User: gearoid

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gearoid200
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Posts by gearoid

<prev • 16 results • page 2 of 2 • next >
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Answer: A: How to remove the last character "," from each row in bed file?
... Remove one trailing ',' from the end of every line in a file: while read line; do echo ${line%,} done < input.file > output.file (If I understand you correctly) ...
written 3.2 years ago by gearoid200
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Comment: C: muscle v3.8.31 large sequence Segmentation fault
... With regards to it taking forever, it's a lot of sequences, but they're quite short, so it's probably not going to be as bad as you'd expect. To get an idea, I just timed Clustal Omega aligning 194775 amino acid sequences of average length 40 (WD40 repeat from Pfam) and it took about 2.5 hours (real ...
written 3.2 years ago by gearoid200
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Comment: C: How to create empty Biopython MultipleSeqAlignment object?
... So the short version is that to use a class or function you either need to define it in the same file or import it from somewhere else. In this case class MultipleSeqAlign is defined in module Bio.Align. So you can get it two ways from Bio.Align import MultipleSeqAlign which then allows you to ...
written 3.2 years ago by gearoid200
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Answer: A: How to create empty Biopython MultipleSeqAlignment object?
... MultipleSeqAlignment is in Bio.Align, so you just need to import that: import Bio.Align empty_align = Bio.Align.MultipleSeqAlignment([]) ...
written 3.2 years ago by gearoid200
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Answer: A: muscle v3.8.31 large sequence Segmentation fault
... I believe this is just an issue with MUSCLE -- it crashes for very large numbers of sequences. I'm not sure exactly how many is too many, but it's on the order of tens of thousands of sequences. As far as I know, MAFFT, Clustal Omega and UPP should be capable of aligning 276188 sequences, so the si ...
written 3.2 years ago by gearoid200
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Comment: C: FASTA file of fixed length
... I think 'if' statements would be more appropriate than assertions in your code. Assertions are really for asserting things that you believe will always be true, not validating user input. They should only be failing when there's a bug in your code, whereas your assertions are going to fail on e.g. a ...
written 3.2 years ago by gearoid200

Latest awards to gearoid

Scholar 3.2 years ago, created an answer that has been accepted. For A: How to create empty Biopython MultipleSeqAlignment object?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How to edit .PDB files fast ?
Scholar 3.2 years ago, created an answer that has been accepted. For A: How to create empty Biopython MultipleSeqAlignment object?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How to edit .PDB files fast ?
Supporter 3.2 years ago, voted at least 25 times.
Scholar 3.2 years ago, created an answer that has been accepted. For A: How to create empty Biopython MultipleSeqAlignment object?

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