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POBiopython (or just Python in general): Most Efficient Way to Parse Species Name From A large .fasta file using gi identifier
 

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  1. POBiopython (or just Python in general): Most Efficient Way to Parse Species Name From A large .fasta file using gi identifier
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    <p>I have a .fasta file (.txt essentiallly) of about 145000 entries that are formatted as below</p> <pre><code>&gt;gi|393182|gb|AAA40101.1| cytokine [Mus musculus] MDAKVVAVLALVLAALCISDGKPVSLSYRCPCRFFESHIARANVKHLKILNTPNCALQIVARLKNNNRQV CIDPKLKWIQEYLEKALNKRLKM &gt;gi|378792467|pdb|3UNH|Y Chain Y, Mouse 20s Immunoproteasome TTTLAFKFQHGVIVAVDSRATAGSYISSLRMNKVIEINPYLLGTMSGCAADCQYWERLLAKECRLYYLRN GERISVSAASKLLSNMMLQYRGMGLSMGSMICGWDKKGPGLYYVDDNGTRLSGQMFSTGSGNTYAYGVMD SGYRQDLSPEEAYDLGRRAIAYATHRDNYSGGVVNMYHMKEDGWVKVESSDVSDLLYKYGEAAL &gt;gi|378792462|pdb|3UNH|T Chain T, Mouse 20s Immunoproteasome MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNV DRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGS YSANDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF ELELSWVGELTKGRHEIVPKDIREEAEKYAKESLKEEDESDDDNM </code></pre> <ol> <li>I have a list of gi's (the first number listed after the |).</li> <li>The size of this list varies between 60 - 600 gi's for a given test</li> <li>I want to return a list with respective species of those gi's</li> <li>The species name is usually seen as in the first example (surrounded by square brackets [Mus musculus]) it is not always present.</li> <li>Order is not particularly important.</li> </ol> <p>I have been using various BioPython parsing bits and pieces but I think because of the size of the search it fails. I was hoping someone on here would know of a more efficient way? </p> <p>Thanks in advance!</p>
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      1. POBiopython (or just Python in general): Most Efficient Way to Parse Species Name From A large .fasta file using gi identifier
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      1. VTUpMod
    1. COSo for the above, return should be `[393182, "Mus musculus"]`?
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      1. USFredrik Pihl
    2. COWhat should be returned for the example above? It would be helpful if you could state three lines of desired output.
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      1. USAdam Matan
    3. COWhat you you mean by Biopython fails? Perhaps you have accidentally loaded all 145000 entries into memory, rather than using an iteration approach.
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      1. USpeterjc
 

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