R and regex - find all occurrences
- 1 minIn R there are many functions that work with a pattern written as a regular expression. Today I needed to deal with one of these functions: str_locate_all (doc) from stringr
My goal was to find "223777_at [Chip: U133B]" in a series of strings like the following one:
text <- "11753227_s_at [Chip: PrimeView]; 223777_at [Chip: HT_HG-U133B]; 223777_PM_at [Chip: U133_Plus_PM]; 48336_at [Chip: U95B]; 223777_at [Chip: GeneProfilingArray]; g13477210_3p_at [Chip: U133_X3P]; MmugDNA.4759.1.S1_at [Chip: Rhesus]; 11753227_s_at [Chip: HG-U219]; ADXECADA.19261_s_at [Chip: Xcel]; ADXECRS.13279_at [Chip: Xcel]; ADXECRS.13279_x_at [Chip: Xcel]; 223777_at [Chip: U133B]; 223777_at [Chip: U133_Plus_2]; RC_T49570_at [Chip: Hu35KsubB]"
The way to find the location (in my case all the locations) of the pattern number slash at white-space bracket Chip two-points U133B brecket follows:
str_locate_all(text, pattern="[0-9]+_at \\[Chip: U133B\\]")
This returns a list of matrix with the locations (start and end point) of all the occurrences found by the given pattern. Take care, so the brackets need to be escaped by double slash.
Carles Hernandez-Ferrer
Bioinformatics, data analysis and software development