User: skbrimer

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skbrimer500
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Posts by skbrimer

<prev • 170 results • page 1 of 17 • next >
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Comment: C: Beginner in Python- translating DNA given in GenBank file format into its six re
... The biopython cookbook actually shows how to do this but instead of translate you could just call your table instead. ...
written 3 months ago by skbrimer500
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Phylogenetic Analysis Reference request
... Hello Hive Mind! I'm trying to understand phylogenetic analysis better; I know how to read a tree and what the bootstrapping numbers imply. I'm more interested in how to pick the correct model to use for the analysis. Last night I was googling trying to find a resource that would explain why and wh ...
alignment snp sequencing written 5 months ago by skbrimer500
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Answer: A: How to read two non-consecutive lines in a file once in python
... Okay its a little hacky and assuming your file is not too large you should be able to do it this way with open("test.txt","r") as f: lines = f.readlines() count = 0 for i in enumerate(lines): print(lines[count:count+5]) count +=1 this will print it the way I ...
written 5 months ago by skbrimer500
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Comment: C: How to read two non-consecutive lines in a file once in python
... I think this should work, if I understand your question correctly. Not 100% on output you want and I'm not sure if this will print in the way tou want so you will need to play around with it. Good luck lines = [1,6,2,7,3,8] with open(file) as pileup: for i in enumerate(pileup): ...
written 5 months ago by skbrimer500
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Comment: C: PuTTY newick utilities
... I'm not sure what your user level is on the HPC and since I have never really used one I'm not going to be the best one to answer this question... however the error is basically saying "I don't know where you put this library, its not in the normal place." so with that in mind this will be helpful t ...
written 5 months ago by skbrimer500
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Answer: A: primer3-py Heterodimer Calculations
... I'm not sure on what the `tm` value is saying, and the primer3 or primer3-py documentation doesn't really clear it up either, however I think it is saying that this structure will not form over 2.88C so it's not a worry. Hopefully if I'm wrong about the Tm someone will let you know. The rest of the ...
written 5 months ago by skbrimer500
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Answer: A: Generating a multi fasta consensus bcftools v1.7
... appearenty the fasta file I was using had extra lines in it, although I thought I was taking care of that, but the bcftools team pointed it out and it did fix the issue that also said I could do this: `cat ref.fasta | grep -v ^$ | bcftools consensus vcf.file ` and that would eliminate any potental l ...
written 5 months ago by skbrimer500
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Answer: A: Generating a multi fasta consensus bcftools v1.7
... So far, I haven't gotten an answer from the bcftools team on github but I did get two workarounds to work, the first one was to just call each segment as a region and append the cns file, which works however it is not quick. The second solution was to use vcftools with the `vcf-consensus` command li ...
written 5 months ago by skbrimer500
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Comment: C: Generating a multi fasta consensus bcftools v1.7
... And submitted. I will post their response as well. ...
written 5 months ago by skbrimer500
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Generating a multi fasta consensus bcftools v1.7
... Hello hive mind, I work with segmented virus and normally I uses freebayes to make the vcf file, bgzip and tabix to compress and index and then the `standard cat ref.fa | bcftools consensus vcf.file > cns.fa` to make a consensus. This has worked for years, but now after upgrading to 1.7 from 1. ...
bcftools samtools bioinformatics written 5 months ago by skbrimer500

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Popular Question 4 months ago, created a question with more than 1,000 views. For SOLVED***EDIT*** BioPython: how to edit a fasta file to include a large deletion
Scholar 5 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 5 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 5 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 6 months ago, created a question with more than 1,000 views. For SOLVED***EDIT*** BioPython: how to edit a fasta file to include a large deletion
Popular Question 6 months ago, created a question with more than 1,000 views. For Bed file loading issues
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 11 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 13 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 2.6 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 2.6 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once

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