pu4468_1/1_1.000_210' +p10998 +aa(lp10999 +S'>Pg115_1/1_1.000_219' +p11000 +aS'>Pu6030_1/1_1.000_522' +p11001 +aa(lp11002 +S'>Pg5795_1/1_1.000_324' +p11003 +aS'>Pu1728_1/1_1.000_213' +p11004 +aa(lp11005 +S'>Ap4494_1/1_1.000_786' +p11006 +aS'>Pg6162_1/1_1.000_372' +p11007 +aS'>Pu552_1/1_1.000_186' +p11008 +aa(lp11009 +S'>Pg6756_1/1_1.000_292' +p11010 +aS'>Pu6803_1/1_1.000_549' +p11011 +aa(lp11012 +S'>Pg2642_1/1_1.000_459' +p11013 +aS'>Pu3370_1/1_1.000_1350' +p11014 +aa(lp11015 +S'>Pg1768_1/1_1.000_347' +p11016 +aS'>Pu3727_1/1_1.000_275' +p11017 +aa(lp11018 +S'>Pg3035_1/1_1.000_220' +p11019 +aS'>Pu1965_1/1_1.000_628' +p11020 +aa(lp11021 +S'>Pg2130_1/1_1.000_183' +p11022 +aS'>Pu2433_1/1_1.000_330' +p11023 +aa(lp11024 +S'>Pg7447_1/1_1.000_355' +p11025 +aS'>Pu2707_1/1_1.000_782' +p11026 +aa(lp11027 +S'>Pg2650_1/1_1.000_249' +p11028 +aS'>Pu1900_1/1_1.000_187' +p11029 +aa(lp11030 +S'>Pg3465_1/1_1.000_198' +p11031 +aS'>Pu3979_1/1_1.000_205' +p11032 +aa(lp11033 +S'>Pg5796_1/1_1.000_217' +p11034 +aS'>Pu2668_1/1_1.000_234' +p11035 +aa(lp11036 +S'>Pg5655_1/1_1.000_174' +p11037 +aS'>Pu3440_1/1_1.000_330' +p11038 +aa(lp11039 +S'>Te4589_1/1_1.000_647' 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+aS'>Th1918_1/1_1.000_433' +p11077 +aa(lp11078 +S'>Te2142_1/1_1.000_300' +p11079 +aS'>Th5252_1/1_1.000_234' +p11080 +aa(lp11081 +S'>Te2839_1/1_1.000_309' +p11082 +aS'>Th770_1/1_1.000_265' +p11083 +aa(lp11084 +S'>Te5579_1/1_1.000_252' +p11085 +aS'>Th6351_1/1_1.000_205' +p11086 +aa(lp11087 +S'>Te5806_1/1_1.000_140' +p11088 +aS'>Th7118_1/1_1.000_190' +p11089 +aa(lp11090 +S'>Te4510_1/1_1.000_348' +p11091 +aS'>Th5676_1/1_1.000_249' +p11092 +aa(lp11093 +S'>Pg941_1/1_1.000_294' +p11094 +aS'>Te6822_1/1_1.000_261' +p11095 +aS'>Th4061_1/1_1.000_495' +p11096 +aa(lp11097 +S'>Te5254_1/1_1.000_1263' +p11098 +aS'>Th35_1/1_1.000_318' +p11099 +aa(lp11100 +S'>Ph7332_1/1_1.000_414' +p11101 +aS'>Te2179_1/1_1.000_408' +p11102 +aS'>Th3959_1/1_1.000_437' +p11103 +aa(lp11104 +S'>Pg4557_1/1_1.000_2178' +p11105 +ag2701 +aS'>Te2802_1/1_1.000_386' +p11106 +aS'>Th7321_1/1_1.000_150' +p11107 +aa(lp11108 +S'>Te3611_1/1_1.000_261' +p11109 +aS'>Th3394_1/1_1.000_511' +p11110 +aa(lp11111 +S'>Am7223_1/1_1.000_378' 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+aS'>Te5438_1/1_1.000_310' +p14103 +aa(lp14104 +S'>Am6733_1/1_1.000_646' +p14105 +aS'>Te4975_1/1_1.000_227' +p14106 +aa(lp14107 +S'>Am4705_1/1_1.000_352' +p14108 +aS'>Te4367_1/1_1.000_233' +p14109 +aa(lp14110 +S'>Am7674_1/1_1.000_774' +p14111 +aS'>Te4931_1/1_1.000_269' +p14112 +aa(lp14113 +S'>Am4273_1/1_1.000_774' +p14114 +aS'>Te66_1/1_1.000_218' +p14115 +aa(lp14116 +S'>Am5367_1/1_1.000_277' +p14117 +aS'>Te465_1/1_1.000_224' +p14118 +aa(lp14119 +S'>Am5464_1/1_1.000_495' +p14120 +aS'>Te2934_1/1_1.000_741' +p14121 +aa(lp14122 +S'>Am6988_1/1_1.000_529' +p14123 +aS'>Te4162_1/1_1.000_327' +p14124 +aa(lp14125 +S'>Am7186_1/1_1.000_171' +p14126 +aS'>Te2771_1/1_1.000_534' +p14127 +aa(lp14128 +S'>Am2323_1/1_1.000_358' +p14129 +aS'>Te2499_1/1_1.000_437' +p14130 +aa(lp14131 +S'>Am3473_1/1_1.000_492' +p14132 +aS'>Te7751_1/1_1.000_329' +p14133 +aa(lp14134 +S'>Am986_1/1_1.000_483' +p14135 +aS'>Te1406_1/1_1.000_277' +p14136 +aa(lp14137 +S'>Am3288_1/1_1.000_711' +p14138 +aS'>Te4403_1/1_1.000_204' 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+aS'>Te2617_1/1_1.000_375' +p14212 +aa(lp14213 +S'>Am468_1/1_1.000_216' +p14214 +aS'>Te227_1/1_1.000_2529' +p14215 +aa(lp14216 +S'>Am7596_1/1_1.000_402' +p14217 +aS'>Te6691_1/1_1.000_1107' +p14218 +aa(lp14219 +S'>Am4720_1/1_1.000_507' +p14220 +aS'>Te1290_1/1_1.000_457' +p14221 +aa(lp14222 +S'>Am4152_1/1_1.000_316' +p14223 +aS'>Pg4663_1/1_1.000_237' +p14224 +aS'>Te97_1/1_1.000_189' +p14225 +aa(lp14226 +S'>Am7437_1/1_1.000_198' +p14227 +aS'>Te3226_1/1_1.000_213' +p14228 +aa(lp14229 +S'>Am6896_1/1_1.000_627' +p14230 +aS'>Te127_1/1_1.000_245' +p14231 +aa(lp14232 +S'>Am7772_1/1_1.000_201' +p14233 +aS'>Te3645_1/1_1.000_322' +p14234 +aa(lp14235 +S'>Am7960_1/1_1.000_426' +p14236 +aS'>Te106_1/1_1.000_361' +p14237 +aa(lp14238 +S'>Am7563_1/1_1.000_239' +p14239 +aS'>Te3662_1/1_1.000_278' +p14240 +aa(lp14241 +S'>Am2761_1/1_1.000_236' +p14242 +aS'>Te5396_1/1_1.000_286' +p14243 +aa(lp14244 +S'>Am2914_1/1_1.000_404' +p14245 +aS'>Te2936_1/1_1.000_404' +p14246 +aa(lp14247 +S'>Am5574_1/1_1.000_442' 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+S'>Am2463_1/1_1.000_564' +p14285 +aS'>Te2799_1/1_1.000_223' +p14286 +aa(lp14287 +S'>Am7133_1/1_1.000_205' +p14288 +aS'>Te7294_1/1_1.000_611' +p14289 +aa(lp14290 +S'>Am2094_1/1_1.000_604' +p14291 +aS'>Te412_1/1_1.000_772' +p14292 +aa(lp14293 +S'>Am3485_1/1_1.000_308' +p14294 +aS'>Te3236_1/1_1.000_281' +p14295 +aa(lp14296 +S'>Am1482_1/1_1.000_183' +p14297 +aS'>Te1025_1/1_1.000_241' +p14298 +aa(lp14299 +S'>Am3258_1/1_1.000_245' +p14300 +aS'>Te4233_1/1_1.000_221' +p14301 +aa(lp14302 +S'>Am2888_1/1_1.000_369' +p14303 +aS'>Te6634_1/1_1.000_256' +p14304 +aa(lp14305 +S'>Am209_1/1_1.000_381' +p14306 +aS'>Ph7790_1/1_1.000_1467' +p14307 +aS'>Te2421_1/1_1.000_288' +p14308 +aa(lp14309 +S'>Am4530_1/1_1.000_264' +p14310 +aS'>Te7643_1/1_1.000_237' +p14311 +aa(lp14312 +S'>Am7951_1/1_1.000_285' +p14313 +aS'>Te2089_1/1_1.000_546' +p14314 +aa(lp14315 +S'>Pg8272_1/1_1.000_297' +p14316 +aS'>Te6215_1/1_1.000_453' +p14317 +aa(lp14318 +S'>Pg2915_1/1_1.000_544' +p14319 +aS'>Ph5816_1/1_1.000_1128' +p14320 +aS'>Te1478_1/1_1.000_546' +p14321 +aa(lp14322 +S'>Pg1275_1/1_1.000_411' +p14323 +aS'>Ph6004_1/1_1.000_249' +p14324 +aS'>Te7611_1/1_1.000_471' +p14325 +aa(lp14326 +S'>Pf6468_1/1_1.000_327' +p14327 +aS'>Pg1692_1/1_1.000_672' +p14328 +aS'>Pg8075_1/1_1.000_427' +p14329 +aS'>Ph158_1/1_1.000_386' +p14330 +aS'>Te2657_1/1_1.000_255' +p14331 +aa(lp14332 +S'>Pg7876_1/1_1.000_248' +p14333 +aS'>Te6991_1/1_1.000_438' +p14334 +aa(lp14335 +S'>Pg2449_1/1_1.000_324' +p14336 +aS'>Te6840_1/1_1.000_282' +p14337 +aa(lp14338 +S'>Pg6178_1/1_1.000_333' +p14339 +aS'>Te1188_1/1_1.000_376' +p14340 +aa(lp14341 +S'>Pg2704_1/1_1.000_143' +p14342 +aS'>Te1601_1/1_1.000_274' +p14343 +aa(lp14344 +S'>Pg2360_1/1_1.000_615' +p14345 +aS'>Te2784_1/1_1.000_201' +p14346 +aa(lp14347 +S'>Pg6842_1/1_1.000_240' +p14348 +aS'>Te3048_1/1_1.000_250' +p14349 +aa(lp14350 +S'>Pg5140_1/1_1.000_762' +p14351 +aS'>Te6069_1/1_1.000_744' +p14352 +aa(lp14353 +S'>Pg3482_1/1_1.000_639' +p14354 +aS'>Te2945_1/1_1.000_1083' +p14355 +aa(lp14356 +S'>Pg122_1/1_1.000_213' +p14357 +aS'>Te89_1/1_1.000_339' +p14358 +aa(lp14359 +S'>Pg7025_1/1_1.000_361' +p14360 +aS'>Te1814_1/1_1.000_894' +p14361 +aa(lp14362 +S'>Pg1471_1/1_1.000_311' +p14363 +aS'>Te425_1/1_1.000_276' +p14364 +aa(lp14365 +S'>Pg6566_1/1_1.000_495' +p14366 +aS'>Te3387_1/1_1.000_268' +p14367 +aa(lp14368 +S'>Pg5562_1/1_1.000_265' +p14369 +aS'>Te5475_1/1_1.000_177' +p14370 +aa(lp14371 +S'>Pg5149_1/1_1.000_303' +p14372 +aS'>Te1096_1/1_1.000_203' +p14373 +aa(lp14374 +S'>Pg7866_1/1_1.000_358' +p14375 +aS'>Te6336_1/1_1.000_420' +p14376 +aa(lp14377 +S'>Pg474_1/1_1.000_228' +p14378 +aS'>Te816_1/1_1.000_289' +p14379 +aa(lp14380 +S'>Pg6388_1/1_1.000_429' +p14381 +aS'>Te6726_1/1_1.000_411' +p14382 +aa(lp14383 +S'>Pg4457_1/1_1.000_804' +p14384 +aS'>Te2335_1/1_1.000_396' +p14385 +aa(lp14386 +S'>Pg7494_1/1_1.000_450' +p14387 +aS'>Te3626_1/1_1.000_264' +p14388 +aa(lp14389 +S'>Pg5836_1/1_1.000_432' +p14390 +aS'>Te7812_1/1_1.000_213' +p14391 +aa(lp14392 +S'>Pg332_1/1_1.000_312' +p14393 +aS'>Te3604_1/1_1.000_223' +p14394 +aa(lp14395 +S'>Pg1278_1/1_1.000_264' +p14396 +aS'>Te2034_1/1_1.000_384' +p14397 +aa(lp14398 +S'>Pg4223_1/1_1.000_474' +p14399 +aS'>Ph4554_1/1_1.000_195' +p14400 +aS'>Ph5129_1/1_1.000_274' +p14401 +aS'>Te6265_1/1_1.000_606' +p14402 +aa(lp14403 +S'>Pg1639_1/1_1.000_165' +p14404 +aS'>Te3114_1/1_1.000_219' +p14405 +aa(lp14406 +S'>Pg16_1/1_1.000_639' +p14407 +aS'>Te6151_1/1_1.000_456' +p14408 +aa(lp14409 +S'>Pg5235_1/1_1.000_561' +p14410 +aS'>Te2759_1/1_1.000_294' +p14411 +aa(lp14412 +S'>Pg5851_1/1_1.000_326' +p14413 +aS'>Te3023_1/1_1.000_369' +p14414 +aa(lp14415 +S'>Pg2992_1/1_1.000_471' +p14416 +aS'>Te5991_1/1_1.000_543' +p14417 +aa(lp14418 +S'>Pg2755_1/1_1.000_218' +p14419 +aS'>Te5370_1/1_1.000_311' +p14420 +aa(lp14421 +S'>Pg1076_1/1_1.000_154' +p14422 +aS'>Te4787_1/1_1.000_487' +p14423 +aa(lp14424 +S'>Pg6665_1/1_1.000_218' +p14425 +aS'>Te7673_1/1_1.000_495' +p14426 +aa(lp14427 +S'>Pg5653_1/1_1.000_990' +p14428 +aS'>Te7554_1/1_1.000_1260' +p14429 +aa(lp14430 +S'>Pg974_1/1_1.000_231' +p14431 +aS'>Te1897_1/1_1.000_330' +p14432 +aa(lp14433 +S'>Pg902_1/1_1.000_213' +p14434 +aS'>Te5268_1/1_1.000_942' +p14435 +aa(lp14436 +S'>Pf6552_1/1_1.000_656' +p14437 +aS'>Pg6575_1/1_1.000_222' +p14438 +aS'>Te6213_1/1_1.000_2454' +p14439 +aa(lp14440 +S'>Pg5680_1/1_1.000_355' +p14441 +aS'>Te1875_1/1_1.000_208' +p14442 +aa(lp14443 +S'>Pg6366_1/1_1.000_691' +p14444 +aS'>Te7494_1/1_1.000_201' +p14445 +aa(lp14446 +S'>Pg2173_1/1_1.000_276' +p14447 +aS'>Te7173_1/1_1.000_393' +p14448 +aa(lp14449 +S'>Pg7219_1/1_1.000_377' +p14450 +aS'>Te7558_1/1_1.000_270' +p14451 +aa(lp14452 +S'>Ph2551_1/1_1.000_372' +p14453 +aS'>Th739_1/1_1.000_208' +p14454 +aa(lp14455 +S'>Ph1157_1/1_1.000_260' +p14456 +aS'>Th909_1/1_1.000_618' +p14457 +aa(lp14458 +S'>Ph6998_1/1_1.000_327' +p14459 +aS'>Th2888_1/1_1.000_339' +p14460 +aa(lp14461 +S'>Ph3758_1/1_1.000_380' +p14462 +aS'>Th4253_1/1_1.000_567' +p14463 +aa(lp14464 +S'>Ph1903_1/1_1.000_293' +p14465 +aS'>Th6307_1/1_1.000_259' +p14466 +aa(lp14467 +S'>Ph6489_1/1_1.000_381' +p14468 +aS'>Th7655_1/1_1.000_192' +p14469 +aa(lp14470 +S'>Ph6755_1/1_1.000_408' +p14471 +aS'>Th114_1/1_1.000_1192' +p14472 +aa(lp14473 +S'>Ph7778_1/1_1.000_570' +p14474 +aS'>Th2938_1/1_1.000_570' +p14475 +aa(lp14476 +S'>Ph2388_1/1_1.000_447' +p14477 +aS'>Th649_1/1_1.000_747' +p14478 +aa(lp14479 +S'>Ph7337_1/1_1.000_258' +p14480 +aS'>Th760_1/1_1.000_844' +p14481 +aa(lp14482 +S'>Ph463_1/1_1.000_330' +p14483 +aS'>Th6602_1/1_1.000_483' +p14484 +aa(lp14485 +S'>Pg3763_1/1_1.000_198' +p14486 +aS'>Ph1926_1/1_1.000_1080' +p14487 +aS'>Th7098_1/1_1.000_372' +p14488 +aa(lp14489 +S'>Pg6145_1/1_1.000_207' +p14490 +aS'>Ph7955_1/1_1.000_897' +p14491 +aS'>Th5392_1/1_1.000_1236' +p14492 +aa(lp14493 +S'>Pg1068_1/1_1.000_1306' +p14494 +aS'>Ph1466_1/1_1.000_358' +p14495 +aS'>Th1754_1/1_1.000_203' +p14496 +aa(lp14497 +S'>Ph3858_1/1_1.000_523' +p14498 +aS'>Th7727_1/1_1.000_567' +p14499 +aa(lp14500 +S'>Ph3325_1/1_1.000_240' +p14501 +aS'>Th7238_1/1_1.000_345' +p14502 +aa(lp14503 +S'>Ph8059_1/1_1.000_231' +p14504 +aS'>Th2374_1/1_1.000_243' +p14505 +aa(lp14506 +S'>Ph3125_1/1_1.000_231' +p14507 +aS'>Th6337_1/1_1.000_279' +p14508 +aa(lp14509 +S'>Ph1616_1/1_1.000_336' +p14510 +aS'>Th6043_1/1_1.000_522' +p14511 +aa(lp14512 +S'>Ph8057_1/1_1.000_453' +p14513 +aS'>Th1029_1/1_1.000_484' +p14514 +aa(lp14515 +S'>Ph183_1/1_1.000_261' +p14516 +aS'>Te5784_1/1_1.000_235' +p14517 +aS'>Th1832_1/1_1.000_408' +p14518 +aa(lp14519 +S'>Ph4057_1/1_1.000_637' +p14520 +aS'>Th2478_1/1_1.000_219' +p14521 +aa(lp14522 +S'>Ph5509_1/1_1.000_249' +p14523 +aS'>Te3270_1/1_1.000_252' +p14524 +aS'>Th4074_1/1_1.000_462' +p14525 +aa(lp14526 +S'>Ph4476_1/1_1.000_1182' +p14527 +aS'>Th344_1/1_1.000_323' +p14528 +aa(lp14529 +S'>Ph1725_1/1_1.000_1125' +p14530 +aS'>Te4733_1/1_1.000_487' +p14531 +aa(lp14532 +S'>Ph2924_1/1_1.000_1392' +p14533 +aS'>Te4630_1/1_1.000_595' +p14534 +aa(lp14535 +S'>Ph4168_1/1_1.000_291' +p14536 +aS'>Te1373_1/1_1.000_1254' +p14537 +aa(lp14538 +S'>Pg3120_1/1_1.000_339' +p14539 +aS'>Ph1249_1/1_1.000_1377' +p14540 +aS'>Te5785_1/1_1.000_331' +p14541 +aa(lp14542 +S'>Ph3616_1/1_1.000_372' +p14543 +aS'>Te3549_1/1_1.000_379' +p14544 +aa(lp14545 +S'>Ph2548_1/1_1.000_263' +p14546 +aS'>Te113_1/1_1.000_336' +p14547 +aa(lp14548 +S'>Ph1464_1/1_1.000_259' +p14549 +aS'>Te2519_1/1_1.000_233' +p14550 +aa(lp14551 +S'>Ph663_1/1_1.000_735' +p14552 +aS'>Te1230_1/1_1.000_189' +p14553 +aa(lp14554 +S'>Ph4423_1/1_1.000_255' +p14555 +aS'>Te5304_1/1_1.000_470' +p14556 +aa(lp14557 +S'>Ph7598_1/1_1.000_573' +p14558 +aS'>Te4788_1/1_1.000_252' +p14559 +aa(lp14560 +S'>Ph8069_1/1_1.000_220' +p14561 +aS'>Te4578_1/1_1.000_214' +p14562 +aa(lp14563 +S'>Ph6873_1/1_1.000_265' +p14564 +aS'>Te4268_1/1_1.000_222' +p14565 +aa(lp14566 +S'>Ph2628_1/1_1.000_228' +p14567 +aS'>Te5034_1/1_1.000_209' +p14568 +aa(lp14569 +S'>Ap1134_1/1_1.000_273' +p14570 +aS'>Pu4925_1/1_1.000_262' +p14571 +aa(lp14572 +S'>Ap1450_1/1_1.000_242' +p14573 +aS'>Pu3518_1/1_1.000_1228' +p14574 +aa(lp14575 +S'>Ap2732_1/1_1.000_227' +p14576 +aS'>Pu8071_1/1_1.000_242' +p14577 +aa(lp14578 +S'>Ap1327_1/1_1.000_177' +p14579 +aS'>Pu872_1/1_1.000_213' +p14580 +aa(lp14581 +S'>Ap4298_1/1_1.000_252' +p14582 +aS'>Pu5455_1/1_1.000_237' +p14583 +aa(lp14584 +S'>Ap4276_1/1_1.000_254' +p14585 +aS'>Pu4104_1/1_1.000_177' +p14586 +aa(lp14587 +S'>Ap2574_1/1_1.000_171' +p14588 +aS'>Pu1625_1/1_1.000_186' +p14589 +aa(lp14590 +S'>Pf3043_1/1_1.000_207' +p14591 +aS'>Te1034_1/1_1.000_332' +p14592 +aa(lp14593 +S'>Pf4127_1/1_1.000_363' +p14594 +aS'>Te797_1/1_1.000_291' +p14595 +aa(lp14596 +S'>Pf127_1/1_1.000_345' +p14597 +aS'>Te1893_1/1_1.000_352' +p14598 +aa(lp14599 +S'>Pf2751_1/1_1.000_210' +p14600 +aS'>Te4010_1/1_1.000_747' +p14601 +aa(lp14602 +S'>Pf5962_1/1_1.000_510' +p14603 +aS'>Te1436_1/1_1.000_358' +p14604 +aa(lp14605 +S'>Pf326_1/1_1.000_420' +p14606 +aS'>Te6153_1/1_1.000_357' +p14607 +aa(lp14608 +S'>Pf301_1/1_1.000_429' +p14609 +aS'>Te6251_1/1_1.000_399' +p14610 +aa(lp14611 +S'>Pf6996_1/1_1.000_1335' +p14612 +aS'>Te200_1/1_1.000_1089' +p14613 +aa(lp14614 +S'>Pg4870_1/1_1.000_297' +p14615 +aS'>Ph5338_1/1_1.000_269' +p14616 +aa(lp14617 +S'>Pg4545_1/1_1.000_168' +p14618 +aS'>Ph2561_1/1_1.000_201' +p14619 +aa(lp14620 +S'>Pg3774_1/1_1.000_406' +p14621 +aS'>Ph6105_1/1_1.000_518' +p14622 +aa(lp14623 +S'>Pg8282_1/1_1.000_298' +p14624 +aS'>Ph3103_1/1_1.000_303' +p14625 +aa(lp14626 +S'>Pg1004_1/1_1.000_208' +p14627 +aS'>Ph3568_1/1_1.000_533' +p14628 +aa(lp14629 +S'>Pg1553_1/1_1.000_269' +p14630 +aS'>Ph7053_1/1_1.000_312' +p14631 +aa(lp14632 +S'>Pg3285_1/1_1.000_1275' +p14633 +aS'>Ph8085_1/1_1.000_552' +p14634 +aa(lp14635 +S'>Pg3589_1/1_1.000_207' +p14636 +aS'>Ph3067_1/1_1.000_304' +p14637 +aa(lp14638 +S'>Pg6683_1/1_1.000_454' +p14639 +aS'>Ph3487_1/1_1.000_329' +p14640 +aa(lp14641 +S'>Pg3241_1/1_1.000_277' +p14642 +aS'>Ph3217_1/1_1.000_282' +p14643 +aa(lp14644 +S'>Pg3988_1/1_1.000_228' +p14645 +aS'>Ph7897_1/1_1.000_311' +p14646 +aa(lp14647 +S'>Pg6274_1/1_1.000_215' +p14648 +aS'>Ph1553_1/1_1.000_204' +p14649 +aa(lp14650 +S'>Pg143_1/1_1.000_274' +p14651 +aS'>Ph79_1/1_1.000_1459' +p14652 +aa(lp14653 +S'>Pg4161_1/1_1.000_257' +p14654 +aS'>Ph3715_1/1_1.000_360' +p14655 +aa(lp14656 +S'>Pg1738_1/1_1.000_661' +p14657 +aS'>Ph194_1/1_1.000_492' +p14658 +aa(lp14659 +S'>Pg3944_1/1_1.000_297' +p14660 +aS'>Ph3917_1/1_1.000_197' +p14661 +aa(lp14662 +S'>Pg5509_1/1_1.000_203' +p14663 +aS'>Ph4435_1/1_1.000_444' +p14664 +aa(lp14665 +S'>Pg1225_1/1_1.000_286' +p14666 +aS'>Ph6514_1/1_1.000_326' +p14667 +aa(lp14668 +S'>Pg3930_1/1_1.000_589' +p14669 +aS'>Ph621_1/1_1.000_368' +p14670 +aa(lp14671 +S'>Pg1436_1/1_1.000_254' +p14672 +aS'>Ph254_1/1_1.000_606' +p14673 +aa(lp14674 +S'>Pg4839_1/1_1.000_515' +p14675 +aS'>Ph501_1/1_1.000_448' +p14676 +aa(lp14677 +S'>Pg2204_1/1_1.000_419' +p14678 +aS'>Ph4698_1/1_1.000_354' +p14679 +aa(lp14680 +S'>Pg6614_1/1_1.000_312' +p14681 +aS'>Ph7500_1/1_1.000_204' +p14682 +aa(lp14683 +S'>Pg4299_1/1_1.000_516' +p14684 +aS'>Ph7174_1/1_1.000_138' +p14685 +aa(lp14686 +S'>Pg5820_1/1_1.000_439' +p14687 +aS'>Ph1286_1/1_1.000_348' +p14688 +aa(lp14689 +S'>Pg7226_1/1_1.000_282' +p14690 +aS'>Ph5282_1/1_1.000_216' +p14691 +aa(lp14692 +S'>Pg121_1/1_1.000_301' +p14693 +aS'>Ph1831_1/1_1.000_338' +p14694 +aa(lp14695 +S'>Pg5101_1/1_1.000_267' +p14696 +aS'>Ph7120_1/1_1.000_411' +p14697 +aa(lp14698 +S'>Pg954_1/1_1.000_243' +p14699 +aS'>Ph5147_1/1_1.000_375' +p14700 +aa(lp14701 +S'>Pg2442_1/1_1.000_389' +p14702 +aS'>Ph2736_1/1_1.000_408' +p14703 +aa(lp14704 +S'>Pg3826_1/1_1.000_212' +p14705 +aS'>Ph2017_1/1_1.000_262' +p14706 +aa(lp14707 +S'>Pg4392_1/1_1.000_485' +p14708 +aS'>Ph1108_1/1_1.000_207' +p14709 +aa(lp14710 +S'>Pg4230_1/1_1.000_385' +p14711 +aS'>Ph7188_1/1_1.000_407' +p14712 +aa(lp14713 +S'>Pg4153_1/1_1.000_207' +p14714 +aS'>Ph1435_1/1_1.000_186' +p14715 +aa(lp14716 +S'>Pg3524_1/1_1.000_232' +p14717 +aS'>Ph5128_1/1_1.000_390' +p14718 +aa(lp14719 +S'>Pg7117_1/1_1.000_1515' +p14720 +aS'>Ph522_1/1_1.000_383' +p14721 +aa(lp14722 +S'>Pg3072_1/1_1.000_263' +p14723 +aS'>Ph4955_1/1_1.000_282' +p14724 +aa(lp14725 +S'>Pg5725_1/1_1.000_330' +p14726 +aS'>Ph1105_1/1_1.000_342' +p14727 +aa(lp14728 +S'>Pg7383_1/1_1.000_553' +p14729 +aS'>Ph4717_1/1_1.000_543' +p14730 +aa(lp14731 +S'>Pg3966_1/1_1.000_209' +p14732 +aS'>Ph358_1/1_1.000_674' +p14733 +aa(lp14734 +S'>Pg3843_1/1_1.000_434' +p14735 +aS'>Ph1723_1/1_1.000_354' +p14736 +aa(lp14737 +S'>Pg3815_1/1_1.000_216' +p14738 +aS'>Ph156_1/1_1.000_261' +p14739 +aa(lp14740 +S'>Pg5191_1/1_1.000_177' +p14741 +aS'>Ph5619_1/1_1.000_780' +p14742 +aa(lp14743 +S'>Pg1134_1/1_1.000_309' +p14744 +aS'>Ph4001_1/1_1.000_375' +p14745 +aa(lp14746 +S'>Pg2596_1/1_1.000_214' +p14747 +aS'>Ph3967_1/1_1.000_351' +p14748 +aa(lp14749 +S'>Pg5543_1/1_1.000_407' +p14750 +aS'>Ph1689_1/1_1.000_337' +p14751 +aa(lp14752 +S'>Pg3370_1/1_1.000_251' +p14753 +aS'>Ph8007_1/1_1.000_1723' +p14754 +aa(lp14755 +S'>Pg5460_1/1_1.000_765' +p14756 +aS'>Ph4073_1/1_1.000_309' +p14757 +aa(lp14758 +S'>Pg5891_1/1_1.000_211' +p14759 +aS'>Ph7904_1/1_1.000_202' +p14760 +aa(lp14761 +S'>Pg6280_1/1_1.000_402' +p14762 +aS'>Ph4861_1/1_1.000_438' +p14763 +aa(lp14764 +S'>Pg4733_1/1_1.000_865' +p14765 +aS'>Ph416_1/1_1.000_639' +p14766 +aa(lp14767 +S'>Pg2643_1/1_1.000_141' +p14768 +aS'>Ph7701_1/1_1.000_234' +p14769 +aa(lp14770 +S'>Pg4420_1/1_1.000_583' +p14771 +aS'>Ph7751_1/1_1.000_1461' +p14772 +aa(lp14773 +S'>Pg7358_1/1_1.000_671' +p14774 +aS'>Ph707_1/1_1.000_572' +p14775 +aa(lp14776 +S'>Pg3732_1/1_1.000_284' +p14777 +aS'>Ph565_1/1_1.000_837' +p14778 +aa(lp14779 +S'>Pg966_1/1_1.000_225' +p14780 +aS'>Ph3163_1/1_1.000_396' +p14781 +aa(lp14782 +S'>Pg1005_1/1_1.000_315' +p14783 +aS'>Ph1709_1/1_1.000_207' +p14784 +aa(lp14785 +S'>Pg6092_1/1_1.000_201' +p14786 +aS'>Ph4044_1/1_1.000_814' +p14787 +aa(lp14788 +S'>Pg2533_1/1_1.000_397' +p14789 +aS'>Ph1500_1/1_1.000_298' +p14790 +aa(lp14791 +S'>Pg7939_1/1_1.000_231' +p14792 +aS'>Ph6708_1/1_1.000_214' +p14793 +aa(lp14794 +S'>Pg6768_1/1_1.000_462' +p14795 +aS'>Ph99_1/1_1.000_541' +p14796 +aa(lp14797 +S'>Pg4388_1/1_1.000_234' +p14798 +aS'>Ph4235_1/1_1.000_1312' +p14799 +aa(lp14800 +S'>Pg3528_1/1_1.000_257' +p14801 +aS'>Ph4268_1/1_1.000_412' +p14802 +aa(lp14803 +S'>Pg1276_1/1_1.000_212' +p14804 +aS'>Ph2933_1/1_1.000_732' +p14805 +aa(lp14806 +S'>Pg1524_1/1_1.000_231' +p14807 +aS'>Ph2855_1/1_1.000_858' +p14808 +aa(lp14809 +S'>Pg6882_1/1_1.000_153' +p14810 +aS'>Ph5828_1/1_1.000_147' +p14811 +aa(lp14812 +S'>Pg131_1/1_1.000_402' +p14813 +aS'>Ph271_1/1_1.000_285' +p14814 +aa(lp14815 +S'>Pg1180_1/1_1.000_285' +p14816 +aS'>Ph7247_1/1_1.000_294' +p14817 +aa(lp14818 +S'>Pg3901_1/1_1.000_214' +p14819 +aS'>Ph2347_1/1_1.000_443' +p14820 +aa(lp14821 +S'>Pg4592_1/1_1.000_327' +p14822 +aS'>Ph1714_1/1_1.000_201' +p14823 +aa(lp14824 +S'>Pg893_1/1_1.000_268' +p14825 +aS'>Ph4300_1/1_1.000_260' +p14826 +aa(lp14827 +S'>Pg4711_1/1_1.000_465' +p14828 +aS'>Ph3259_1/1_1.000_246' +p14829 +aa(lp14830 +S'>Pg2136_1/1_1.000_855' +p14831 +aS'>Ph4067_1/1_1.000_447' +p14832 +aa(lp14833 +S'>Pg7149_1/1_1.000_369' +p14834 +aS'>Ph2190_1/1_1.000_219' +p14835 +aa(lp14836 +S'>Pg5664_1/1_1.000_513' +p14837 +aS'>Ph6587_1/1_1.000_541' +p14838 +aa(lp14839 +S'>Pg4553_1/1_1.000_262' +p14840 +aS'>Ph5657_1/1_1.000_376' +p14841 +aa(lp14842 +S'>Pg5067_1/1_1.000_516' +p14843 +aS'>Ph262_1/1_1.000_456' +p14844 +aa(lp14845 +S'>Pg5414_1/1_1.000_207' +p14846 +aS'>Ph6607_1/1_1.000_253' +p14847 +aa(lp14848 +S'>Pg2393_1/1_1.000_237' +p14849 +aS'>Ph430_1/1_1.000_378' +p14850 +aa(lp14851 +S'>Pg423_1/1_1.000_354' +p14852 +aS'>Ph497_1/1_1.000_435' +p14853 +aa(lp14854 +S'>Pg1529_1/1_1.000_376' +p14855 +aS'>Ph1055_1/1_1.000_370' +p14856 +aa(lp14857 +S'>Pg5546_1/1_1.000_411' +p14858 +aS'>Ph124_1/1_1.000_426' +p14859 +aa. \ No newline at end of file
--- a/POGs.xml Mon May 29 04:09:04 2017 -0400 +++ b/POGs.xml Mon May 29 07:45:07 2017 -0400 @@ -26,7 +26,7 @@ <param name="zip" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Contains the files filter after the tool oase" /> <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file " help="Contains homologous sequences in PROTEIC format, ONLY A ZIP FILE" /> <param name="minseq" type="integer" value="3" label="Drop orthogroups with less than n species" /> - <param name="paralogs" type="select" label="Paralogs filtering" help="Yes : paralogs sequences will be (naively) filtered to keep only one sequence. No : the whole orthogroup will be removed." > + <param name="paralogs" type="select" label="Paralogs savage removal" help="Yes : orthogroups with paralogs will be fully removed. No : paralogs sequences will be (naively) filtered to keep only one sequence." > <option value="yes">Yes</option> <option value="no">No</option> </param> @@ -39,15 +39,15 @@ <tests> <test> - <param name="zip" ftype="zip" value="filter_oase_results_for_pogs.zip" /> - <param name="zip_file" ftype="zip" value="test_03_output_Pairwise_PROT_inputPOGS.zip" /> + <param name="zip" ftype="zip" value="outputfilter.zip" /> + <param name="zip_file" ftype="zip" value="outputpairwise.zip" /> <param name="minseq" value="2" /> <param name="paralogs" value="no" /> <output name="output" value="test_03.out" /> </test> <test> - <param name="zip" ftype="zip" value="filter_oase_results_for_pogs.zip" /> - <param name="zip_file" ftype="zip" value="test_03_output_Pairwise_PROT_inputPOGS.zip" /> + <param name="zip" ftype="zip" value="outputfilter.zip" /> + <param name="zip_file" ftype="zip" value="outputpairwise.zip" /> <param name="minseq" value="2" /> <param name="paralogs" value="yes" /> <output name="output" value="test_03b.out" />
--- a/scripts/S02_get_locus_orthologs_part2_v2.py Mon May 29 04:09:04 2017 -0400 +++ b/scripts/S02_get_locus_orthologs_part2_v2.py Mon May 29 07:45:07 2017 -0400 @@ -56,7 +56,9 @@ elif loci[0:3] != new_group[rang][0:3]: new_group.append(loci) rang += 1 - list_orthogroups_filtered.append(new_group) + #print new_group + list_orthogroups_filtered.append(new_group) + #print list_orthogroups_filtered return list_orthogroups_filtered @@ -161,10 +163,10 @@ ## 2 ## intra LOCUS treatment ############################################################################################################################ LOCUS_without_DUPLI = [] -if sys.argv[3] == "oui": +if sys.argv[3] == "yes": LOCUS_without_DUPLI = intraLocusTreatment(list_LOCUS) #DEF1 print "\nNUMBER OF REMAINING LOCUS AFTER INTRA LOCUS TREATMENT [REMOVE GROUPS WITH PARALOGS] = %d" %len(LOCUS_without_DUPLI) -elif sys.argv[3] == "non": +elif sys.argv[3] == "no": LOCUS_without_DUPLI = removeParalogous(list_LOCUS) print "\nNUMBER OF REMAINING LOCUS AFTER INTRA LOCUS TREATMENT [PARALOGS NAIVE FILTERING] = %d" %len(LOCUS_without_DUPLI)