diff --git a/modulector/files/miraccs.csv b/modulector/files/miraccs.csv new file mode 100644 index 0000000..6cb3c60 --- /dev/null +++ b/modulector/files/miraccs.csv @@ -0,0 +1,2880 @@ +ID,Sequence +hsa-miR-548ap-3p,AAAAACCACAAUUACUUUU +hsa-miR-548aa,AAAAACCACAAUUACUUUUGCACCA +hsa-miR-548aa,AAAAACCACAAUUACUUUUGCACCA +hsa-miR-548t-3p,AAAAACCACAAUUACUUUUGCACCA +hsa-miR-548e-3p,AAAAACUGAGACUACUUUUGCA +hsa-miR-548az-3p,AAAAACUGCAAUCACUUUUGC +hsa-miR-548f-3p,AAAAACUGUAAUUACUUUU +hsa-miR-548f-3p,AAAAACUGUAAUUACUUUU +hsa-miR-548f-3p,AAAAACUGUAAUUACUUUU +hsa-miR-548f-3p,AAAAACUGUAAUUACUUUU +hsa-miR-548f-3p,AAAAACUGUAAUUACUUUU +hsa-miR-548bc,AAAAACUGUGAUUACUUUUGC +hsa-miR-1537-3p,AAAACCGUCUAGUUACAGUUGU +hsa-miR-553,AAAACGGUGAGAUUUUGUUUU +hsa-miR-7844-5p,AAAACUAGGACUGUGUGGUGUA +hsa-miR-548av-3p,AAAACUGCAGUUACUUUUGC +hsa-miR-548g-3p,AAAACUGUAAUUACUUUUGUAC +hsa-miR-6835-3p,AAAAGCACUUUUCUGUCUCCCAG +hsa-miR-4422,AAAAGCAUCAGGAAGUACCCA +hsa-miR-4429,AAAAGCUGGGCUGAGAGGCG +hsa-miR-320d,AAAAGCUGGGUUGAGAGGA +hsa-miR-320d,AAAAGCUGGGUUGAGAGGA +hsa-miR-320b,AAAAGCUGGGUUGAGAGGGCAA +hsa-miR-320b,AAAAGCUGGGUUGAGAGGGCAA +hsa-miR-320a-3p,AAAAGCUGGGUUGAGAGGGCGA +hsa-miR-320c,AAAAGCUGGGUUGAGAGGGU +hsa-miR-320c,AAAAGCUGGGUUGAGAGGGU +hsa-miR-548an,AAAAGGCAUUGUGGUUUUUG +hsa-miR-4484,AAAAGGCGGGAGAAGCCCCA +hsa-miR-10526-3p,AAAAGGGGGCUGAGGUGGAG +hsa-miR-548bb-5p,AAAAGUAACUAUGGUUUUUGCC +hsa-miR-548ak,AAAAGUAACUGCGGUUUUUGA +hsa-miR-548w,AAAAGUAACUGCGGUUUUUGCCU +hsa-miR-548y,AAAAGUAAUCACUGUUUUUGCC +hsa-miR-548h-5p,AAAAGUAAUCGCGGUUUUUGUC +hsa-miR-548h-5p,AAAAGUAAUCGCGGUUUUUGUC +hsa-miR-548h-5p,AAAAGUAAUCGCGGUUUUUGUC +hsa-miR-548h-5p,AAAAGUAAUCGCGGUUUUUGUC +hsa-miR-548h-5p,AAAAGUAAUCGCGGUUUUUGUC +hsa-miR-548ar-5p,AAAAGUAAUUGCAGUUUUUGC +hsa-miR-548a-5p,AAAAGUAAUUGCGAGUUUUACC +hsa-miR-548i,AAAAGUAAUUGCGGAUUUUGCC +hsa-miR-548i,AAAAGUAAUUGCGGAUUUUGCC +hsa-miR-548i,AAAAGUAAUUGCGGAUUUUGCC +hsa-miR-548i,AAAAGUAAUUGCGGAUUUUGCC +hsa-miR-548as-5p,AAAAGUAAUUGCGGGUUUUGCC +hsa-miR-548ap-5p,AAAAGUAAUUGCGGUCUUU +hsa-miR-548j-5p,AAAAGUAAUUGCGGUCUUUGGU +hsa-miR-548au-5p,AAAAGUAAUUGCGGUUUUUGC +hsa-miR-548c-5p,AAAAGUAAUUGCGGUUUUUGCC +hsa-miR-548o-5p,AAAAGUAAUUGCGGUUUUUGCC +hsa-miR-548am-5p,AAAAGUAAUUGCGGUUUUUGCC +hsa-miR-548ab,AAAAGUAAUUGUGGAUUUUGCU +hsa-miR-548b-5p,AAAAGUAAUUGUGGUUUUGGCC +hsa-miR-548ad-5p,AAAAGUAAUUGUGGUUUUUG +hsa-miR-548ae-5p,AAAAGUAAUUGUGGUUUUUG +hsa-miR-548ay-5p,AAAAGUAAUUGUGGUUUUUGC +hsa-miR-548d-5p,AAAAGUAAUUGUGGUUUUUGCC +hsa-miR-548d-5p,AAAAGUAAUUGUGGUUUUUGCC +hsa-miR-548av-5p,AAAAGUACUUGCGGAUUU +hsa-miR-548k,AAAAGUACUUGCGGAUUUUGCU +hsa-miR-548l,AAAAGUAUUUGCGGGUUUUGUC +hsa-miR-548ah-5p,AAAAGUGAUUGCAGUGUUUG +hsa-miR-106a-5p,AAAAGUGCUUACAGUGCAGGUAG +hsa-miR-548at-5p,AAAAGUUAUUGCGGUUUUGGCU +hsa-miR-3646,AAAAUGAAAUGAGCCCAGCCCA +hsa-miR-224-3p,AAAAUGGUGCCCUAGUGACUACA +hsa-miR-522-3p,AAAAUGGUUCCCUUUAGAGUGU +hsa-miR-3606-3p,AAAAUUUCUUUCACUACUUAG +hsa-miR-495-3p,AAACAAACAUGGUGCACUUCUU +hsa-miR-122b-3p,AAACACCAUUGUCACACUCCAC +hsa-miR-543,AAACAUUCGCGGUGCACUUCUU +hsa-miR-451a,AAACCGUUACCAUUACUGAGUU +hsa-miR-649,AAACCUGUGUUGUUCAAGAGUC +hsa-miR-5583-5p,AAACUAAUAUACCCAUAUUCUG +hsa-miR-5583-5p,AAACUAAUAUACCCAUAUUCUG +hsa-miR-3129-3p,AAACUAAUCUCUACACUGCUGC +hsa-miR-606,AAACUACUGAAAAUCAAAGAU +hsa-miR-618,AAACUCUACUUGUCCUUCUGAGU +hsa-miR-641,AAAGACAUAGGAUAGAGUCACCUC +hsa-miR-3617-5p,AAAGACAUAGUUGCAAGAUGGG +hsa-miR-3667-5p,AAAGACCCAUUGAGGAGAAGGU +hsa-miR-548ao-3p,AAAGACCGUGACUACUUUUGCA +hsa-miR-4432,AAAGACUCUGCAAGAUGCCU +hsa-miR-4662a-3p,AAAGAUAGACAAUUGGCUAAAU +hsa-miR-3156-5p,AAAGAUCUGGAAGUGGGAGACA +hsa-miR-3156-5p,AAAGAUCUGGAAGUGGGAGACA +hsa-miR-3156-5p,AAAGAUCUGGAAGUGGGAGACA +hsa-miR-4662b,AAAGAUGGACAAUUGGCUAAAU +hsa-miR-10527-5p,AAAGCAAAUGUUGGGUGAACGGC +hsa-miR-498-3p,AAAGCACCUCCAGAGCUUGAAGC +hsa-miR-518e-3p,AAAGCGCUUCCCUUCAGAGUG +hsa-miR-320e,AAAGCUGGGUUGAGAAGG +hsa-miR-651-3p,AAAGGAAAGUGUAUCCUAAAAG +hsa-miR-3173-3p,AAAGGAGGAAAUAGGCAGGCCA +hsa-miR-541-5p,AAAGGAUUCUGCUGUCGGUCCCACU +hsa-miR-3910,AAAGGCAUAAAACCAAGACA +hsa-miR-3910,AAAGGCAUAAAACCAAGACA +hsa-miR-548ba,AAAGGUAACUGUGAUUUUUGCU +hsa-miR-570-5p,AAAGGUAAUUGCAGUUUUUCCC +hsa-miR-548ai,AAAGGUAAUUGCAGUUUUUCCC +hsa-miR-548ag,AAAGGUAAUUGUGGUUUCUGC +hsa-miR-548ag,AAAGGUAAUUGUGGUUUCUGC +hsa-miR-3974,AAAGGUCAUUGUAAGGUUAAUGC +hsa-miR-4735-3p,AAAGGUGCUCAAAUUAGACAU +hsa-miR-562,AAAGUAGCUGUACCAUUUGC +hsa-miR-3184-3p,AAAGUCUCGCUCUCUGCCCCUCA +hsa-miR-519b-3p,AAAGUGCAUCCUUUUAGAGGUU +hsa-miR-519a-3p,AAAGUGCAUCCUUUUAGAGUGU +hsa-miR-519a-3p,AAAGUGCAUCCUUUUAGAGUGU +hsa-miR-519c-3p,AAAGUGCAUCUUUUUAGAGGAU +hsa-miR-372-3p,AAAGUGCUGCGACAUUUGAGCGU +hsa-miR-520a-3p,AAAGUGCUUCCCUUUGGACUGU +hsa-miR-520b-3p,AAAGUGCUUCCUUUUAGAGGG +hsa-miR-520c-3p,AAAGUGCUUCCUUUUAGAGGGU +hsa-miR-520e-3p,AAAGUGCUUCCUUUUUGAGGG +hsa-miR-520d-3p,AAAGUGCUUCUCUUUGGUGGGU +hsa-miR-148a-5p,AAAGUUCUGAGACACUCCGACU +hsa-miR-1277-5p,AAAUAUAUAUAUAUAUGUACGUAU +hsa-miR-4517,AAAUAUGAUGAAACUCACAGCUGAG +hsa-miR-216b-5p,AAAUCUCUGCAGGCAAAUGUGA +hsa-miR-4506,AAAUGGGUGGUCUGAGGCAA +hsa-miR-513b-3p,AAAUGUCACCUUUUUGAGAGGA +hsa-miR-944,AAAUUAUUGUACAUCGGAUGAG +hsa-miR-4760-3p,AAAUUCAUGUUCAAUCUAAACC +hsa-miR-3529-3p,AACAACAAAAUCACUAGUCUUCCA +hsa-miR-338-5p,AACAAUAUCCUGGUGCUGAGUG +hsa-miR-362-3p,AACACACCUAUUCAAGGAUUCA +hsa-miR-329-3p,AACACACCUGGUUAACCUCUUU +hsa-miR-329-3p,AACACACCUGGUUAACCUCUUU +hsa-miR-6757-3p,AACACUGGCCUUGCUAUCCCCA +hsa-miR-552-3p,AACAGGUGACUGGUUAGACAA +hsa-miR-376c-3p,AACAUAGAGGAAAUUCCACGU +hsa-miR-499a-3p,AACAUCACAGCAAGUCUGUGCU +hsa-miR-499b-3p,AACAUCACUGCAAGUCUUAACA +hsa-miR-181c-5p,AACAUUCAACCUGUCGGUGAGU +hsa-miR-181a-5p,AACAUUCAACGCUGUCGGUGAGU +hsa-miR-181a-5p,AACAUUCAACGCUGUCGGUGAGU +hsa-miR-181b-5p,AACAUUCAUUGCUGUCGGUGGGU +hsa-miR-181b-5p,AACAUUCAUUGCUGUCGGUGGGU +hsa-miR-181d-5p,AACAUUCAUUGUUGUCGGUGGGU +hsa-miR-1255b-2-3p,AACCACUUUCUUUGCUCAUCCA +hsa-miR-634,AACCAGCACCCCAACUUUGGAC +hsa-miR-181c-3p,AACCAUCGACCGUUGAGUGGAC +hsa-miR-4482-5p,AACCCAGUGGGCUAUGGAAAUG +hsa-miR-5195-5p,AACCCCUAAGGCAACUGGAUGG +hsa-miR-100-5p,AACCCGUAGAUCCGAACUUGUG +hsa-miR-99a-5p,AACCCGUAGAUCCGAUCUUGUG +hsa-miR-6813-3p,AACCUUGGCCCCUCUCCCCAG +hsa-miR-521,AACGCACUUCCCUUUAGAGUGU +hsa-miR-521,AACGCACUUCCCUUUAGAGUGU +hsa-miR-122-3p,AACGCCAUUAUCACACUAAAUA +hsa-miR-548al,AACGGCAAUGACUUUUGUACCA +hsa-miR-4681,AACGGGAAUGCAGGCUGUAUCU +hsa-miR-4661-5p,AACUAGCUCUGUGGAUCCUGAC +hsa-miR-3923,AACUAGUAAUGUUGGAUUAGGG +hsa-miR-4798-3p,AACUCACGAAGUAUACCGAAGU +hsa-miR-3145-5p,AACUCCAAACACUCAAAACUCA +hsa-miR-4636,AACUCGUGUUCAAAGCCUUUAG +hsa-miR-5684,AACUCUAGCCUGAGCAACAG +hsa-miR-4714-5p,AACUCUGACCCCUUAGGUUGAU +hsa-miR-3664-5p,AACUCUGUCUUCACUCAUGAGU +hsa-miR-4724-5p,AACUGAACCAGGAGUGAGCUUCG +hsa-miR-1243,AACUGGAUCAAUUAUAGGAGUG +hsa-miR-193b-3p,AACUGGCCCUCAAAGUCCCGCU +hsa-miR-193a-3p,AACUGGCCUACAAAGUCCCAGU +hsa-miR-452-5p,AACUGUUUGCAGAGGAAACUGA +hsa-miR-5197-3p,AAGAAGAGACUGAGUCAUCGAAU +hsa-miR-483-5p,AAGACGGGAGGAAAGAAGGGAG +hsa-miR-4499,AAGACUGAGAGGAGGGA +hsa-miR-3925-5p,AAGAGAACUGAAAGUGGAGCCU +hsa-miR-6856-5p,AAGAGAGGAGCAGUGGUGCUGUGG +hsa-miR-3916,AAGAGGAAGAAAUGGCUGGUUCUCAG +hsa-miR-576-3p,AAGAUGUGGAAAAAUUGGAAUC +hsa-miR-3942-5p,AAGCAAUACUGUUACCUGAAAU +hsa-miR-6838-5p,AAGCAGCAGUGGCAAGACUCCU +hsa-miR-646,AAGCAGCUGCCUCUGAGGC +hsa-miR-1179,AAGCAUUCUUUCAUUGGUUGG +hsa-miR-6779-3p,AAGCCCUGUCUCCUCCCAUCU +hsa-miR-129-2-3p,AAGCCCUUACCCCAAAAAGCAU +hsa-miR-129-1-3p,AAGCCCUUACCCCAAAAAGUAU +hsa-miR-6819-3p,AAGCCUCUGUCCCCACCCCAG +hsa-miR-596,AAGCCUGCCCGGCUCCUCGGG +hsa-miR-4670-5p,AAGCGACCAUGAUGUAACUUCA +hsa-miR-6854-5p,AAGCUCAGGUUUGAGAACUGCUGA +hsa-miR-22-3p,AAGCUGCCAGUUGAAGAACUGU +hsa-miR-208b-5p,AAGCUUUUUGCUCGAAUUAUGU +hsa-miR-3914,AAGGAACCAGAAAAUGAGAAGU +hsa-miR-3914,AAGGAACCAGAAAAUGAGAAGU +hsa-miR-6888-5p,AAGGAGAUGCUCAGGCAGAU +hsa-miR-28-5p,AAGGAGCUCACAGUCUAUUGAG +hsa-miR-708-5p,AAGGAGCUUACAAUCUAGCUGGG +hsa-miR-940,AAGGCAGGGCCCCCGCUCCCC +hsa-miR-4747-3p,AAGGCCCGGGCUUUCCUCCCAG +hsa-miR-3142,AAGGCCUUUCUGAACCUUCAGA +hsa-miR-9500,AAGGGAAGAUGGUGACCAC +hsa-miR-7845-5p,AAGGGACAGGGAGGGUCGUGG +hsa-miR-4739,AAGGGAGGAGGAGCGGAGGGGCCCU +hsa-miR-3158-3p,AAGGGCUUCCUCUCUGCAGGAC +hsa-miR-3158-3p,AAGGGCUUCCUCUCUGCAGGAC +hsa-miR-6743-5p,AAGGGGCAGGGACGGGUGGCCC +hsa-miR-6085,AAGGGGCUGGGGGAGCACA +hsa-miR-4716-3p,AAGGGGGAAGGAAACAUGGAGA +hsa-miR-4678,AAGGUAUUGUUCAGACUUAUGA +hsa-miR-4464,AAGGUUUGGAUAGAUGCAAUA +hsa-miR-1244,AAGUAGUUGGUUUGUAUGAGAUGGUU +hsa-miR-1244,AAGUAGUUGGUUUGUAUGAGAUGGUU +hsa-miR-1244,AAGUAGUUGGUUUGUAUGAGAUGGUU +hsa-miR-1244,AAGUAGUUGGUUUGUAUGAGAUGGUU +hsa-miR-5588-3p,AAGUCCCACUAAUGCCAGC +hsa-miR-6838-3p,AAGUCCUGCUUCUGUUGCAG +hsa-miR-1245a,AAGUGAUCUAAAGGCCUACAU +hsa-miR-371b-3p,AAGUGCCCCCACAGUUUGAGUGC +hsa-miR-371a-3p,AAGUGCCGCCAUCUUUUGAGUGU +hsa-miR-519e-3p,AAGUGCCUCCUUUUAGAGUGUU +hsa-miR-512-3p,AAGUGCUGUCAUAGCUGAGGUC +hsa-miR-512-3p,AAGUGCUGUCAUAGCUGAGGUC +hsa-miR-520f-3p,AAGUGCUUCCUUUUAGAGGGUU +hsa-miR-648,AAGUGUGCAGGGCACUGGU +hsa-miR-148b-5p,AAGUUCUGUUAUACACUCAGGC +hsa-miR-4715-5p,AAGUUGGCUGCAGUUAAGGUGG +hsa-miR-5590-3p,AAUAAAGUUCAUGUAUGGCAA +hsa-miR-369-3p,AAUAAUACAUGGUUGAUCUUU +hsa-miR-5692b,AAUAAUAUCACAGUAGGUGU +hsa-miR-5692c,AAUAAUAUCACAGUAGGUGUAC +hsa-miR-5692c,AAUAAUAUCACAGUAGGUGUAC +hsa-miR-7705,AAUAGCUCAGAAUGUCAGUUCUG +hsa-miR-1295b-3p,AAUAGGCCACGGAUCUGGGCAA +hsa-miR-410-3p,AAUAUAACACAGAUGGCCUGU +hsa-miR-656-3p,AAUAUUAUACAGUCAACCUCU +hsa-miR-34c-3p,AAUCACUAACCACACGGCCAGG +hsa-miR-5094,AAUCAGUGAAUGCCUUGAACCU +hsa-miR-154-3p,AAUCAUACACGGUUGACCUAUU +hsa-miR-487a-3p,AAUCAUACAGGGACAUCCAGUU +hsa-miR-96-3p,AAUCAUGUGCAGUGCCAAUAUG +hsa-miR-382-3p,AAUCAUUCACGGACAACACUU +hsa-miR-5092,AAUCCACGCUGAGCUUGGCAUC +hsa-miR-4733-5p,AAUCCCAAUGCUAGACCCGGUG +hsa-miR-500b-5p,AAUCCUUGCUACCUGGGU +hsa-miR-362-5p,AAUCCUUGGAACCUAGGUGUGAGU +hsa-miR-501-5p,AAUCCUUUGUCCCUGGGUGAGA +hsa-miR-5188,AAUCGGACCCAUUUAAACCGGAG +hsa-miR-487b-3p,AAUCGUACAGGGUCAUCCACUU +hsa-miR-3200-5p,AAUCUGAGAAGGCGCACAAGGU +hsa-miR-425-5p,AAUGACACGAUCACUCCCGUUGA +hsa-miR-4712-3p,AAUGAGAGACCUGUACUGUAU +hsa-miR-501-3p,AAUGCACCCGGGCAAGGAUUCU +hsa-miR-502-3p,AAUGCACCUGGGCAAGGAUUCA +hsa-miR-1246,AAUGGAUUUUUGGAGCAGG +hsa-miR-652-3p,AAUGGCGCCACUAGGGUUGUG +hsa-miR-889-5p,AAUGGCUGUCCGUAGUAUGGUC +hsa-miR-4495,AAUGUAAACAGGCUUUUUGCU +hsa-miR-3668,AAUGUAGAGAUUGAUCAAAAU +hsa-miR-4657,AAUGUGGAAGUGGUCUGAGGCAU +hsa-miR-4491,AAUGUGGACUGGUGUGACCAAA +hsa-miR-511-3p,AAUGUGUAGCAAAAGACAGA +hsa-miR-4781-3p,AAUGUUGGAAUCCUCGCUAGAG +hsa-miR-4307,AAUGUUUUUUCCUGUUUCC +hsa-miR-10399-5p,AAUUACAGAUUGUCUCAGAGA +hsa-miR-3938,AAUUCCCUUGUAGAUAACCCGG +hsa-miR-4778-5p,AAUUCUGUAAAGGAAGAAGAGG +hsa-miR-363-3p,AAUUGCACGGUAUCCAUCUGUA +hsa-miR-367-3p,AAUUGCACUUUAGCAAUGGUGA +hsa-miR-4699-3p,AAUUUACUCUGCAAUCUUCUCC +hsa-miR-5002-5p,AAUUUGGUUUCUGAGGCACUUAGU +hsa-miR-3613-3p,ACAAAAAAAAAAGCCCAACCCUUC +hsa-miR-3973,ACAAAGUACAGCAUUAGCCUUAG +hsa-miR-520h,ACAAAGUGCUUCCCUUUAGAGU +hsa-miR-520g-3p,ACAAAGUGCUUCCCUUUAGAGUGU +hsa-miR-4709-5p,ACAACAGUGACUUGCUCUCCAA +hsa-miR-4761-5p,ACAAGGUGUGCAUGCCUGACC +hsa-miR-216b-3p,ACACACUUACCCGUAGAGAUUCUA 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+hsa-miR-1302,UUGGGACAUACUUAUGCUAAA +hsa-miR-1302,UUGGGACAUACUUAUGCUAAA +hsa-miR-1302,UUGGGACAUACUUAUGCUAAA +hsa-miR-6780a-5p,UUGGGAGGGAAGACAGCUGGAGA +hsa-miR-450b-3p,UUGGGAUCAUUUUGCAUCCAUA +hsa-miR-6728-5p,UUGGGAUGGUAGGACCAGAGGGG +hsa-miR-6773-5p,UUGGGCCCAGGAGUAAACAGGAU +hsa-miR-1587,UUGGGCUGGGCUGGGUUGGG +hsa-miR-2110,UUGGGGAAACGGCCGCUGAGUG +hsa-miR-6857-5p,UUGGGGAUUGGGUCAGGCCAGU +hsa-miR-6751-5p,UUGGGGGUGAGGUUGGUGUCUGG +hsa-miR-6819-5p,UUGGGGUGGAGGGCCAAGGAGC +hsa-miR-6737-5p,UUGGGGUGGUCGGCCCUGGAG +hsa-miR-6855-5p,UUGGGGUUUGGGGUGCAGACAUUGC +hsa-miR-6839-3p,UUGGGUUUUCUCUUCAAUCCAG +hsa-miR-7855-5p,UUGGUGAGGACCCCAAGCUCGG +hsa-miR-493-5p,UUGUACAUGGUAGGCUUUCAUU +hsa-miR-6818-3p,UUGUCUCUUGUUCCUCACACAG +hsa-miR-4288,UUGUCUGCUGAGUUUCC +hsa-miR-3611,UUGUGAAGAAAGAAAUUCUUA +hsa-miR-218-5p,UUGUGCUUGAUCUAACCAUGU +hsa-miR-218-5p,UUGUGCUUGAUCUAACCAUGU +hsa-miR-4752,UUGUGGAUCUCAAGGAUGUGCU +hsa-miR-4474-3p,UUGUGGCUGGUCAUGAGGCUAA +hsa-miR-6796-5p,UUGUGGGGUUGGAGAGCUGGCUG +hsa-miR-6759-5p,UUGUGGGUGGGCAGAAGUCUGU +hsa-miR-592,UUGUGUCAAUAUGCGAUGAUGU +hsa-miR-6818-5p,UUGUGUGAGUACAGAGAGCAUC +hsa-miR-7156-5p,UUGUUCUCAAACUGGCUGUCAGA +hsa-miR-4677-5p,UUGUUCUUUGGUCUUUCAGCCA +hsa-miR-302c-5p,UUUAACAUGGGGGUACCUGCUG +hsa-miR-3658,UUUAAGAAAACACCAUGGAGAU +hsa-miR-4503,UUUAAGCAGGAAAUAGAAUUUA +hsa-miR-1303,UUUAGAGACGGGGUCUUGCUCU +hsa-miR-4760-5p,UUUAGAUUGAACAUGAAGUUAG +hsa-miR-651-5p,UUUAGGAUAAGCUUGACUUUUG +hsa-miR-122b-5p,UUUAGUGUGAUAAUGGCGUUUGA +hsa-miR-498-5p,UUUCAAGCCAGGGGGCGUUUUUC +hsa-miR-3942-3p,UUUCAGAUAACAGUAUUACAU +hsa-miR-587,UUUCCAUAGGUGAUGAGUCAC +hsa-miR-4755-5p,UUUCCCUUCAGAGCCUGGCUUU +hsa-miR-5006-3p,UUUCCCUUUCCAUCCUGGCAG +hsa-miR-1180-3p,UUUCCGGCUCGCGUGGGUGUGU +hsa-miR-3685,UUUCCUACCCUACCUGAAGACU +hsa-miR-670-3p,UUUCCUCAUAUUCAUUCAGGA +hsa-miR-3059-5p,UUUCCUCUCUGCCCCAUAGGGUGU +hsa-miR-7152-5p,UUUCCUGUCCUCCAACCAGACC +hsa-miR-7159-3p,UUUCUAUGUUAGUUGGAAG +hsa-miR-4482-3p,UUUCUAUUUCUCAGUGGGGCUC +hsa-miR-6833-3p,UUUCUCUCUCCACUUCCUCAG +hsa-miR-4743-3p,UUUCUGUCUUUUCUGGUCCAG +hsa-miR-4659a-3p,UUUCUUCUUAGACAUGGCAACG +hsa-miR-4659b-3p,UUUCUUCUUAGACAUGGCAGCU +hsa-miR-1304-5p,UUUGAGGCUACAGUGAGAUGUG +hsa-miR-6516-5p,UUUGCAGUAACAGGUGUGAGCA +hsa-miR-4520-2-3p,UUUGGACAGAAAACACGCAGGU +hsa-miR-12131,UUUGGAGAGGUGUACUCCCA +hsa-miR-182-5p,UUUGGCAAUGGUAGAACUCACACU +hsa-miR-96-5p,UUUGGCACUAGCACAUUUUUGCU +hsa-miR-3913-5p,UUUGGGACUGAUCUUGAUGUCU +hsa-miR-3913-5p,UUUGGGACUGAUCUUGAUGUCU +hsa-miR-6513-5p,UUUGGGAUUGACGCCACAUGUCU +hsa-miR-133b,UUUGGUCCCCUUCAACCAGCUA +hsa-miR-133a-3p,UUUGGUCCCCUUCAACCAGCUG +hsa-miR-133a-3p,UUUGGUCCCCUUCAACCAGCUG +hsa-miR-3149,UUUGUAUGGAUAUGUGUGUGUAU +hsa-miR-758-3p,UUUGUGACCUGGUCCACUAACC +hsa-miR-375-3p,UUUGUUCGUUCGGCUCGCGUGA +hsa-miR-7856-5p,UUUUAAGGACACUGAGGGAUC +hsa-miR-1305,UUUUCAACUCUAAUGGGAGAGA +hsa-miR-450b-5p,UUUUGCAAUAUGUUCCUGAAUA +hsa-miR-507,UUUUGCACCUUUUGGAGUGAA +hsa-miR-3680-3p,UUUUGCAUGACCCUGGGAGUAGG +hsa-miR-3680-3p,UUUUGCAUGACCCUGGGAGUAGG +hsa-miR-450a-5p,UUUUGCGAUGUGUUCCUAAUAU +hsa-miR-450a-5p,UUUUGCGAUGUGUUCCUAAUAU +hsa-miR-5010-3p,UUUUGUGUCUCCCAUUCCCCAG +hsa-miR-335-3p,UUUUUCAUUAUUGCUCCUGACC +hsa-miR-9983-3p,UUUUUUGCUGGAACAUUUCUGG diff --git a/modulector/migrations/0019_mirna_mirna_sequence.py b/modulector/migrations/0019_mirna_mirna_sequence.py new file mode 100644 index 0000000..102af33 --- /dev/null +++ b/modulector/migrations/0019_mirna_mirna_sequence.py @@ -0,0 +1,18 @@ +# Generated by Django 3.0.8 on 2021-01-28 00:34 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('modulector', '0018_auto_20210118_1355'), + ] + + operations = [ + migrations.AddField( + model_name='mirna', + name='mirna_sequence', + field=models.CharField(max_length=40, null=True), + ), + ] diff --git a/modulector/models.py b/modulector/models.py index 761dfd4..f0324dd 100644 --- a/modulector/models.py +++ b/modulector/models.py @@ -24,6 +24,11 @@ class UrlTemplate(models.Model): class Mirna(models.Model): mirna_code = models.CharField(max_length=40, unique=True) + mirna_sequence = models.CharField(max_length=40, null=True) + + @property + def mirbase_id(self) -> List: + return MirbaseIdMirna.objects.filter(mature_mirna__contains=self.mirna_code)[0] class OldRefSeqMapping(models.Model): @@ -85,6 +90,10 @@ class MirnaDisease(models.Model): pubmed_id = models.DecimalField(max_digits=10, decimal_places=0, null=False) description = models.TextField(blank=False) + @property + def mirna_object(self) -> List: + return Mirna.objects.filter(mirna_code__contains=self.mirna) + class Meta: db_table = 'modulector_mirnadisease' @@ -101,5 +110,9 @@ class MirnaDrugs(models.Model): support = models.TextField(blank=False) expression_pattern = models.CharField(max_length=30) + @property + def mirna_object(self) -> List: + return Mirna.objects.filter(mirna_code__contains=self.mature_mirna) + class Meta: db_table = 'modulector_mirnadrugs' diff --git a/modulector/processors/sequence_processor.py b/modulector/processors/sequence_processor.py new file mode 100644 index 0000000..ca631e6 --- /dev/null +++ b/modulector/processors/sequence_processor.py @@ -0,0 +1,34 @@ +import logging +import os +import pathlib +import sys + +import pandas as pd +from django.db import transaction, connection + +from modulector.models import Mirna + +logger = logging.getLogger(__name__) +logger.addHandler(logging.StreamHandler(sys.stdout)) +logger.setLevel(logging.INFO) + + +def process(): + parent_dir = pathlib.Path(__file__).parent.absolute().parent + file_path = os.path.join(parent_dir, "files/miraccs.csv") + logger.info("loading sequence info") + mirna_table = Mirna._meta.db_table + update_template = "UPDATE {} set mirna_sequence= '{}' where mirna_code = '{}'" + + # loading files + data = pd.read_csv(filepath_or_buffer=file_path, encoding="ISO-8859-1") + + with transaction.atomic(): + updates = [] + for index, row in data.iterrows(): + mirna, sequence = row + updates.append(update_template.format(mirna_table, sequence, mirna)) + for update in updates: + with connection.cursor() as cursor: + cursor.execute(update) + logger.info("mirna sequence updated") diff --git a/modulector/serializers.py b/modulector/serializers.py index a4a1a91..0093ca8 100644 --- a/modulector/serializers.py +++ b/modulector/serializers.py @@ -39,11 +39,16 @@ class Meta: class MirnaXGenSerializer(serializers.ModelSerializer): source_name = serializers.CharField(read_only=True, source='mirna_source.name') mirna = serializers.CharField(read_only=True, source='mirna.mirna_code') + sequence = serializers.CharField(read_only=True, source='mirna.mirna_sequence') + mirbase_id = serializers.SerializerMethodField() pubmed = PubmedSerializer(read_only=True, many=True) class Meta: model = MirnaXGene - fields = ['id', 'mirna', 'gene', 'score', 'source_name', 'pubmed'] + fields = ['id', 'mirna', 'sequence', 'mirbase_id', 'gene', 'score', 'source_name', 'pubmed'] + + def get_mirbase_id(self, mirnaxgene): + return mirnaxgene.mirna.mirbase_id.mirbase_id class MirnaSourceListSerializer(serializers.ModelSerializer): @@ -54,26 +59,34 @@ class Meta: depth = 1 -class MirnaSerializer(serializers.ModelSerializer): - class Meta: - model = Mirna - fields = ['mirna_code'] - - class MirbaseMatureMirnaSerializer(serializers.ModelSerializer): class Meta: model = MirbaseIdMirna fields = ['mirbase_id', 'mature_mirna'] +class MirnaSerializer(serializers.ModelSerializer): + mirbase = serializers.CharField(read_only=True, source='mirbase_id.mirbase_id') + + class Meta: + model = Mirna + fields = ['mirna_code', 'mirna_sequence', 'mirbase'] + + class MirnaDiseaseSerializer(serializers.ModelSerializer): + matching_mirnas = MirnaSerializer(read_only=True, many=True, source='mirna_object', allow_null=True) + class Meta: model = MirnaDisease - fields = ['id', 'category', 'mirna', 'disease', 'pubmed_id', 'description'] + fields = ['id', 'category', 'mirna', 'matching_mirnas', 'disease', 'pubmed_id', 'description'] class MirnaDrugsSerializer(serializers.ModelSerializer): + matching_mirnas = MirnaSerializer(read_only=True, many=True, source='mirna_object', allow_null=True) + class Meta: model = MirnaDrugs - fields = ['id', 'mature_mirna', 'mirbase_id', 'small_molecule', 'fda_approved', 'detection_method', 'condition', + fields = ['id', 'mature_mirna', 'matching_mirnas', + 'mirbase_id', 'small_molecule', 'fda_approved', + 'detection_method', 'condition', 'pubmed_id', 'reference', 'expression_pattern', 'support'] diff --git a/modulector/services/data_loading_service.py b/modulector/services/data_loading_service.py index 879a073..3a6a7a9 100644 --- a/modulector/services/data_loading_service.py +++ b/modulector/services/data_loading_service.py @@ -3,7 +3,7 @@ import sys from modulector.mappers import ref_seq_mapper, gene_mapper, mature_mirna_mapper -from modulector.processors import disease_processor, drugs_processor +from modulector.processors import disease_processor, drugs_processor, sequence_processor logger = logging.getLogger(__name__) logger.addHandler(logging.StreamHandler(sys.stdout)) @@ -14,9 +14,11 @@ def load_data(): # this variable show be set when you before running the code should_load_data = os.environ['LOAD_DATA'] if should_load_data == '1': + sequence_processor.process() logger.info("preloading required data") drugs_processor.process() mature_mirna_mapper.execute() disease_processor.process() ref_seq_mapper.execute() gene_mapper.execute() + sequence_processor() diff --git a/modulector/views.py b/modulector/views.py index 2a18548..f555bf1 100644 --- a/modulector/views.py +++ b/modulector/views.py @@ -1,11 +1,13 @@ import re + from django.shortcuts import render +from django_filters.rest_framework import DjangoFilterBackend from rest_framework import status, generics, filters from rest_framework.response import Response from rest_framework.views import APIView + from modulector.models import MirnaXGene, MirnaSource, Mirna, MirnaColumns, MirbaseIdMirna, MirnaDisease, MirnaDrugs from modulector.pagination import StandardResultsSetPagination -from django_filters.rest_framework import DjangoFilterBackend from modulector.serializers import MirnaXGenSerializer, MirnaSourceSerializer, MirnaSerializer, \ MirnaSourceListSerializer, MirbaseMatureMirnaSerializer, MirnaDiseaseSerializer, MirnaDrugsSerializer from modulector.services import url_service, processor_service @@ -25,8 +27,14 @@ def get_queryset(self): mirna = self.request.query_params.get("mirna") if mirna is None: return MirnaXGene.objects.none() - - return MirnaXGene.objects.filter(mirna__mirna_code=mirna) + else: + if mirna.startswith('MI'): + mirbase_mirna_record = MirbaseIdMirna.objects.filter(mirbase_id=mirna) + if mirbase_mirna_record: + mirna = [record[2] for record in mirbase_mirna_record.values_list()] + return MirnaXGene.objects.filter(mirna__mirna_code__in=mirna) + else: + return MirnaXGene.objects.filter(mirna__mirna_code=mirna) class MirnaSourcePostAndList(APIView): @@ -76,13 +84,19 @@ def get_queryset(self): mirna = self.request.query_params.get("mirna", None) result = Mirna.objects.all() if mirna: - result = result.filter(mirna_code=mirna) + if mirna.startswith('MI'): + mirbase_mirna_record = MirbaseIdMirna.objects.filter(mirbase_id=mirna) + if mirbase_mirna_record: + mirna = [record[2] for record in mirbase_mirna_record.values_list()] + result = result.filter(mirna_code__in=mirna) + else: + result = result.filter(mirna_code=mirna) return result class LinksList(APIView): - def get(self): - mirna = self.request.query_params.get("mirna", None) + def get(self, request): + mirna = request.query_params.get("mirna", None) links = url_service.build_urls(mirna) return Response(links, status=status.HTTP_200_OK) @@ -99,8 +113,9 @@ def get_queryset(self): result = MirnaDisease.objects.all() if mirna: mirna = mirna.lower() - mirna = re.sub(regex, "", mirna) - result = result.filter(mirna__startswith=mirna) + if mirna.count('-') == 3: + mirna = re.sub(regex, "", mirna) + result = result.filter(mirna__contains=mirna) return result @@ -118,7 +133,7 @@ def get_queryset(self): mirbase = self.request.query_params.get("mirbase") query_set = MirnaDrugs.objects.all() if mirna: - query_set = query_set.filter(mature_mirna__endswith=mirna) + query_set = query_set.filter(mature_mirna__contains=mirna) if mirbase: query_set = query_set.filter(mirbase_id=mirbase) return query_set