User: skbrimer

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skbrimer490
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Posts by skbrimer

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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 19 days ago by skbrimer490
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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 8 weeks ago by skbrimer490
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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 10 weeks ago by skbrimer490
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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 10 weeks ago by skbrimer490
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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 10 weeks ago by skbrimer490
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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 10 weeks ago by skbrimer490
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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 10 weeks ago by skbrimer490
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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 11 weeks ago by skbrimer490
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Comment: C: Generating a multi fasta consensus bcftools v1.7
... And submitted. I will post their response as well. ...
written 11 weeks ago by skbrimer490
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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 11 weeks ago by skbrimer490

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Popular Question 5 weeks 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 10 weeks ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 10 weeks ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 11 weeks ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 3 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 3 months ago, created a question with more than 1,000 views. For Bed file loading issues
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 8 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 10 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Popular Question 11 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Scholar 12 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 2.1 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 2.1 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 2.2 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once

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