Unable to plot some secondary RNA structures

[Biocanter]

Hi, I'm unable to plot some secondary RNA structures: For example when I want to visualize these secondary structures:

ss_2='((.....))......((.(((.(((.((((((...)))))))))..)))))......((((((((.((.(((((((.(((((.((..(((((.(.((((.((.(((((.(((((..((.(((((((......)))....)))).))....))))).))))).)).)))).))).(((.((((((.....)))))).))))))..))..)))))))))))).)).)).....(((((((....))))))).))))))'

ss_3='.......(((..((((((((..((((((..((((..((.((.((((((((((.((((((((((....((((..((..(((.(((((((((.(((....((((((((((........)))).)))))).....))))))))).))))))..)).)))).((((((..(((((((.(((............))).....)))))))))))))..))))).))))).))).)..)))))).))..)).)))).)))((((......)))).))).))))))))...((((((....)))))).)))'

I got this error: -- IndexError: list index out of range

This error comes from here -- _RiboGraphViz/RiboGraphViz/RG_utils.py] in intersect(x, y, lineA, lineB)

These are the RNA sequences I've used to calculate the previous secondary RNA structures:

seq_2='GCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGG'

seq_3='AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGGCCGGCGAGGGUGGAAGAUCCGGGCGAGCAGAGCUGCGCUCCGGGCGUCGUGGGAAGGGAGAUCCGGAGCGAAAAGGGGGCUUCGCCUCCGGCCCAGCCCUCCCGCUGACCCCCCAGACAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGGGGGCGGACACUUUGCACUGGAACUUACAACACCCUAGCAAGGACGCUACUCUCCCGACGCGGGGAGGCUAUUCUGCCUAUUUGGGGACACUUCCCCGCCGC'

Thanks Ángel Cantero-Camacho, PhD

[HWaymentSteele]

What is your code for plotting?

On Oct 5, 2022, at 10:05 AM, Biocanter @.***> wrote:

Hi, I'm unable to plot some secondary RNA structures: For example when I want to visualize these secondary structures:

ss_2='((.....))......((.(((.(((.((((((...)))))))))..)))))......((((((((.((.(((((((.(((((.((..(((((.(.((((.((.(((((.(((((..((.(((((((......)))....)))).))....))))).))))).)).)))).))).(((.((((((.....)))))).))))))..))..)))))))))))).)).)).....(((((((....))))))).))))))'

ss_3='.......(((..((((((((..((((((..((((..((.((.((((((((((.((((((((((....((((..((..(((.(((((((((.(((....((((((((((........)))).)))))).....))))))))).))))))..)).)))).((((((..(((((((.(((............))).....)))))))))))))..))))).))))).))).)..)))))).))..)).)))).)))((((......)))).))).))))))))...((((((....)))))).)))'

I got this error: -- IndexError: list index out of range

This error comes from here -- _RiboGraphViz/RiboGraphViz/RG_utils.py] in intersect(x, y, lineA, lineB)

These are the RNA sequences I've used to calculate the previous secondary RNA structures:

seq_2='GCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGG'

seq_3='AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGGCCGGCGAGGGUGGAAGAUCCGGGCGAGCAGAGCUGCGCUCCGGGCGUCGUGGGAAGGGAGAUCCGGAGCGAAAAGGGGGCUUCGCCUCCGGCCCAGCCCUCCCGCUGACCCCCCAGACAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGGGGGCGGACACUUUGCACUGGAACUUACAACACCCUAGCAAGGACGCUACUCUCCCGACGCGGGGAGGCUAUUCUGCCUAUUUGGGGACACUUCCCCGCCGC'

Thanks Ángel Cantero-Camacho, PhD

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[Biocanter]

`##this sequence works seq_0='ACUGAACAUAAACUCCUAGCCUUAGUGUCUACGUUGUUGUGUUUUUCUAACAAUAUGAUGCUCUGGCCGUGGCUUUAAGCCACCAGGGUGCGAGGUAGAAAUGCCUGCAUCUCCCGUAUUUGGAAAGGUGUUAUGGUACAACUGAC' ss_0='......(((((.(.(((.(((..((((((...(((((((........)))))))..))))))..))).((((((...))))))..((((((.(((((....))))))))))).(((....)))..))).))))))...........'

this sequences doesn't work

seq_3='AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGGCCGGCGAGGGUGGAAGAUCCGGGCGAGCAGAGCUGCGCUCCGGGCGUCGUGGGAAGGGAGAUCCGGAGCGAAAAGGGGGCUUCGCCUCCGGCCCAGCCCUCCCGCUGACCCCCCAGACAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGGGGGCGGACACUUUGCACUGGAACUUACAACACCCUAGCAAGGACGCUACUCUCCCGACGCGGGGAGGCUAUUCUGCCUAUUUGGGGACACUUCCCCGCCGC' ss_3='.......(((..((((((((..((((((..((((..((.((.((((((((((.((((((((((....((((..((..(((.(((((((((.(((....((((((((((........)))).)))))).....))))))))).))))))..)).)))).((((((..(((((((.(((............))).....)))))))))))))..))))).))))).))).)..)))))).))..)).)))).)))((((......)))).))).))))))))...((((((....)))))).)))' struct = mfe(seq_3, package='vienna_2') bpp_vec = 1 - np.sum(bpps(seq_3, package='vienna_2'),axis=0) rg = RGV(struct) figure(figsize=(12,12)) rg.draw(c=bpp_vec, cmap='plasma')`