Category : genome

I am absolutely new to Python and any help will be really appreciated. I am working on Bioinformatics. I have created a json file whose entries look like this: {"0": ["47d0143b-af1a-8c33-b9b0-54daae4ce7d3", "40e548a3-6bd1-0772-12fd-753269eb46fb", "5be638d6-c39b-ba83-85db-69fab9d9fa50", "92a7495a-ff4b-043e-8b14-5da61ba83327", "227c8787- a2dc-5afd-cc6d-bed0cf2ec9f7"], "1": ["3f26a469-b618-9342-4bc5-42537b44cd86",…..} where 0,1,.. denotes the contig ID and the big number denotes the long read ID to which ..

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I previously posted a question asking how to separate a file (How would I pull multiple partial match strings out of rows and keep them in the same order on the same lines?) and figured out how to pull partial matches out using prefixes = ["Zm00018ab","Zm00001eb","Zm00039ab"] with open("MaizeGDB_maize_pangene_2020_08.txt","r") as infile: with open("pangene_adjusted_2021_06.txt","w") as outfile: for ..

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I am trying to run a snakemake-based software https://github.com/MeHelmy/princess with SLURM on our cluster https://gitlab.com/cigene/computational/orion-support. In brief, the issue is that when I run the software on the login node, it works. However, when I submit a slurm script to run this software, it gives me an error that "snakemake/temp file is not found." It ..

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I just started learning Python and I’m facing a task I can’t comprehend. I have a bed file containing genomic information and I have to extract from It a column and count how many of them are greater than my 0.05 threshold. I tried to import the file with pandas couldn’t manage to make it ..

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I have little experience in python programming and I have just beginning to learn this scripting language. I have a script and a bunch of .gff genome files. I am using this script to summarize the information in my gff files. #!/usr/bin/env python2 from Bio.SeqIO.FastaIO import SimpleFastaParser from Bio.Seq import translate from Bio.Seq import reverse_complement ..

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