User: UBodenhofer

gravatar for UBodenhofer
UBodenhofer200
Reputation:
200
Status:
Trusted
Location:
Johannes Kepler University, Linz, Austria
Website:
http://www.bioinf.jku.at/
Twitter:
u_bode
Scholar ID:
Google Scholar Page
Last seen:
4 days, 4 hours ago
Joined:
5 years, 3 months ago
Email:
b*********@bioinf.jku.at

Associate Professor in Bioinformatics at Johannes Kepler University, Linz, Austria. Maintainer of the following packages: 'msa', 'kebabs', 'procoil', 'podkat' (Bioconductor) / 'apcluster', 'rococo' (CRAN)

Posts by UBodenhofer

<prev • 29 results • page 1 of 3 • next >
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Answer: A: msa: How to obtain a subset of an alignment
... Thanks for your positive feedback, Christof!  Regarding your question: yes, it is true that objects of class 'MultipleAlignment' and classes derived from 'MultipleAlignment' do not support subsetting. Presently, I can offer the following workaround (... continuing your example code): alnSubset &l ...
written 8 weeks ago by UBodenhofer200
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Comment: C: Can't install msa on FreeBSD
... That's why GNU make is listed as system requirement. ;-) ...
written 12 weeks ago by UBodenhofer200
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Comment: C: Can't install msa on FreeBSD
... Great to know that you managed to solve this issue. I will make some tests to see if your workaround also works on other systems and compilers. If so, I can include it in the release. Note, however, that this code is shipped with ClustalOmega. Can you compile ClustalOmega from source on your system? ...
written 12 weeks ago by UBodenhofer200
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Comment: C: untranslate AAstringset {Biostrings} or MsaAAMultipleAlignment {msa}
... Please note that more or less exactly the same question has been discussed previously (thread https://support.bioconductor.org/p/96231/). And the answer was the same as by hakunamatata: use DECIPHER. ...
written 3 months ago by UBodenhofer200 • updated 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... These are not directly related to msaPrettyPrint() or any other 'msa' functionality. Olorin used them for his example posted above. He reads FASTA files from 'workdir' and writes the output of msaPrettyPrint() to 'outdir'. 'bdir' is just the base directory, of which 'workdir' and 'outdir' are sub-di ...
written 5 months ago by UBodenhofer200
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Answer: A: Outputting a multiple alignment to file error: could not find function write.XSt
... The correct name of the function is 'writeXStringSet' (without period). I don't recall precisely when the function name was changed, but I think it was several Bioconductor releases ago. The correct usage is the following: writeXStringSet(unmasked(z), file="test.fasta") The function 'unmasked' ma ...
written 8 months ago by UBodenhofer200
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Comment: C: msaPrettyPrint cannot handle long sequences?
... Of course, that is exactly what I would have answered. If you have any other questions or issues, please let us know. All the best! ...
written 8 months ago by UBodenhofer200
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Comment: C: msa alignement: sorted sequences by sequence name
... That is true, 'code' overrides everything else. However, if you just want to add some customizations on top of what msaPrettyPrint() configures by itself, you can use the 'furtherCode' argument which only adds TeX code without overriding the rest. ...
written 9 months ago by UBodenhofer200
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Comment: C: msa alignement: sorted sequences by sequence name
... There is not always the space to display full names if they are longer. I suggest to use some string processing to shorten the names properly, e.g. to remove "Escherichia coli" entirely (if you only have E.coli sequences anyway) or to abbreviate it by "E.coli". This can be done by altering the names ...
written 9 months ago by UBodenhofer200
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Comment: C: msa alignement: sorted sequences by sequence name
... Awesome, Olorin! May I add a few more bits: Not all of your customizations really need to be done in the LaTeX source. The most common customizations can be made using optional arguments of the msaPrettyPrint() function. See '?msaPrettyPrint' for details.  Those interested in where more details ...
written 9 months ago by UBodenhofer200

Latest awards to UBodenhofer

Scholar 8 months ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Autobiographer 17 months ago, has more than 80 characters in the information field of the user's profile.

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