User: dylan.storey

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dylan.storey60
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@dylanbstorey
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3 years, 4 months ago
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Posts by dylan.storey

<prev • 16 results • page 1 of 2 • next >
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Answer: A: gbk2faa: why is it not working for refseq gbk?
... 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.storey60
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Comment: C: Assemble short reads based on k-mers
... You could try google ...
written 3.9 years ago by dylan.storey60 • updated 3.9 years ago by Devon Ryan90k
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Comment: C: Perl :Help to match two IDs from two tables and print to a .txt file
... his test cases don't show that. =D  ...
written 4.0 years ago by dylan.storey60
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Comment: C: Perl :Help to match two IDs from two tables and print to a .txt file
... 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.storey60
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Comment: C: Efficient means of mass converting Affy SNP IDs to dbSNP rs ids
... 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.storey60
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Comment: C: Efficient means of mass converting Affy SNP IDs to dbSNP rs ids
... 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.storey60
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Comment: C: Efficient means of mass converting Affy SNP IDs to dbSNP rs ids
... It sounded like you had a sed solution. ...
written 4.1 years ago by dylan.storey60
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Answer: A: Efficient means of mass converting Affy SNP IDs to dbSNP rs ids
... 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.storey60
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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.storey60
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Answer: A: Optimal minimum read length PE HiSeq reads for denovo assembly
... 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.storey60

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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