A tidyverse approach to manipulating BMG Labtech OMGEA and stacker output

Here is some R code for dealing with ASCII files as output by BMG MARS analysis

csm_microplate-stacker_317840ffa5.png

software, specifically to make use of data spread across different plates as a result of using the BMG Microplate Stacker.

I had a few problems with the stacker jamming when we first got it, but this was solved by (1) lubricating the magazines with a silicon spray (food-grade, not sure if that matters), (2) periodic cleaning with a degreaser, and (3) making the first step of any protocol a ‘restack’ all plates command, so that the plates are positioned more accurately. Since doing these steps, I’ve had minimal problems. In general, I like BMG plate readers for the exact reason most people don’t: the scripting language. Although it isn’t the most sophisticated, the scripting language is powerful enough to design some fairly complex protocols. Combined with the stacker, which can hold either 25 or 50 microplates depending on which magazine set you have, it’s useful for running high-throughput phenotype assays.

require(lubridate)
require(tidyverse)
require(growthcurver)

# Some functions for importing BMG-style CSV files in a tidy way
BMGtime = function(otime){
# A function to convert BMG's default time format to fractional hours (can also set in MARS)
missing.s=grep("[0-9] s",otime, value=F,invert=T)
missing.m=grep("[0-9] min",otime, value=F,invert=T)
missing.h=grep("[0-9] h",otime, value=F,invert=T)
otime[missing.s]=sub("$"," 0 s", otime[missing.s])
otime[missing.h]=sub("^","0 h ", otime[missing.h])
otime[missing.m]=sub("h", "h 0 min ", otime[missing.m])
otime=period_to_seconds(hms(gsub("[a-z ]+",":", otime)))/3600
return(otime)
}

# BMG MARS CSV exports have a trailing comma, so this drops the empty last column
read_csv_drop = function(...) read_csv(...) %>% select(-ncol(.))

# Read a single BMG Mars wide-format time series table into long format
readBMG = function(file){
growthdata = read_csv_drop(file, skip=0) %>%
select(-contains("Blank corrected"))
ndescriptors = ifelse("Group"%in%names(growthdata), 4, 3)
header = tolower(gsub("Well ", "", names(growthdata)[1:ndescriptors]))
time = growthdata %>% select(-(1:ndescriptors)) %>% slice(1) %>% t()
if(grepl("[a-z]", time)) time = BMGtime(time)
names(growthdata) = c(header, time)
growthdata = growthdata %>%
slice(2:n()) %>%
type_convert() %>%
gather("time","value",-header)
return(growthdata)
}
# Read multiple files from the same experiment (resulting from a stacker run)
readStack = function(path=NULL, pattern, parse.name=F, prefix=NULL, suffix=NULL, into=NULL, sep=NULL, ...){
stackdata = data_frame(id = list.files(pattern=pattern, path=path, ...), data = map2(id, path, ~readBMG(paste0(.y,"/",.x))))
if(parse.name){
if(!is.null(prefix)){
stackdata = stackdata %>%
mutate(id = gsub(prefix, "", id))
}
if(!is.null(suffix)){
stackdata = stackdata %>%
mutate(id = gsub(suffix, "", id))
}
stackdata = stackdata %>% separate(id, sep=sep, into=into)
}
stackdata = stackdata %>% unnest(data) %>% type_convert()
return(stackdata)}

SNPsvg

I wrote a quick Perl script to visualize SNPs in a gene from experimental evolution sequencing data.  Useful for making figures when one gene is hit by mutations in multiple lineages.  It outputs an SVG file with the reference sequence and the changes.

For the moment, it only visualizes substitutions, not insertions/deletions or anything more exotic.  More to come.

Example: SNPs found in Pseudomonas aeruginosa gene PA2449 (converted to PNG)

figure

(Thanks to Sofia Robb for teaching Perl as part of Programming for Evolutionary Biology!)

Download SNPsvg here.

 

Regex to change bracket citations into bibtex keys

Useful for converting in-text citations (from e.g. Word) into a LaTeX document.  Converts bracket notation into first 3 chars of first author’s last name (or 2 chars, if only 2 chars long), plus two-digit year: e.g. (Bobby 2009) becomes \citep{Bob09}.  See also my post on how to insert bibtex references into Word.

Search for:

\(([A-Za-z]{2,3})[A-Za-z -.]* (18|19|20)([0-9a-z]{2,3})\)

Replace with:

\\citep{\1\3}

Test citations:

(Bobby 2009)
(Bobby and Jonny 1909)
(Bobby et al. 1923)

(Maynard Smith 1989)
(Maynard Smith and Haigh 1974)
(Maynard Smith and Bobby-Jonny 1974)
(Maynard Smith and Maynard Smith 1974)
(Maynard Smith et al. 1993)

(Maisnier-Patin 1900)
(Maisnier-Patin and Bobby-Jonny 1956)
(Maisnier-Patin et al. 2002)

(Aa 1932)
(Aaa 1932)

Fluctuation test calculator: FALCOR copy/paste issue

Update 2018-10-10 Since people still seem to look at this post regularly, consider switching to the R package flan for fluctuation tests.  There’s even a FALCOR-style web app through Shiny (interactive websites powered by R), ShinyFlan.

FALCOR (Fluctuation AnaLysis CalculatOR) is a handy Java applet designed to estimate mutation rates from fluctuation test data. A Java update prevents access to the clipboard to unsigned Java applets. If you are having trouble copy/pasting your data into FALCOR, try modifying your java.policy file to include the line: permission java.awt.AWTPermission “accessClipboard” under where it says //”standard” properties that can be read by anyone.

// "standard" properties that can be read by anyone
permission java.awt.AWTPermission "accessClipboard"

Save the file, exit and restart Java (or any programs using it, like Firefox or LibreOffice), and copy/paste should work again. You may wish to consider removing the clipboard access after using FALCOR for security reasons.

Abbreviate journal titles with Jabref

I use KBibTeX to manage my references database, but I used to use Jabref.  Jabref has a handy feature that can automatically abbreviate journal names to their standard (ISO) abbreviation format.  The built-in list of abbreviations is missing a lot of common biology journals, but I have updated it with many biology journals.  You can get the most recent version of my abbreviations list from my Dropbox.