User: charles.bridges

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Posts by charles.bridges

<prev • 28 results • page 1 of 3 • next >
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Comment: C: "missing value where TRUE/FALSE needed" in 16Stimator R script
... So after a bit of investigation, here's what I've come up with: 1. The RDPerGene variable does contain the information that it should. 2. It is (seemingly) correctly written and formatted to a*.csv file. 3. The following `print` commands showed what each variable contains: ---------- print(RD ...
written 18 months ago by charles.bridges70
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Comment: C: "missing value where TRUE/FALSE needed" in 16Stimator R script
... Hi Jean-Karim Heriche, Thanks for your reply. I'm not well versed in R, how would I check to see what Df16S contains? Charles ...
written 19 months ago by charles.bridges70
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"missing value where TRUE/FALSE needed" in 16Stimator R script
... Hello, I'm using the program 16Stimator ([paper here][1] and [source here][2]) to estimate 16S rRNA gene copy number from draft genomes. It's comprised of a shell script that calls several other programs and R scripts. I run R on a linux cluster and have gotten most scripts to run successfully, but ...
R 16s copy number is.na 16stimator written 19 months ago by charles.bridges70 • updated 19 months ago by zx87549.1k
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Answer: A: Calculating Average Amino Acid Identity (AAI) using CompareM
... @the.good.doctor.is.in, Thanks, but I cited that link in my initial question. The conversation you've found is my own, with the user that I cited. Problem has been resolved. ...
written 20 months ago by charles.bridges70
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Answer: A: Busco result interpretation
... Not sure if [CheckM][1] will work for you, but I've found it extremely useful for bacterial genomes [1]: https://github.com/Ecogenomics/CheckM ...
written 2.1 years ago by charles.bridges70
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Calculating Average Amino Acid Identity (AAI) using CompareM
... Hi all, I'm trying to calculate Average Amino-acid Identity (AAI) between a set of ~15 genomes. A program called CompareM (https://github.com/dparks1134/CompareM from the same set of minds who created the increasingly popular CheckM suite) was created to do this, among other things. It's made to ru ...
sort ani checkm comparem aai written 2.1 years ago by charles.bridges70
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Answer: A: Attribute Error Using Biopython Bio.Searchio.Convert
... Thank you both for your help. Instead of editing PyShell.py, I've added the following code as a prefix to my own: import warnings with warnings.catch_warnings(): warnings.simplefilter('ignore') from Bio import SearchIO It didn't fix the root of the problem, but allowed the script to ...
written 6.4 years ago by charles.bridges70
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Comment: C: Attribute Error Using Biopython Bio.Searchio.Convert
... Yes, I can use python without using any Biopython modules. Any suggestions to modify PyShell.py? ...
written 6.4 years ago by charles.bridges70
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Attribute Error Using Biopython Bio.Searchio.Convert
... Hello, writing a script in Python using Biopython modules that will convert Blast XML output to Tabular form. I get an attribute error as follows: Traceback (most recent call last): File "C:\Python33\myscripts\Working\Convert_Blast_XML_to_Tabular.py", line 4, in <module> from Bio import Sea ...
python biopython convert written 6.4 years ago by charles.bridges70
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Adding Submodules To Biopython?
... Hello, I'm an infrequent user of Python (v 3.23) and Biopython (v 1.59), but when I need it I can usually hack my way through some code to get what I want done. My problem is this -- I need to use a sub-module 'Bio.SearchIO' that is not included with my version of Biopython, and am very weary of up ...
python windows biopython written 6.4 years ago by charles.bridges70 • updated 6.4 years ago by Brad Chapman9.5k

Latest awards to charles.bridges

Scholar 20 months ago, created an answer that has been accepted. For A: Calculating Average Amino Acid Identity (AAI) using CompareM
Great Question 6.4 years ago, created a question with more than 5,000 views. For Concatenate Multiple .Fasta Files
Epic Question 6.4 years ago, created a question with more than 10,000 views. For Concatenate Multiple .Fasta Files
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Extract Specific Entries From Blastx Output File, Write To New File
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Adding Submodules To Biopython?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Attribute Error Using Biopython Bio.Searchio.Convert
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Trouble Calling Emboss Program From Python
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Split Large Fasta Into Mulitple Files, Can'T Name Them With Gi Number
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Trouble Calling Biopython Sequtils Six_Frame_Translations
Popular Question 7.7 years ago, created a question with more than 1,000 views. For Concatenate Multiple .Fasta Files
Student 7.8 years ago, asked a question with at least 3 up-votes. For Trouble Calling Emboss Program From Python

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