User: dylan.storey
dylan.storey • 60
- Reputation:
- 60
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- Location:
- United States
- Twitter:
- @dylanbstorey
- Last seen:
- 3 years, 4 months ago
- Joined:
- 6 years, 6 months ago
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Posts by dylan.storey
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... I don't know python well but -
I'd guess that the translation key doesn't exist
Add a switch statement in to test for the existence of the key 'translation' before you.
Something like
if (defined seq_feature.qualifiers['translation']){
do something
}
else{
warn you - po ...
written 3.4 years ago by
dylan.storey • 60
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3
answers
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... You could try google
...
written 3.9 years ago by
dylan.storey • 60
• updated
3.9 years ago by
Devon Ryan ♦ 90k
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... his test cases don't show that. =D
...
written 4.0 years ago by
dylan.storey • 60
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... if it's space delimited you can use \s+ for your regex , it will match tabs and spaces both.
...
written 4.0 years ago by
dylan.storey • 60
0
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... If you already have the one to one mappings in a file. Build a hash (or
dict) in perl (python) by reading in and parsing previously mentioned file.
(maybe 5 lines) .
Then read your other file in and do look ups and replacements.
-- Dylan B. Storey
Post Doctoral Researcher
University of Calif ...
written 4.1 years ago by
dylan.storey • 60
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... why do you think it would re read the file every time? Sed works on a stream. You literally posted the exact solution you needed as a one line sed solution. Am I missing something about the replacement pattern ?
...
written 4.1 years ago by
dylan.storey • 60
0
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... It sounded like you had a sed solution. ...
written 4.1 years ago by
dylan.storey • 60
0
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... if you can use a command line tool it will likely be the more efficient
than relying on perl.
I'd suggest you pipe your output instead of doing an inline replace just to
ensure you have an un-tainted file to come back to in the event of a
mistake.
-- Dylan B. Storey
Post Doctoral Researcher
...
written 4.1 years ago by
dylan.storey • 60
0
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Comment:
C: Make multi-fasta using perl
... I was looking for a mic drop gif but just gave up myself.
...
written 4.2 years ago by
dylan.storey • 60
1
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1.6k
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... If most of your reads are that short , your assembly is going to be bad no question about it. Seeing as it is RADSeq data though I don't think you're overly interested in getting long contigs. I would suggest running your assembler with multiple parameters to test for the configuration that works be ...
written 4.2 years ago by
dylan.storey • 60
Latest awards to dylan.storey
Scholar
4.2 years ago,
created an answer that has been accepted.
For A: how to find and replace the atypical aas in a protein fasta-file, remembering th
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: how to find and replace the atypical aas in a protein fasta-file, remembering th
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