User: Shred

gravatar for Shred
Shred150
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d************@studenti.unipr.it

Posts by Shred

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Avoid download limit from NCBI entrez with Biopython using API key
... Yeah, solved by using retmax and timeout error exception to handle timeout from server. ...
written 6 weeks ago by Shred150
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Comment: C: Remove duplicates in an extremely large text file
... Sort loads file into memory too. ...
written 6 weeks ago by Shred150
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Comment: C: Remove duplicates in an extremely large text file
... Shit happens. But if a file is too large for ram, in bash there's no way to map into memory. Maybe a solution would be in python, as explained [here][1] [1]: https://unix.stackexchange.com/a/413729 ...
written 6 weeks ago by Shred150
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Answer: A: Remove duplicates in an extremely large text file
... Split the text file into smaller one using the `split` command. You could split by size, as example: split -b 200m filename This will produce files named ' xaa, xab, xac..' . Now use awk, but with simpler syntax awk -F"\t" '!seen[$1]++' xa* And after that, join files using a sample `cat` ...
written 6 weeks ago by Shred150
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Comment: C: Avoid download limit from NCBI entrez with Biopython using API key
... Added. Using a timeout with the `sleep` function could be a nice workaround, but I don't know how could be implemented in this case. I don't want to use FTP here because Entrez gives be directly the `gbk` file without doing extraction from gzip archives. ...
written 6 weeks ago by Shred150
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Comment: C: Avoid download limit from NCBI entrez with Biopython using API key
... Okay but how could I put some delay between request? I've added above the code used. ...
written 6 weeks ago by Shred150
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Avoid download limit from NCBI entrez with Biopython using API key
... Hello guys, I'm trying to download several genomes from ncbi using Entrez module in Biopython. I'm using obviously an API key, but it seems that after 20 records, download it's stopped. It's just me? I don't see explicit limit in Entrez documentation. I'm expecting around 773 records, as obtained w ...
ncbi biopython entrez written 6 weeks ago by Shred150
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Comment: C: Bioinformatician, Center for Translational Data Science at the University of Chi
... Linked page does not exists. RAL? ...
written 9 weeks ago by Shred150
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Answer: A: GenBank features don't extract sequences based on condition Biopython
... Many many thanks for this solution goes to @jrj.healey . Apparently the logic of features selection is the same, so I suddenly don't realize why this selection works instead of the previous. for f in glob.glob(cwd+'/genomes/*.gbk'): gbank = SeqIO.parse(open(f,'r'), "genbank") w ...
written 9 weeks ago by Shred150
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Comment: C: GenBank features don't extract sequences based on condition Biopython
... Found a way, thanks for your precious help. I'll post the code as soon as it tested on real-life application. ...
written 9 weeks ago by Shred150

Latest awards to Shred

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Scholar 9 weeks ago, created an answer that has been accepted. For A: Faster way to get GC content and Coverage from .fasta
Popular Question 8 months ago, created a question with more than 1,000 views. For Faster way to get GC content and Coverage from .fasta
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Scholar 12 months ago, created an answer that has been accepted. For A: Faster way to get GC content and Coverage from .fasta

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