User: chrisgbeldam

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chrisgbeldam20
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2 years, 4 months ago
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Posts by chrisgbeldam

<prev • 9 results • page 1 of 1 • next >
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BioPython ESearch XML File & Dates
... Hi, So I am attempting to do an esearch like the following in Biopython: handle = Entrez.esearch( db="pubmed", sort="relevance", term=disease, mindate=year, retmode="xml", ) results = Entrez.read(handle) handle.close() How would I go about ...
search esearch written 7 months ago by chrisgbeldam20
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Comment: C: BioPython Error Messaging
... I'm asking here because it's in relation to BioPython and fasta files which are Bioinformatics ...
written 2.4 years ago by chrisgbeldam20
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BioPython Error Messaging
... Hi All I've written some BioPython but I want to be able to generate an error message if the protein searched for is not in my fasta file? I've use try and except but there must be a better way to do it than that? for myuniprot in myuniprots: try: for record in SeqIO.parse("uniprot ...
errormessage python biopython error written 2.4 years ago by chrisgbeldam20 • updated 2.4 years ago by Bioaln310
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... So now if I want to grab the CD4_HUMAN aspect as the species. Would I do something like this? species = record.id.split('|')[2] if '|' in record.id else record.species? ...
written 2.4 years ago by chrisgbeldam20
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Last question, why does that only return P01731 as opposed to both of them? ...
written 2.4 years ago by chrisgbeldam20
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Thank you! I didn't realise that's how BioPython see's ids ...
written 2.4 years ago by chrisgbeldam20
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Yeap runs but prints nothing Here is the fasta file format: >sp|P01730|CD4_HUMAN T-cell surface glycoprotein CD4 OS=Homo sapiens GN=CD4 PE=1 SV=1 M NRGVPFRHLLLVLQLALLPAATQGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIK ILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQL LVFGLTANSDTHLLQGQSLTLTLESP ...
written 2.4 years ago by chrisgbeldam20
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Thanks! Silly comment to make but the script runs and prints nothing. Am I safe to then assume that uniprot is not in the FASTA file? ...
written 2.4 years ago by chrisgbeldam20
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Using Biopython to search a fasta file for specific uniprots
... I am trying to use BioPython to search through a fasta file. I can get BioPython to search and return the entire fasta file. However, I want to be able to then specify a specific uniprot in that fasta file and have BioPython search for it and returns its attributes e.g. ID, seq and so on. This is t ...
python uniprot biopython written 2.4 years ago by chrisgbeldam20 • updated 2.4 years ago by a.zielezinski8.8k

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