User: aproposdiver
aproposdiver • 10
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Posts by aproposdiver
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... 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.
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written 5.4 years ago by
aproposdiver • 10
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... 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
aproposdiver • 10
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... 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 ...
written 5.6 years ago by
aproposdiver • 10
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... 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.
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written 5.6 years ago by
aproposdiver • 10
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5 follow
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... 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 ...
written 5.6 years ago by
aproposdiver • 10
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... 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
aproposdiver • 10
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