User: massa.kassa.sc3na

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Posts by massa.kassa.sc3na

<prev • 74 results • page 1 of 8 • next >
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Comment: C: Extracting CDS using python
... Hi, good for you and GJ for creating gbk parser. Although the Biopython parsers are not very fast, they are not worst. As I've wrote, the extract and the creating of the `Seq` and `SeqRecord` objects is what is slow here. ...
written 1 day ago by massa.kassa.sc3na320
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Comment: C: Extracting CDS using python
... Ok, I've looked into your code, and single most expensive line is this one `feature_sequence = feature.location.extract(seq_record).seq` You don't specify, if you want to have the DNA or the protein sequence for your CDS, and originally I've thought that you want the protein sequence. If that is ...
written 2 days ago by massa.kassa.sc3na320
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Comment: C: Extracting CDS using python
... Can you share your code? How big are your files? From my experience, in some gb files the coding sequence is directly associated within the feature, if that is your case, than you can just read the feature, which should be blazing fast, once the SeqRecord is parsed. If not, then on each cds the tr ...
written 4 days ago by massa.kassa.sc3na320
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Answer: C: Building a BLAST database with the python subprocess module
... Hi, I'm not an expert for python subprocess module on windows, so take my suggestions with grain of salt. However, it seems to me, that your usage of subprocess module is wierd. There are two modes 1) you build a string and pass `shell=True` 2) you build a list of parameters like this `[exepath, v ...
written 4 days ago by massa.kassa.sc3na320
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Answer: C: Joining multiple query keys in entrez Efetch
... Hi, I've had a glimpse at your code and it does seems overly complicated. I'm regularly obtaining 500 - 1000 records per query. The queries can fail, but it is not very common (at least for me). You should know, that you should pass the accessions directly to the `Entrez.efetch` (without the "AND" ...
written 15 days ago by massa.kassa.sc3na320
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Comment: C: Blast output representation
... I can imagine the use for histogram (e.g. to plot HSP score distributions) and pie-chart (e.g. to plot % of sequences from the db hit by your query), but this is limited to special use-cases. It really depends on what you want to show. ...
written 9 weeks ago by massa.kassa.sc3na320
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Difference between "nucleotide" and "nuccore" entrez databases
... Hello, I was wondering what is the difference between the `nucleotide` and `nuccore` entrez databases. It seems that both index the same number of terms, but `nuccore` appears to contain links to other databases, while `nucleotide` does not (based on `einfo` output). Thanks ...
ncbi entrez written 3 months ago by massa.kassa.sc3na320
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Comment: C: How to use entrezpy and Biopython Entrez libraries to access ClinVar data from
... Hi, as far as I know, the `Biopython Entrez` and `entrezpy` use the same ncbi api (https://www.ncbi.nlm.nih.gov/books/NBK25500/), so I would choose one of them. It seems to me that the `entrezpy`is implementing a lot of `Entrez Direct` behaviour (and that is much easier to use then Biopython entrez) ...
written 3 months ago by massa.kassa.sc3na320
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Comment: C: How to use entrezpy and Biopython Entrez libraries to access ClinVar data from
... Why do you combine entrezpy and Biopyton? Entrezpy is (according to documentation) well equipped with chaining commands (so esearch | efetch) should be piece of cake (https://entrezpy.readthedocs.io/en/master/tutorials/conduit/pipeline.html). No need to fetch UIDs and download them separately. Coul ...
written 3 months ago by massa.kassa.sc3na320
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Comment: C: ClustalOmegaCommandline (multiple sequence alignment) no output file
... From the documentation (https://biopython.org/DIST/docs/api/Bio.Align.Applications._ClustalOmega.ClustalOmegaCommandline-class.html) You need to **execute** the clustalomega_cline (imagine it as if you've formatted parameters to a string, and you need to paste it to terminal). Use the `clustalomega ...
written 4 months ago by massa.kassa.sc3na320

Latest awards to massa.kassa.sc3na

Scholar 4 days ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 15 days ago, created an answer that has been accepted. For C: BLAST using Biopython
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to pass multiple seq_start and seq_stop statements to NCBI efetch
Scholar 11 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 11 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Programatically (Python) Navigate from BLASTp results to Genbank file
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: rRNA and bacteria: Absence and duplicates
Scholar 12 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 13 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 17 months ago, created an answer that has been accepted. For C: BLAST using Biopython

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