User: yarmda

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yarmda0
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Posts by yarmda

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Maximum number of efetch
... Hi Pierre, do you know if looping through the records returned maintains an open ftp connection to NCBI? I have a firewall that doesn't allow ftps connections to remain open for long and my loop fails somewhere between 3 and 10 iterations. I suspect this is due to the ftp connection. I don't believe ...
written 5 days ago by yarmda0
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How to limit/filter BLAST results using NcbiblastnCommandline
... I am using a command like NcbiblastnCommandline(query="fasta.fasta", db=nt, outfmt=5, out="out.xml", show_gis=True) And that is returning results. However, I want to limit the results to only returning the gi number/taxID (not the alignment or the bulk of the data) and to limit the hitlist si ...
ncbiblastncommandline biopython blast written 6 weeks ago by yarmda0 • updated 6 weeks ago by Pierre Lindenbaum100k
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NCBIXML parser get hit sequence
... I want to retrieve the complete sequences of BLAST results that are stored in an XML file. I can see that hsp_hseq is not the complete sequence. Is there an easier way to do this than by pulling the identifier and downloading with Entrez? 2 gi|755995789|gb|CP009605.1| Bacillu ...
parse biopython blast ncbixml written 6 weeks ago by yarmda0 • updated 6 weeks ago by Pierre Lindenbaum100k
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Biopython BLAST or Blast parser returns "no"
... I'm trying to parse my BLAST results and keep only records that don't have a gi identifier in a list. However, parsing the file is not quite working and the result is not informative. Sorry if this type of question has been posted before. Search engines don't do well with the term "no" from Bi ...
searchio biopython blast ncbixml written 7 weeks ago by yarmda0 • updated 7 weeks ago by Pierre Lindenbaum100k
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Comment: C: biopython esearch not giving all children taxIDs
... Actually, I think it may have been an issue with a default retmax of 20. ...
written 8 weeks ago by yarmda0
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biopython esearch not giving all children taxIDs
... I know similar questions have been posted before.. https://www.biostars.org/p/58955/ https://www.biostars.org/p/17715/#273935 But, I am having trouble retrieving the children sequences of a given taxID. For instance, from Bio import Entrez record = Entrez.read(Entrez.esearch(db='protein ...
ncbi biopython entrez written 8 weeks ago by yarmda0 • updated 8 weeks ago by Renesh1.1k
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Comment: C: Refseq Proteins For A Given Taxid
... I don't know if this will still get any attention, but I am running into RuntimeError: Search Backend failed: or no elements found. Any thoughts? I've gotten around this by not using so many variables. It's a little less clean, but it works. ...
written 8 weeks ago by yarmda0
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Comment: C: Command line to download fasta sequences from PATRIC DB
... These files seem to have fewer proteins than were indicated by the protein families page for a given strain. That may be fine, but can you explain why? For instance, genome 1392.82 has a protein families page that would have 5400 or so sequences, while the file from the ftp stops around 4500 or so. ...
written 9 weeks ago by yarmda0
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Comment: C: Command line to download fasta sequences from PATRIC DB
... That downloads the table. I want the fasta sequences. That is also not a command line option that would be scalable to an arbitrary number of organisms and their strains. ...
written 9 weeks ago by yarmda0
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Command line to download fasta sequences from PATRIC DB
... I am seeking to download every available protein sequence for a series of organisms and all of their strains. PATRIC offers more strains than NCBI has listed (as far as I can tell, feel free to correct that and please indicate how I can find the corresponding sequences on NCBI), but I can't tell how ...
command patric download written 9 weeks ago by yarmda0

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Supporter 7 months ago, voted at least 25 times.

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