bdaisley / isolater Goto Github PK
View Code? Open in Web Editor NEWAutomated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries
License: Other
isolater's People
Contributors
Stargazers
Watchers
Forkers
sophieseulesonisolater's Issues
Error with isoTAX db specification
IsolateR version 0.0.0.9003
The database variable in isoTax should be able to accept the argument "16S|ITS" for the use of multiple databases in vsearch but results in an error. Also noted that setting to ITS will just result in the 16S database being installed.
> isoTAX.S4 <- isoTAX(input=in2,
+ export_html=TRUE,
+ export_csv=TRUE,
+ db="16S|ITS",
+ quick_search=FALSE)
Detecting operating system...
Operating system is ---> Windows-based <---
VSEARCH already downloaded
Staging files
Error in utils::download.file(eval(parse(text = paste(dblink.list)[names(dblink.list) %in% :
invalid 'url' argument
> isoTAX.S4 <- isoTAX(input=in2,
+ export_html=TRUE,
+ export_csv=TRUE,
+ db="16S,ITS",
+ quick_search=FALSE)
Detecting operating system...
Operating system is ---> Windows-based <---
VSEARCH already downloaded
Staging files
Error in utils::download.file(eval(parse(text = paste(dblink.list)[names(dblink.list) %in% :
invalid 'url' argument
> isoTAX.S4 <- isoTAX(input=in2,
+ export_html=TRUE,
+ export_csv=TRUE,
+ db="ITS",
+ quick_search=FALSE)
Detecting operating system...
Operating system is ---> Windows-based <---
VSEARCH already downloaded
Staging files
trying URL 'https://ftp.ncbi.nlm.nih.gov/refseq/TargetedLoci/Bacteria/bacteria.16SrRNA.fna.gz'
Content type 'application/x-gzip' length 7820305 bytes (7.5 MB)
downloaded 7.5 MB
FASTA as input for `isoTAX`?
Hi,
This looks like such a useful wrapper for handling large collections of Sanger sequences, thank you for publishing it!
I've read the tutorial and manual, but was wondering if it would be possible to pass entries made only from FASTA sequences (and not .ab1 files) as an output of isoQC into isoTAX? Or what could a possible workaround be to still input samples where only FASTA sequences exist (e.g. make up mock ab1 quality values, make them into .ab1 files, and process it in isoQC)?
The motivation being, that in-house we of course have .ab1 files from which FASTA sequences were eventually extracted and worked with for tax. identification and etc. But in order to have sequences from other labs used in the same collection/pipeline (e.g. for taxonomic identity), only FASTA sequences are usually available and made public.
It would be great if this were possible all within isolateR, otherwise it's again a chore to process own samples with .ab1 files here, make collections, export FASTA, add external FASTA collections, redo taxonomic identifications with whatever tool, summarize taxonomy on your own.
Do you see any possible workaround at the moment or possibly implementing a similar feature in the future?
Thanks.
using a custom db
Hello. I'm curious to try this with the SILVA 138.1 SSU ref database. Can you please give me a bit more information as to what is required in the header of each sequence? At the moment, I have gotten it to work but with an offset- the Class information is showing in the Phylum column. Thank you!
ERROR: lazy loading failed for package 'isolateR'
Error when installing isolateR in R 4.3.2
* installing *source* package 'isolateR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object 'patchworkGrob' is not exported by 'namespace:patchwork'
Execution halted
ERROR: lazy loading failed for package 'isolateR'
This has to do with multiple versions of patchwork package being available, as described here
Current workaround:
remove.packages('patchwork')
install.packages('patchwork', repos='http://cran.us.r-project.org')
#now the package version should appear as 1.1.3 not 2.4
devtools::install_github("bdaisley/isolateR")
#select 'None' when prompted to update dependencies, assuming all other packages have already been installed
Error when running isoQC step on a single sample
The following error occurs for isoQC when the input directory has only one .ab1 file present.
isoQC(input="~/dir_containing_one_ab1_file")
- Error in [email protected][[index]] : subscript out of boundsError installing isolateR in R 4.4.0 on Windows 10 and 11
When running the install command in a new R environment on Windows systems it has been noted that Bioconductor dependencies fail to install, resulting in a failed isolateR installation:
Installing package into ‘C:/Users/cambr/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
ERROR: dependencies 'Biostrings', 'msa', 'sangeranalyseR', 'sangerseqR' are not available for package 'isolateR'
* removing 'C:/Users/cambr/AppData/Local/R/win-library/4.4/isolateR'
Warning messages:
1: In i.p(...) :
installation of package ‘sangerseqR’ had non-zero exit status
2: In i.p(...) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In i.p(...) :
installation of package ‘sangeranalyseR’ had non-zero exit status
4: In i.p(...) :
installation of package ‘C:/Users/cambr/AppData/Local/Temp/RtmpUjesIT/file8dc715e6ae2/isolateR_0.0.0.9003.tar.gz’ had non-zero exit status
The current work around for this issue is to install the Bioconductor packages separately, as demonstrated below.
BiocManager::install("sangerseqR", force =TRUE)
BiocManager::install("GenomeInfoDb", force =TRUE)
BiocManager::install("sangeranalyseR", force =TRUE)
BiocManager::install("msa", force =TRUE)
devtools::install_github("bdaisley/isolateR")
IsolateR will then successfully install and can be called like normal with library(isolateR).
Error with isoLIB function when combining new + old strain libraries together
The following error occurs when trying to combine new + old strain libraries using the isoLIB function:
Error in `mutate()`:
i In argument: `strain_group = sapply(...)`.
Caused by error in `str_sub()`:
! could not find function "str_sub"
Run `rlang::last_trace()` to see where the error occurred.
isoQC step sometimes does not fail sequences below the trim threshold
The attached sample sequences result in a PASS in the isoQC step (leading to their inclusion in the taxonomy and library steps) despite having a trimmed sequencing length below the set threshold (400).
isoQC_badtrimlen.zip
Example command:
isoQC.S4 <- isoQC(input=in1,
export_html=TRUE,
export_csv=TRUE,
export_fasta=TRUE,
verbose=FALSE,
min_phred_score = 20,
min_length = 400,
sliding_window_cutoff = NULL,
sliding_window_size = 15,
date=NULL)
Output:
ERROR: isoLIB issue with combining libraries
isoLIB function does not maintain original strain reference order of "old_lib_csv" input when attempting to combine old and new library CSV files together.
Which version of R is recommended to install the isolateR?
Hello,
Thanks for developing the library.
I got the following error messages
- building ‘isolateR_0.0.0.9003.tar.gz’
ERROR: dependencies ‘cowplot’, ‘ggtree’, ‘ggbeeswarm’, ‘ggiraph’, ‘plotly’, ‘msa’, ‘rentrez’, ‘sangeranalyseR’, ‘seqinr’, ‘xmlconvert’ are not available for package ‘isolateR - removing ‘/home/ec2-user/miniconda3/envs/R4.3/lib/R/library/isolateR’
when installing the isolateR under R4.3 .
I was wondering which version of R is recommended to install the isolateR.
Thanks,
xmeng
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.