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Faheem Mitha  committed ebb3cec

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 diff -r 93dca9262560 checkfasta.py
 --- /dev/null
 +++ b/checkfasta.py
-@@ -0,0 +1,105 @@
+@@ -0,0 +1,109 @@
 +def checkfasta(accnum, rss):
 +    import os
 +    from corrmodel.utils import get_conf
 +        rss_in_seqlst = rss_in_seq
 +        seqcontainsrss.append(rss_in_seqlst)
 +
++    return seqcontainsrss
++
 +if __name__ == '__main__':
 +    accnum = "AJ231222"
 +    rss = "cacagtg atacagactgga acaaaaacc"
 +    #checkfasta(accnum, rss)
 +
-+    accnumlst = ['AC003057', 'AC003994', 'AC003994', 'AC003994', 'AC003996', 'AC003997', 'AC003997', 'AC004096', 'AC004101', 'AC004101', 'AC004102', 'AC004406', 'AC004406', 'AC004407', 'AC005240', 'AC005240', 'AC005402', 'AC005402', 'AC005855', 'AC005855', 'AC005938', 'AE000663', 'AE000664', 'AE000665', 'AE000665', 'AF003294', 'AF003295', 'AF019412', 'AF021335', 'AF021335', 'AF029261', 'AF037352', 'AF037352', 'AF037352', 'AF044198', 'AF259073', 'AF259074', 'AJ132683', 'AJ23119', 'AJ231200', 'AJ231206', 'AJ231207', 'AJ231209', 'AJ231211', 'AJ231212', 'AJ231213', 'AJ231214', 'AJ231215', 'AJ231216', 'AJ231217', 'AJ231218', 'AJ231219', 'AJ231221', 'AJ231222', 'AJ231223', 'AJ231224', 'AJ231225', 'AJ231226', 'AJ231228', 'AJ231229', 'AJ231231', 'AJ231234', 'AJ231241', 'AJ231243', 'AJ231244', 'AJ231247', 'AJ231248', 'AJ231250', 'AJ231256', 'AJ231258', 'AJ231259', 'AJ231263', 'AJ231264', 'AJ231269', 'AJ231273', 'AJ231274', 'AJ235935', 'AJ235936', 'AJ235938', 'AJ235940', 'AJ235942', 'AJ235943', 'AJ235944', 'AJ235946', 'AJ235947', 'AJ235948', 'AJ235949', 'AJ235950', 'AJ235951', 'AJ235953', 'AJ235955', 'AJ235956', 'AJ235958', 'AJ235961', 'AJ235962', 'AJ235963', 'AJ235964', 'AJ235966', 'AJ235967', 'AJ235968', 'AJ235973', 'AJ235974', 'AJ239197', 'AJ239198', 'D00080', 'D00081', 'D00082', 'D13199', 'D13201', 'D13203', 'D14633', 'D14634', 'D29793', 'D29794', 'J00431', 'J00432', 'J00433', 'J00434', 'J00435', 'J00436', 'J00437', 'J00438', 'J00439', 'J00440', 'J00488', 'J00492', 'J00502', 'J00503', 'J00507', 'J00511', 'J00525', 'J00526', 'J00530', 'J00532', 'J00533', 'J00534', 'J00535', 'J00536', 'J00537', 'J00538', 'J00545', 'J00562', 'J00583', 'J00590', 'J00593', 'J00599', 'K00706', 'K00884', 'K02153', 'K02158', 'K02159', 'K02160', 'K02161', 'K02162', 'K02418', 'K02548', 'K02802', 'K02890', 'L14547', 'L14548', 'L32868', 'L77148', 'L77149', 'L77150', 'L77154', 'M12816', 'M12831', 'M12832', 'M14360', 'M15520', 'M15559', 'M15559', 'M16724', 'M16725', 'M16726', 'M19403', 'M23095', 'M23243', 'M26763', 'M27021', 'M27036', 'M28132', 'M28134', 'M33586', 'M34597', 'M35156', 'M35332', 'M36690', 'M37280', 'M54906', 'M60955', 'M60961', 'M64239', 'M64239', 'M94080', 'S37664', 'V00762', 'V00770', 'V00774', 'V00777', 'V00813', 'V01563', 'V01564', 'V01565', 'X00163', 'X00933', 'X00934', 'X01018', 'X01134', 'X02458', 'X02459', 'X02460', 'X02462', 'X02466', 'X02467', 'X02833', 'X02843', 'X03254', 'X03255', 'X03256', 'X03571', 'X03572', 'X03573', 'X04332', 'X05502', 'X05555', 'X06305', 'X06306', 'X06307', 'X06308', 'X06864', 'X06866', 'X06867', 'X06868', 'X16954', 'X16955', 'X17173', 'X17178', 'X17179', 'X56701', 'X56725', 'X58412', 'X58417', 'X59817', 'Y15968', 'Y15972', 'Y15975', 'Y15976', 'Y15977', 'Y15978', 'Y15980', 'Y15981', 'Y15982', 'Z72382', 'Z72384']
++    # Remove 'AJ23119'
++
++    accnumlst = ['AC003057', 'AC003994', 'AC003994', 'AC003994', 'AC003996', 'AC003997', 'AC003997', 'AC004096', 'AC004101', 'AC004101', 'AC004102', 'AC004406', 'AC004406', 'AC004407', 'AC005240', 'AC005240', 'AC005402', 'AC005402', 'AC005855', 'AC005855', 'AC005938', 'AE000663', 'AE000664', 'AE000665', 'AE000665', 'AF003294', 'AF003295', 'AF019412', 'AF021335', 'AF021335', 'AF029261', 'AF037352', 'AF037352', 'AF037352', 'AF044198', 'AF259073', 'AF259074', 'AJ132683', 'AJ231200', 'AJ231206', 'AJ231207', 'AJ231209', 'AJ231211', 'AJ231212', 'AJ231213', 'AJ231214', 'AJ231215', 'AJ231216', 'AJ231217', 'AJ231218', 'AJ231219', 'AJ231221', 'AJ231222', 'AJ231223', 'AJ231224', 'AJ231225', 'AJ231226', 'AJ231228', 'AJ231229', 'AJ231231', 'AJ231234', 'AJ231241', 'AJ231243', 'AJ231244', 'AJ231247', 'AJ231248', 'AJ231250', 'AJ231256', 'AJ231258', 'AJ231259', 'AJ231263', 'AJ231264', 'AJ231269', 'AJ231273', 'AJ231274', 'AJ235935', 'AJ235936', 'AJ235938', 'AJ235940', 'AJ235942', 'AJ235943', 'AJ235944', 'AJ235946', 'AJ235947', 'AJ235948', 'AJ235949', 'AJ235950', 'AJ235951', 'AJ235953', 'AJ235955', 'AJ235956', 'AJ235958', 'AJ235961', 'AJ235962', 'AJ235963', 'AJ235964', 'AJ235966', 'AJ235967', 'AJ235968', 'AJ235973', 'AJ235974', 'AJ239197', 'AJ239198', 'D00080', 'D00081', 'D00082', 'D13199', 'D13201', 'D13203', 'D14633', 'D14634', 'D29793', 'D29794', 'J00431', 'J00432', 'J00433', 'J00434', 'J00435', 'J00436', 'J00437', 'J00438', 'J00439', 'J00440', 'J00488', 'J00492', 'J00502', 'J00503', 'J00507', 'J00511', 'J00525', 'J00526', 'J00530', 'J00532', 'J00533', 'J00534', 'J00535', 'J00536', 'J00537', 'J00538', 'J00545', 'J00562', 'J00583', 'J00590', 'J00593', 'J00599', 'K00706', 'K00884', 'K02153', 'K02158', 'K02159', 'K02160', 'K02161', 'K02162', 'K02418', 'K02548', 'K02802', 'K02890', 'L14547', 'L14548', 'L32868', 'L77148', 'L77149', 'L77150', 'L77154', 'M12816', 'M12831', 'M12832', 'M14360', 'M15520', 'M15559', 'M15559', 'M16724', 'M16725', 'M16726', 'M19403', 'M23095', 'M23243', 'M26763', 'M27021', 'M27036', 'M28132', 'M28134', 'M33586', 'M34597', 'M35156', 'M35332', 'M36690', 'M37280', 'M54906', 'M60955', 'M60961', 'M64239', 'M64239', 'M94080', 'S37664', 'V00762', 'V00770', 'V00774', 'V00777', 'V00813', 'V01563', 'V01564', 'V01565', 'X00163', 'X00933', 'X00934', 'X01018', 'X01134', 'X02458', 'X02459', 'X02460', 'X02462', 'X02466', 'X02467', 'X02833', 'X02843', 'X03254', 'X03255', 'X03256', 'X03571', 'X03572', 'X03573', 'X04332', 'X05502', 'X05555', 'X06305', 'X06306', 'X06307', 'X06308', 'X06864', 'X06866', 'X06867', 'X06868', 'X16954', 'X16955', 'X17173', 'X17178', 'X17179', 'X56701', 'X56725', 'X58412', 'X58417', 'X59817', 'Y15968', 'Y15972', 'Y15975', 'Y15976', 'Y15977', 'Y15978', 'Y15980', 'Y15981', 'Y15982', 'Z72382', 'Z72384']
 +
 +    schema = "mouse12rss"
 +    from sqlalchemy.orm import sessionmaker
 +    #print rsslst
 +    #("SELECT sequence from motif inner join motifgroup on motif.motifgroup_id=motifgroup.id")
 +    fastafile = "accnum.fasta"
-+    checkfasta2(fastafile, accnumlst, rsslst)
++    print checkfasta2(fastafile, accnumlst, rsslst)
 diff -r 93dca9262560 corrmodel/load.py
 --- a/corrmodel/load.py
 +++ b/corrmodel/load.py
 diff -r 93dca9262560 getfasta2.py
 --- /dev/null
 +++ b/getfasta2.py
-@@ -0,0 +1,64 @@
+@@ -0,0 +1,65 @@
 +#!/usr/bin/python
 +
 +def wgetcmd(accnumlst, dataset):
 +    args = parser.parse_args()
 +    #getfasta(args.dataset)
 +
-+    l = ['AC003057', 'AC003994', 'AC003994', 'AC003994', 'AC003996', 'AC003997', 'AC003997', 'AC004096', 'AC004101', 'AC004101', 'AC004102', 'AC004406', 'AC004406', 'AC004407', 'AC005240', 'AC005240', 'AC005402', 'AC005402', 'AC005855', 'AC005855', 'AC005938', 'AE000663', 'AE000664', 'AE000665', 'AE000665', 'AF003294', 'AF003295', 'AF019412', 'AF021335', 'AF021335', 'AF029261', 'AF037352', 'AF037352', 'AF037352', 'AF044198', 'AF259073', 'AF259074', 'AJ132683', 'AJ23119', 'AJ231200', 'AJ231206', 'AJ231207', 'AJ231209', 'AJ231211', 'AJ231212', 'AJ231213', 'AJ231214', 'AJ231215', 'AJ231216', 'AJ231217', 'AJ231218', 'AJ231219', 'AJ231221', 'AJ231222', 'AJ231223', 'AJ231224', 'AJ231225', 'AJ231226', 'AJ231228', 'AJ231229', 'AJ231231', 'AJ231234', 'AJ231241', 'AJ231243', 'AJ231244', 'AJ231247', 'AJ231248', 'AJ231250', 'AJ231256', 'AJ231258', 'AJ231259', 'AJ231263', 'AJ231264', 'AJ231269', 'AJ231273', 'AJ231274', 'AJ235935', 'AJ235936', 'AJ235938', 'AJ235940', 'AJ235942', 'AJ235943', 'AJ235944', 'AJ235946', 'AJ235947', 'AJ235948', 'AJ235949', 'AJ235950', 'AJ235951', 'AJ235953', 'AJ235955', 'AJ235956', 'AJ235958', 'AJ235961', 'AJ235962', 'AJ235963', 'AJ235964', 'AJ235966', 'AJ235967', 'AJ235968', 'AJ235973', 'AJ235974', 'AJ239197', 'AJ239198', 'D00080', 'D00081', 'D00082', 'D13199', 'D13201', 'D13203', 'D14633', 'D14634', 'D29793', 'D29794', 'J00431', 'J00432', 'J00433', 'J00434', 'J00435', 'J00436', 'J00437', 'J00438', 'J00439', 'J00440', 'J00488', 'J00492', 'J00502', 'J00503', 'J00507', 'J00511', 'J00525', 'J00526', 'J00530', 'J00532', 'J00533', 'J00534', 'J00535', 'J00536', 'J00537', 'J00538', 'J00545', 'J00562', 'J00583', 'J00590', 'J00593', 'J00599', 'K00706', 'K00884', 'K02153', 'K02158', 'K02159', 'K02160', 'K02161', 'K02162', 'K02418', 'K02548', 'K02802', 'K02890', 'L14547', 'L14548', 'L32868', 'L77148', 'L77149', 'L77150', 'L77154', 'M12816', 'M12831', 'M12832', 'M14360', 'M15520', 'M15559', 'M15559', 'M16724', 'M16725', 'M16726', 'M19403', 'M23095', 'M23243', 'M26763', 'M27021', 'M27036', 'M28132', 'M28134', 'M33586', 'M34597', 'M35156', 'M35332', 'M36690', 'M37280', 'M54906', 'M60955', 'M60961', 'M64239', 'M64239', 'M94080', 'S37664', 'V00762', 'V00770', 'V00774', 'V00777', 'V00813', 'V01563', 'V01564', 'V01565', 'X00163', 'X00933', 'X00934', 'X01018', 'X01134', 'X02458', 'X02459', 'X02460', 'X02462', 'X02466', 'X02467', 'X02833', 'X02843', 'X03254', 'X03255', 'X03256', 'X03571', 'X03572', 'X03573', 'X04332', 'X05502', 'X05555', 'X06305', 'X06306', 'X06307', 'X06308', 'X06864', 'X06866', 'X06867', 'X06868', 'X16954', 'X16955', 'X17173', 'X17178', 'X17179', 'X56701', 'X56725', 'X58412', 'X58417', 'X59817', 'Y15968', 'Y15972', 'Y15975', 'Y15976', 'Y15977', 'Y15978', 'Y15980', 'Y15981', 'Y15982', 'Z72382', 'Z72384']
++    #l = ['AC003057', 'AC003994', 'AC003994', 'AC003994', 'AC003996', 'AC003997', 'AC003997', 'AC004096', 'AC004101', 'AC004101', 'AC004102', 'AC004406', 'AC004406', 'AC004407', 'AC005240', 'AC005240', 'AC005402', 'AC005402', 'AC005855', 'AC005855', 'AC005938', 'AE000663', 'AE000664', 'AE000665', 'AE000665', 'AF003294', 'AF003295', 'AF019412', 'AF021335', 'AF021335', 'AF029261', 'AF037352', 'AF037352', 'AF037352', 'AF044198', 'AF259073', 'AF259074', 'AJ132683', 'AJ23119', 'AJ231200', 'AJ231206', 'AJ231207', 'AJ231209', 'AJ231211', 'AJ231212', 'AJ231213', 'AJ231214', 'AJ231215', 'AJ231216', 'AJ231217', 'AJ231218', 'AJ231219', 'AJ231221', 'AJ231222', 'AJ231223', 'AJ231224', 'AJ231225', 'AJ231226', 'AJ231228', 'AJ231229', 'AJ231231', 'AJ231234', 'AJ231241', 'AJ231243', 'AJ231244', 'AJ231247', 'AJ231248', 'AJ231250', 'AJ231256', 'AJ231258', 'AJ231259', 'AJ231263', 'AJ231264', 'AJ231269', 'AJ231273', 'AJ231274', 'AJ235935', 'AJ235936', 'AJ235938', 'AJ235940', 'AJ235942', 'AJ235943', 'AJ235944', 'AJ235946', 'AJ235947', 'AJ235948', 'AJ235949', 'AJ235950', 'AJ235951', 'AJ235953', 'AJ235955', 'AJ235956', 'AJ235958', 'AJ235961', 'AJ235962', 'AJ235963', 'AJ235964', 'AJ235966', 'AJ235967', 'AJ235968', 'AJ235973', 'AJ235974', 'AJ239197', 'AJ239198', 'D00080', 'D00081', 'D00082', 'D13199', 'D13201', 'D13203', 'D14633', 'D14634', 'D29793', 'D29794', 'J00431', 'J00432', 'J00433', 'J00434', 'J00435', 'J00436', 'J00437', 'J00438', 'J00439', 'J00440', 'J00488', 'J00492', 'J00502', 'J00503', 'J00507', 'J00511', 'J00525', 'J00526', 'J00530', 'J00532', 'J00533', 'J00534', 'J00535', 'J00536', 'J00537', 'J00538', 'J00545', 'J00562', 'J00583', 'J00590', 'J00593', 'J00599', 'K00706', 'K00884', 'K02153', 'K02158', 'K02159', 'K02160', 'K02161', 'K02162', 'K02418', 'K02548', 'K02802', 'K02890', 'L14547', 'L14548', 'L32868', 'L77148', 'L77149', 'L77150', 'L77154', 'M12816', 'M12831', 'M12832', 'M14360', 'M15520', 'M15559', 'M15559', 'M16724', 'M16725', 'M16726', 'M19403', 'M23095', 'M23243', 'M26763', 'M27021', 'M27036', 'M28132', 'M28134', 'M33586', 'M34597', 'M35156', 'M35332', 'M36690', 'M37280', 'M54906', 'M60955', 'M60961', 'M64239', 'M64239', 'M94080', 'S37664', 'V00762', 'V00770', 'V00774', 'V00777', 'V00813', 'V01563', 'V01564', 'V01565', 'X00163', 'X00933', 'X00934', 'X01018', 'X01134', 'X02458', 'X02459', 'X02460', 'X02462', 'X02466', 'X02467', 'X02833', 'X02843', 'X03254', 'X03255', 'X03256', 'X03571', 'X03572', 'X03573', 'X04332', 'X05502', 'X05555', 'X06305', 'X06306', 'X06307', 'X06308', 'X06864', 'X06866', 'X06867', 'X06868', 'X16954', 'X16955', 'X17173', 'X17178', 'X17179', 'X56701', 'X56725', 'X58412', 'X58417', 'X59817', 'Y15968', 'Y15972', 'Y15975', 'Y15976', 'Y15977', 'Y15978', 'Y15980', 'Y15981', 'Y15982', 'Z72382', 'Z72384']
++
++    l = ['AJ23119']
 +
 +    getfasta2(l, args.dataset)
 +
 +#['AE000665', 'AF018146', 'AF029261', 'AF044198', 'AJ132683', 'AJ231200', 'AJ231206', 'AJ231207', 'AJ231209', 'AJ231212', 'AJ231213', 'AJ231214', 'AJ231215', 'AJ231216', 'AJ231217', 'AJ231218', 'AJ231219', 'AJ231221', 'AJ231222', 'AJ231223', 'AJ231224', 'AJ231225', 'AJ231226', 'AJ231229', 'AJ231231', 'AJ231234', 'AJ231241', 'AJ231243', 'AJ231244', 'AJ231247']
 +
 +# l = ['AC003057', 'AC003994', 'AC003996', 'AC003997', 'AC004096', 'AC004101', 'AC004102', 'AC004406', 'AC004407', 'AC005240', 'AC005402', 'AC005855', 'AC005938', 'AE000663', 'AE000664', 'AE000665', 'AF018146', 'AF019412', 'AF021335', 'AF029261', 'AF037352', 'AF044198', 'AF259073', 'AF259074', 'AJ132683', 'AJ23119', 'AJ231200', 'AJ231206', 'AJ231207', 'AJ231209', 'AJ231211', 'AJ231212', 'AJ231213', 'AJ231214', 'AJ231215', 'AJ231216', 'AJ231217', 'AJ231218', 'AJ231219', 'AJ231221', 'AJ231222', 'AJ231223', 'AJ231224', 'AJ231225', 'AJ231226', 'AJ231229', 'AJ231231', 'AJ231234', 'AJ231234|S37664', 'AJ231241', 'AJ231243', 'AJ231244', 'AJ231247', 'AJ231248', 'AJ231248|AF003294', 'AJ231250', 'AJ231250|AF003295', 'AJ231256', 'AJ231258', 'AJ231259', 'AJ231263', 'AJ231264', 'AJ231269', 'AJ231273', 'AJ231273|M35156', 'AJ231274', 'AJ235935', 'AJ235936', 'AJ235938', 'AJ235940', 'AJ235942', 'AJ235943', 'AJ235944', 'AJ235946', 'AJ235947', 'AJ235948', 'AJ235949', 'AJ235950', 'AJ235951', 'AJ235953', 'AJ235955', 'AJ235956', 'AJ235958', 'AJ235961', 'AJ235962', 'AJ235963', 'AJ235964', 'AJ235966', 'AJ235967', 'AJ235968', 'AJ235973', 'AJ235974', 'AJ239197', 'AJ239198', 'D00080', 'D00081', 'D00082', 'D13199', 'D13201', 'D13203', 'D14633', 'D14634', 'D29793', 'D29794', 'J00431', 'J00432', 'J00433', 'J00434', 'J00435', 'J00436', 'J00437', 'J00438', 'J00439', 'J00440', 'J00488', 'J00492', 'J00502', 'J00503', 'J00507', 'J00511', 'J00525', 'J00526', 'J00530', 'J00532', 'J00533', 'J00534', 'J00535', 'J00536', 'J00537', 'J00538', 'J00545', 'J00562', 'J00583', 'J00590', 'J00593', 'J00599', 'K00706', 'K00884', 'K02153', 'K02158', 'K02159', 'K02160', 'K02161', 'K02162', 'K02418', 'K02548', 'K02802', 'K02890', 'L14547', 'L14548', 'L32868', 'L77148', 'L77149', 'L77150', 'L77154', 'M12816', 'M12831', 'M12832', 'M14360', 'M15520', 'M15559', 'M16724', 'M16725', 'M16726', 'M19403', 'M23095', 'M23243', 'M26763', 'M27021', 'M27036', 'M28132', 'M28134', 'M33586', 'M34597', 'M35332', 'M36690', 'M37280', 'M38103', 'M38105', 'M54906', 'M60955', 'M60961', 'M64239', 'M94080', 'V00762', 'V00770', 'V00774', 'V00777', 'V00813', 'V01563', 'V01564', 'V01565', 'X00163', 'X00933', 'X00934', 'X01018', 'X01134', 'X02458', 'X02459', 'X02460', 'X02462', 'X02466', 'X02467', 'X02833', 'X02843', 'X02858', 'X02859', 'X02862', 'X03056', 'X03057', 'X03058', 'X03059', 'X03254', 'X03255', 'X03256', 'X03571', 'X03572', 'X03573', 'X03761', 'X04332', 'X05502', 'X05555|AJ231228', 'X06305', 'X06306', 'X06307', 'X06308', 'X06864', 'X06866', 'X06867', 'X06868', 'X16954', 'X16955', 'X17173', 'X17177', 'X17178', 'X17179', 'X56701', 'X56725', 'X58411', 'X58412', 'X58414', 'X58417', 'X59817', 'Y15968', 'Y15972', 'Y15975', 'Y15976', 'Y15977', 'Y15978', 'Y15980', 'Y15981', 'Y15982', 'Z72382', 'Z72384']
-+