In [9]:

    

# Create a fasta file first
%load_ext autoreload
%autoreload
import rna_alignment as ra
a = ra.RNAalignment('test_data/IE2.gissd.sto')


    

    




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

In [10]:

    

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


    

    




Cpin.S516/1-368
Mal.S516/1-409
Ede.S516/1-460
Ddi.S516/1-318
Tpa.S516-1/1-442
Tpa.S516-2/1-443
Par.S516-1/1-432
Par.S516-2/1-432
Par.S516-3/1-427
Pob.S516/1-416
Clu.S516/1-265
Gvi.S516/1-371
Sda.S516/1-424
Ufl.S516/1-440
Ti_fl.S516-1/1-347
Ti_fl.S516-2/1-353
Pbr.S516/1-409
Cmu-2.S516-2/1-417
Cps.S516/1-373
Cre.S516/1-381
Ppl.S516/1-382
Sc_sp.S516/1-416
Aha.S516/1-378
Rpo.S516-1/1-384
Rpo.S516-2/1-418
Msp.S516/1-476
Pau.S516-1/1-378
Pau.S516-2/1-385
Kap.S516/1-397
Afu.S516/1-399
Qcl.S516/1-395
Chlo_sp-10.S516/1-363
Chlo_sp-11.S651/1-353
Chlo_lu.S516-1/1-371
Chlo_lu.S516-2/1-373
Wre.S516/1-385
Sba.S516/1-480
Tar.S516/1-400
Tus.S516/1-400
Am_sp.S516/1-441
Kfl.S516/1-444
Kni.S516-1/1-445
Kni.S516-2/1-445
Ksu.S516/1-400
Ksp.S516/1-379
Cka.L2066/1-404
Cpro.L2066/1-407
Pte.L2066/1-424
Co_sp-3.L2066/1-403
Man.L2066-2/1-361
Man.L2066-1/1-358
Cal.L1923/1-403
Cal.L1923,1/1-394
Cdu.L1923-1/1-393
Cdu.L1923-2/1-396
Sps.L1926/1-439

In [11]:

    

print a.describe()


    

    




SingleLetterAlphabet() alignment with 56 rows and 710 columns

In [12]:

    

s = a[1]


    

In [13]:

    

s.draw_ss()


    

    
Out[13]:

In [14]:

    

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


    

    
Out[14]:

In [15]:

    

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 AAGUCUGUCGAAACCACAGUAUUCUCUUACUGCUGACGCCGGAAAUAGCGGGG......UUC.......ACCCUCGCUAGUCGAGCAUCCAUAUGUAGCGAUGGGU.GAUGCCGGCAGGUGACCUGGUACGG.GGAAGCCUACG......GGCCGUGA.CG.UAU.GGUGAU.CCGUGGCGAGCCAACC....UCCG.......GGUGGCCGUCGUAACCGCGCGCAAAGGCACCGGCCGCCUGUCCUCCAAGGAUCAGGUGGCUCAGGUACGUGCUGUCCAUCUGAAA.GAUGCCUGAAGCUGGAGCAACCCAUCG.UGCAAAGGUUUCGGGGGUAAGCUGC...UCCAUU..GCAGGUUAUCCGGGUCUACUCAACACCCCGUGAGGGACAUGAGGGGGCUUGUGGGUGGGGGUGUUGAAGCGCAGAACAAUUUAACGGCCAGCAGCCGC -structureDBN '...((((.((..........................)).))))..(((((((....................)))))))(((..(....(.................)....)))).((((.(((...((((.(..(.(...........................).)..).))))((((.((((....................))))))))...[..[[[[[...)))))))(((((((((............)))))))))......]]]]]]((.((((......))))((((((((.....((.........)).....))))))))(((((.....................))))).........................................................................)).............' -o /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpeMUWJm.png -title '' -resolution '1.5'
/var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpeMUWJm.png






    
Out[15]:

In [16]:

    

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 AAGUCUGUCGAAACCACAGUAUUCUCUUACUGCUGACGCCGGAAAUAGCGGGGUUCACCCUCGCUAGUCGAGCAUCCAUAUGUAGCGAUGGGUGAUGCCGGCAGGUGACCUGGUACGGGGAAGCCUACGGGCCGUGACGUAUGGUGAUCCGUGGCGAGCCAACCUCCGGGUGGCCGUCGUAACCGCGCGCAAAGGCACCGGCCGCCUGUCCUCCAAGGAUCAGGUGGCUCAGGUACGUGCUGUCCAUCUGAAAGAUGCCUGAAGCUGGAGCAACCCAUCGUGCAAAGGUUUCGGGGGUAAGCUGCUCCAUUGCAGGUUAUCCGGGUCUACUCAACACCCCGUGAGGGACAUGAGGGGGCUUGUGGGUGGGGGUGUUGAAGCGCAGAACAAUUUAACGGCCAGCAGCCGC -structureDBN '...((((.((..........................)).))))..(((((((.......)))))))(((..(....(................)....)))).((((.(((...(((((..(.(..................).)..)))))((((.((((.........))))))))...[..[[[[[...)))))))(((((((((............)))))))))......]]]]]]((.((((.....))))((((((((.....((........)).....))))))))(((((................))))).........................................................................)).............' -o /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpvHpXvG.png -title '' -resolution '5'
/var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmpvHpXvG.png






    
Out[16]:

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