User: yarmda

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yarmda40
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Posts by yarmda

<prev • 48 results • page 1 of 5 • next >
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Answer: A: BadProteinStart errors when uploading PGAP .sqn file to NCBI
... This might be because I was changing the header format that came from asn2gb to match what I was using for tbl2asn. This made sense because I was combining two tbl files and the information I was removing didn't seem significant, but was apparently an issue. What had said ">Feature lcl|1" from P ...
written 9 weeks ago by yarmda40
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Comment: C: BadProteinStart errors when uploading PGAP .sqn file to NCBI
... This might be because I was changing the header format that came from asn2gb to match what I was using for tbl2asn. This made sense because I was combining two tbl files and the information I was removing didn't seem significant, but was apparently an issue. What had said ">Feature lcl|1" from P ...
written 9 weeks ago by yarmda40
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BadProteinStart errors when uploading PGAP .sqn file to NCBI
... I am trying to upload an annotation file to NCBI. NCBI will run PGAP - their prokaryote annotation tool - but not if I have additional annotations. Since I do, from my own source, I am trying to combine them into a single upload file because NCBI will not take multiple. So, PGAP produces a .sqn file ...
ncbi annotation pgap sequin written 9 weeks ago by yarmda40
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What does BLAST command line - gilist option refer to?
... https://www.ncbi.nlm.nih.gov/books/NBK431010/#news_03-02-2016-phase-out-of-GI-numbers describes the phasing out of GI numbers two years ago. Has BLAST caught up with that, but they haven't renamed the flag in blastn/t command line tools? ...
ncbi gi blast number written 2.1 years ago by yarmda40 • updated 2.1 years ago by Joe18k
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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 2.9 years ago by yarmda40
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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 3.1 years ago by yarmda40 • updated 3.1 years ago by Pierre Lindenbaum131k
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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 3.1 years ago by yarmda40 • updated 3.1 years ago by Pierre Lindenbaum131k
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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 3.1 years ago by yarmda40 • updated 3.1 years ago by Pierre Lindenbaum131k
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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 3.1 years ago by yarmda40
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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 3.1 years ago by yarmda40 • updated 2.1 years ago by tsrmhathesh0

Latest awards to yarmda

Scholar 9 weeks ago, created an answer that has been accepted. For A: BadProteinStart errors when uploading PGAP .sqn file to NCBI
Popular Question 13 months ago, created a question with more than 1,000 views. For How to retrieve any and all NCBI/GenBank accession numbers from a Taxonomy ID?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For pysam fetch with partial reference name
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to generate a multiple HMM file with HMMER?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to retrieve any and all NCBI/GenBank accession numbers from a Taxonomy ID?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Trouble with bedtools groupby - not summarizing by columns
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How best to parse samtools mpileup results?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Trouble with bedtools groupby - not summarizing by columns
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to retrieve any and all NCBI/GenBank accession numbers from a Taxonomy ID?
Supporter 3.5 years ago, voted at least 25 times.

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