From cbd0b94a50acdbede1c8762968d4d1f439bd9b6c Mon Sep 17 00:00:00 2001 From: fabrice <fabrice.allain@pasteur.fr> Date: Thu, 21 Jan 2016 18:01:27 +0100 Subject: [PATCH] Add new formats (metapsicov_stg1/2,pconsc1/2) --- ariaec/commands.py | 7 ++++--- ariaec/commands.pyc | Bin 9835 -> 9939 bytes ariaec/protmap.py | 2 +- ariaec/protmap.pyc | Bin 39469 -> 39488 bytes ariaec/reader.py | 27 ++++++++++++++++++++++++++- ariaec/reader.pyc | Bin 17440 -> 17652 bytes 6 files changed, 31 insertions(+), 5 deletions(-) diff --git a/ariaec/commands.py b/ariaec/commands.py index bcdf35d..9bb45c5 100644 --- a/ariaec/commands.py +++ b/ariaec/commands.py @@ -48,9 +48,10 @@ class AriaEcCommand: u"into ARIA restraints", u"Convert contacts in bbcontact format", u"Contactmap tool") - contact_types = ("plmdca", "evfold", "bbcontacts", "pconsc", "gremlin", - "metapsicov", "pdb", "native", "native_full", - "contactlist") + contact_types = ("plmdca", "evfold", "bbcontacts", "pconsc", "pconsc1", + "pconsc2", "psicov", "metapsicovhb", "metapsicov_stg1", + "metapsicov_stg2", "gremlin", "pdb", "native", + "native_full", "contactlist") default_confile = "conf/aria_ec.ini" def __init__(self, custom_logging=None): diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc index 7c8986d2a6e6b569ba7916bde0c9c7d57ac41e8b..dd3a1f06de367d2488b513a28012a210a5706243 100644 GIT binary patch delta 1115 zcmaFubJ>@j`7<w<8Rx={?EY-^{0s~XP6><*#q$^#7*ZJ+q8J%c7#O0M7*doOqL>*{ zR2ZUI7*bRjqF5PH#2BL37*f<2Qp6cr7#X5C7*Zq{S{N9jI2lqT!3-{j6e%!+8>~zk ztc(ZDmI1SQ!E9MDn~xzyjzJHkpPwN`9;{7(Aw>bq5M)SE1T%yfQk1|9VTPb!4fV~; z>=KO01<Cn&#mR;x><kPH5VlbX8;D(;nVer%!o$G8kegbPSODf`B$a^th!BV`E=f1U zB4z|OFTE%=HzzZ1vmr+!BctWy$(##BO&J&%O1Kyp7>ZL%;`2*OQZkEzEGK(#&15xW zU|?|E{ESN!r1TGWDWmP=BAy?t#taM$?wj*@+Zh>cCx7S5XZ2)YU<lrv&3}xM(P6TY zpaGjR0|P^l)8sdjvYT543z-;QCw~_<V04?TA)>160g@90*~!Adzz|YYni`bAz`&pZ z;suF=Bz-3rh%_+9Z~iEf%P8#t5(xt-=VoAFNY2kINlY$D%gjj)a++KzrXmBjDuRK5 zp%@e{1;v>KMX4zYU<KhI2XK`zgTkvgF(_*C1F>M4c#wHwAoD=#q2|SxR2HNLB~JDi 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sort_field allow sorting lines with values into this field # TODO: wrong regex for native_full ? + # TODO: smarter dict ... types = { "plmdca": { "regex": re.compile("^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+" @@ -74,7 +75,31 @@ class MapFile(RegexFile): '(?P<ec_score>\-?\d+\.\d+e?\-?\d*)$'), "score_field": "ec_score" }, - "metapsicov": { + "pconsc1": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) ' + '(?P<ec_score>\-?\d+\.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "pconsc2": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) ' + '(?P<ec_score>\-?\d+\.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "metapsicov_stg1": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) ' + '(?P<ec_score>\-?\d+.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "metapsicov_stg2": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) ' + '(?P<ec_score>\-?\d+.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "psicov": { "regex": re.compile( '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) ' '(?P<ec_score>\-?\d+.\d+e?\-?\d*)$'), diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc index 5eeb4d61ab4ba9568ce24f11b49683d31a4434f0..634fc3685c92e411635247e68d197a2fa87372bd 100644 GIT binary patch delta 2020 zcmZ3`!T6<<k)8Q7FPACz!j0^^*mx9~7#LC+7@`;%GWjQ;WlNnb!Y;_jHJO85cCs_O zcs(0K3NwRQ3NM3MCKE#{6GIj=LkbT=Gb2L^BZFBARF)5~EI+cW09>yi#AG34Sz)-W zCPcPg1h2FxvaA@oW^rU$33ORWWLYV=tTe=88Hj8>#K*F5X*r0rJcC&jD?=(9Lliqh ziULCm149%CLy9ItiXuobMTwz>nIVdkAw?N1#l?`K0%mYCq^N=!JYdCY3@Pehh6Y0m z3quqyLr}1W76SuAaRUPbL!5?vfX(Jw4q+yV5_Sd#hJxh$yy9d-B(~Ay30!G9{0s~X zxv3?I1;v@k`DO9NCFzDGm|{jHYzzzxoBwg?ureA<))wexTsC>9z)eYe1_lPORDN1o zacW5kGsybN+#tuvf)cTlIfVEbw{DgYn!?1mYw}u=DmEtu28JN#$-1I#jK?-_5&g-? z=sS6xxGba1<TK)nS*;lu7*1_2k(k2FXfT;mW)qtiNV(7CgEG>LA(QXQNHY3O{w~ug z_zq+V$UU4a%#31;K}M4&$|}PY?~+wu1Gy^5eewg@O2+8PQF290LX4Bo$=Na{PUex1 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