User: Spencer D.

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Spencer D.0
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Posts by Spencer D.

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Comment: C: How to count files/folders on NCBI ftp server?
... Ah yea I checked it on my local directory. Looks like the script would do the job for you anyways! ...
written 2.5 years ago by Spencer D.0
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Answer: A: How to count files/folders on NCBI ftp server?
... you could probably just pipe instead of saving to a local file. i.e. ls -l | wc -l disclosure: haven't checked it for bugs or reliability ...
written 2.5 years ago by Spencer D.0
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Comment: C: makeblastdb of refseq_genomic for sequences with subspecies
... Hi, Thanks a lot for the info. I assumed as much for the taxonomic metadata (I've observed differences at the genus level even between sequence names and GB entries). I'm actually looking to iteratively search the entirety of the refseq_genomic DB. I devised a hacky workaround using a python script ...
written 2.5 years ago by Spencer D.0
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makeblastdb of refseq_genomic for sequences with subspecies
... So I am running a lot of BLAST+ requests on a local refseq_genomic db I have set up in a UNIX environment. My big issue right now is that I only want to look at sequences that have subspecies definitions. i.e I'm interested in *Cervus nippon taiouanus*, but not a sequence defined just as *Cervus nip ...
python unix blast written 2.5 years ago by Spencer D.0 • updated 2.5 years ago by piet1.6k
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Comment: C: Problem using Biopython qblast (NCBIWWW) with refseq_genomic database
... UPDATE for anyone who has struggled / may struggle with this issue in the future A field I hadn't looked at in my XML output, <Iteration_message>, held an error: <Iteration_message>[blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).</Iteration_message& ...
written 3.0 years ago by Spencer D.0
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Comment: C: Problem using Biopython qblast (NCBIWWW) with refseq_genomic database
... Just a quick bump. If this is too general of a question let me know and I can dive a little more deeply in a few directions,  but it would be great to know where someone with more experience might think the issue lies. ...
written 3.0 years ago by Spencer D.0
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(Closed) Problem using Biopython qblast (NCBIWWW) with refseq_genomic database
... I am having difficulty with using qblast to search for sequence similarity just in the RefSeq database and hopefully someone can point me in the right direction. My qblast query is formatted like so: query_handle = NCBIWWW.qblast('blastn', 'refseq_genomic', fasta_string) This query works perfectl ...
genome python blast written 3.0 years ago by Spencer D.0

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