In [3]:

    

# Create a fasta file first
%load_ext autoreload
%autoreload
import rna_alignment as ra
a = ra.RNAalignment('test_data/IA1.gissd.sto')


    

    




The autoreload extension is already loaded. To reload it, use:
  %reload_ext autoreload

In [9]:

    

for s in a:
    print(s.id)
    #print(s.seq)
    #print(s.ss)


    

    




Ceu.cL958/1-413
Cca.cL958/1-470
Ceu.cL1065/1-451
Csp.cL1065/1-417
Dpa.cL1065/1-362
Hla.cL1065/1-437
She.cL1065/1-360
Naq.cL1255/1-257
Cca.cL1255/1-290
Cko.cL1255/1-347
Cfr.cL1255/1-292
Pan.mL1699/1-1261
Ceu.cL1766/1-373
Cec.cL1766/1-382
Smi.mL2449/1-409
Scar.mL2449/1-422
Scas.mL2449/1-373
Spa.mL2449/1-349
Sce.mL2449-1/1-1163
Sdo.mL2449/1-350
Sse.mL2449/1-346
Sex.mL2449/1-1131
Zro.mL2449/1-335
Zbi.mL2449/1-1169
Tgl.mL2449/1-434
Tpr.mL2449/1-340
Tde.mL2449/1-1163
Kla.mL2449/1-401
Kdo.mL2449/1-447
Kth.mL2449/1-1094
Pca.mL2449/1-1078
Ncr.mL2449/1-1190
Eni.mL2449/1-336
Pch.mL2449/1-1149
Pur.mL2449/1-1149
Pma.mL2449/1-1117
Slu.mL2449/1-542
Aae.mL2449/1-563
Cne.mL2449/1-320
Ama.mL2449/1-320
Ceu.mL2449/1-371
Cbr.cL2449/1-1061
Cps.cL2449/1-504
Csp.cL2449/1-407
Cpa.cL2449/1-499
Col.cL2449/1-1135
Dpa.cL2449/1-1097
Cec.cL2449/1-900
Pbi.cL2449/1-441
Ptu.cL2449/1-294
Pwi.mL2449/1-395
Lmu.mL2449/1-1103
Hje.mL2449/1-1110
Slu.mL2504/1-368
Cne.mL2504/1-437
Ama.mL2504/1-377
Ddi.mL2504/1-546
Sob.mL2504-1/1-1200
Pwi.mL2504/1-520
Rsp.mL2585/1-1104
Sce.m.COB,5/1-498
Tru.m.A9,1/1-260
Tpa.m.COX2,1/1-216
Tpa.m.ND1,1/1-219
Ama.m.COX2,1/1-373
Ama.m.COB,4/1-283
Ceu.c.psbC,2/1-389
Ncr.m.COB,2-1/1-316
Ncr.m.COB,2-2/1-316
Cmo.c.psbA,1/1-308
Cmo.m.psaB,1/1-332
Cre.c.psbA,1/1-250
Cre.c.psbA,4/1-309
Pan.m.COX2,2/1-334
Pan.m.ND1,3/1-1129
Pan.mL2449/1-1153

In [13]:

    

print a.describe()


    

    




SingleLetterAlphabet() alignment with 76 rows and 1471 columns

In [21]:

    

s = a[1]


    

In [22]:

    

s.draw_ss()


    

    
Out[22]:

In [23]:

    

s.remove_gaps(check_bps=False, only_canonical=False)
s.draw_ss()


    

    
Out[23]:

In [24]:

    

s.remove_gaps(check_bps=True, only_canonical=True)
s.draw_ss(verbose=True)


    

    




/Users/magnus/work/opt/varna
java -cp VARNA.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN AGUGGGGGAUAAGAGGAAGCUUGUCCGUUCUAAAUAAGA.AUUUAGAAUUAAACUACUAGGUGAAUUGCGAGAAAGCUAAGGUUCCUGAGCUAUGCUCUUCCCUACGGGGAAAGGUUACUAUGCUAACUUGCAGCGUAUCUAAGCUACUUUCAUUUAAGUCACCGCCUAUUUUCUUCGUAGACAAUAAGGCGAAAGACUAAACGUAGCUAAGCACGUUCAACGACUAGGAAAUGAGGAUUGAAAAUCCAAUAAAUAUUCCCAAGAGUGCCUGGCAACUUU..UAUUGCCCCGAAGGGGGACUCGCAUAAUCCGUCUUCUAAGUUAUAAUCCCUUGGGAUUAUUACUAACAAGGGGAUUAUACGACAU..AAAGUUGAUGACAUAGUCUGAUCUUUAGGGAAACCUAAAGAAGCAGGAGAUAAAGAGCUCCUGCGCUUUACUUAAUUUUUUAAGUAAAGCAACAAGAAGCUUCAUU -structureDBN '......((((((........))))))..(..((........))..)..........(((((((...((((((.....((.(((..................................))).))....))))))(((...((.(((((.........................................................))))).))..)))...[.[[[[[(((.(......................).))).......)))))))(((((((.........................................................................................)))))))......]]]]]]..((((((((....))))))).....((.(.........).))...............................)............' -o /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpaQdEvR.png -title '' -resolution '1.5'
/var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpaQdEvR.png






    
Out[24]:

In [25]:

    

s.remove_gaps(check_bps=True, only_canonical=True)
s.draw_ss(verbose=True, resolution=5)


    

    




/Users/magnus/work/opt/varna
java -cp VARNA.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN AGUGGGGGAUAAGAGGAAGCUUGUCCGUUCUAAAUAAGAAUUUAGAAUUAAACUACUAGGUGAAUUGCGAGAAAGCUAAGGUUCCUGAGCUAUGCUCUUCCCUACGGGGAAAGGUUACUAUGCUAACUUGCAGCGUAUCUAAGCUACUUUCAUUUAAGUCACCGCCUAUUUUCUUCGUAGACAAUAAGGCGAAAGACUAAACGUAGCUAAGCACGUUCAACGACUAGGAAAUGAGGAUUGAAAAUCCAAUAAAUAUUCCCAAGAGUGCCUGGCAACUUUUAUUGCCCCGAAGGGGGACUCGCAUAAUCCGUCUUCUAAGUUAUAAUCCCUUGGGAUUAUUACUAACAAGGGGAUUAUACGACAUAAAGUUGAUGACAUAGUCUGAUCUUUAGGGAAACCUAAAGAAGCAGGAGAUAAAGAGCUCCUGCGCUUUACUUAAUUUUUUAAGUAAAGCAACAAGAAGCUUCAUU -structureDBN '......((((((........))))))..(..((.......))..)..........(((((((...((((((.....((.(((..................................))).))....))))))(((...((.(((((.........................................................))))).))..)))...[.[[[[[(((.(......................).))).......)))))))(((((((.....................................................................................)))))))......]]]]]]..((((((((....))))))).....((.(.........).))...............................)............' -o /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpA4PYlz.png -title '' -resolution '5'
/var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpA4PYlz.png






    
Out[25]:

In [ ]: