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Unable to plot some secondary RNA structures #3
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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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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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