User: toth.joe

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toth.joe20
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Posts by toth.joe

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solved :use pandas dataframe column result to slice data in other columns
... I want a workflow to take raw sequence reads as a multi-entry fasta, then process them with hmmer and regex patterns to yield trimmed gene DNA and protein sequences. I am able to assemble a dataframe with the raw DNA, the upstream trimmed DNA and protein. For the downstream trimming, I need to use ...
python pandas written 5 months ago by toth.joe20 • updated 5 months ago by Biostar ♦♦ 20
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Answer: A: Code for splitting long string into Genbank record gives error
... Thanks for the help everyone. I was able to get the Genbank feature writer to work. It wasn't a problem with long strings, rather I had to pass the Qualifier key and value attributes correctly to the Feature method. container = Record() container.locus = row['Sample'] container.size = len(row ...
written 8 months ago by toth.joe20
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Comment: C: Code for splitting long string into Genbank record gives error
... Thanks for clarifying the source code. I entered the format as you suggest but still get an error. feature = Feature() feature.key = "CDS" feature.location = "1..{}".format(len(row['DNA'])) feature.qualifiers = [ Qualifier("/translation=", "% ...
written 8 months ago by toth.joe20
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Code for splitting long string into Genbank record gives error
... I am trying to read a long amino acid string into a Biopython Genbank record object so that a Genbank file can be written. Here is a truncated example > FEATURES Location/Qualifiers CDS 687..3158 /gene="AXL2" ...
biopython genbank written 8 months ago by toth.joe20
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Answer: A: Creating Genbank files with Python using BioGenBankRecord
... Thanks for the information. I realized that I had a problem with the Genbank record format. Here is the code that works: from Bio.GenBank.Record import Record def main(): /# open csv read entries row by row then insert in a dictionary with open(args.sampleFile,'r') ...
written 8 months ago by toth.joe20
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Creating Genbank files with Python using BioGenBankRecord
... I want to create my own Genbank files for import of sequence and annotations into a commercial DNA Software package. I have a working version using Bio.SeqRecord but the SeqRecord format is limiting (I can't specify organism and some other attributes). I am looking at Bio.GenBank.Record as a bet ...
python biopython genbank written 8 months ago by toth.joe20

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