User: malj

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malj10
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Posts by malj

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Answer: A: [Errno 13] Permission denied Reading Genome Fasta
... Solved. The problem was that must be a list with all the fasta files of the genome. so the solution will be: import glob transcript_fasta_paths_or_urls=(glob.glob("D:\\DATA\\ensembl\\fasta\\*.fa")) ...
written 10 days ago by malj10
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[Errno 13] Permission denied Reading Genome Fasta
... Hello everyone, I trying to load the fasta genome from D:\\ but it seems doesn't allow me to read it from there (working with Jupyter notebook). I'm working on Windows 10 and I already changed the permissions for that specific folder, but still doesn't work. Here the code: import pyensembl ...
genome windows permissions written 11 days ago by malj10
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Comment: C: Writing Genbank files
... I got this error, AttributeError: 'SeqRecord' object has no attribute 'get_strand' what I'm missing? That's for CDS sequences, but what if I want the same complete file that is downloaded from the browser? Thanks! ...
written 23 days ago by malj10
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Multi Blast NCBIWWW Filtering Human Genome and excluding Models and Uncultured sample sequences
... Hello everyone! I have been looking at the NCBIWWW documentation but I still don't know how to do this search done in NCBI Blastn from the browser (input explained below) but with Biopython command line. Input: Fasta file with huge number of sequences to blast. Database Human genomic plus transcri ...
ncbiwww biopython blast written 26 days ago by malj10
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Answer: A: Blast Multi queries output
... Finally I took the position like this: from Bio.Blast import NCBIXML result=open(folder+"Blast-Alignment.xml","r") records= NCBIXML.parse(result) item=next(records) for alignment in item.alignments: for hsp in alignment.hsps: if hsp.expect < 0.01: ...
written 27 days ago by malj10
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Comment: C: How to get gene name from coordinates using python.
... I'm getting this error on Windows with Anaconda prompt. pyensembl install --release 93 --species homo_sapiens urllib.error.URLError: I tried also downloading it manually but where I should place it or which is the variable path to change? Thanks ...
written 27 days ago by malj10
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Comment: A: Blast Multi queries output
... I forgot to mention that the region I want to blast is intronic and quite short (20 nt), so when I follow your advice it doesn't detect anything. The only way I think it could be possible is taking the position and search for it like here is described with biopython here with exons ( I have to check ...
written 27 days ago by malj10
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Blast Multi queries output
... Hello, Following this post: https://www.biostars.org/p/98693/#344810 I'm trying to get also the features of the alignment (the one is written in the picture) but I can't figure out how to do it. My file is a xml that corresponds to several blast sequences, so I also have the question how to dist ...
biopython blast written 28 days ago by malj10
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Comment: A: how to parse blast output using biopython
... Hello, I'm trying to get also the features of the alignment (the one is written in the picture) but I can't figure out how to do it. My file is a xml that corresponds to several blast sequences, so I also have the question how to distinguish between queries. For each query I would have to get the o ...
written 28 days ago by malj10

Latest awards to malj

Scholar 10 days ago, created an answer that has been accepted. For A: Blast Multi queries output
Scholar 27 days ago, created an answer that has been accepted. For A: Blast Multi queries output

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