User: aproposdiver

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aproposdiver10
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Posts by aproposdiver

<prev • 6 results • page 1 of 1 • next >
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Answer: A: get protein sequences from genbank
... I cant seem to figure out how to modify this script to extract just the coding sequence in DNA format.  I am pretty sure I need to use extract but have not been able to modify this properly to get that.     ...
written 5.4 years ago by aproposdiver10
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Comment: C: get protein sequences from genbank
... Thanks for this. I tried it but got the error: line 3 SyntaxError: Non-ASCII character '\xe2' in file /home/kpenn/Python.scripts.dir/Split.Genbank.to.faa.std.input.py on line 3, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details     This is the script: #!/usr/bin ...
written 5.6 years ago by aproposdiver10
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Parsing Hmmsearch tblout format
... I have a tblout format for search of sequences against all Pfams.  I would like to find the HMM that each of my sequences matches best which means I want to get the sequence that has the lowest evalue for one Hmm model.  I wonder if anyone know of a way to do this?  I basically want to be able to so ...
hmmsearch written 5.6 years ago by aproposdiver10
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Comment: C: get protein sequences from genbank
... Yes but the main function I am looking for is to get the sequences parsed into separate files based on the different gb accession for the overall contig.   ...
written 5.6 years ago by aproposdiver10
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get protein sequences from genbank
... I have this script below and it seems to be hard coded for files in the working directory. I basically know nothing about python but I want to make this script so it can read in a many genbank files instead of just be coded for one file at a time. from Bio import GenBank   gbk_filename = "NC_005213 ...
biopython genbank written 5.6 years ago by aproposdiver10
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Comment: C: How can I convert a genbank file to a FASTA file? IOError
... Can you explain this a little more? I am trying to get the same script to work but  dont like the hard coding of NC_005213.gbk. I want to be able to read many files and have each of them parsed to a new file. Can you explain how this can be done? ...
written 5.6 years ago by aproposdiver10

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