pmcLoop: Loop through PMC search results
In cstubben/pmcXML: Tools to parse full text XML documents from PMC Open Access

Description Usage Arguments Details Value Author(s) Examples

Loops through PMC search results and downloads and extracts locus tags in text and tables

1	pmcLoop(pmcresults, tags, prefix, suffix, file = "locus.tab", notStartingWith, expand = TRUE, digits = 4)

`pmcresults`	PMC search results from `ncbiPMC`
`tags`	an ordered list of locus tags, used for expanding locus tag pairs
`prefix`	locus tag prefix, can be a regular expression such as "BPS[SL]" or "VCA?"
`suffix`	locus tag suffix, should be a single letter "a" or character class "[ac]" or grouping brackets "(a\|c\|\.1)"
`file`	name of output file
`notStartingWith`	optional single letter to exclude matches, eg, use "J" to match "HP" but not "JHP" tags in Helicobacter
`expand`	expand locus tags pairs marking the start and end of a operon, island or other region
`digits`	number of digits in locus tags, use NA for 1 or more

Downloads XML using pmcOAI and then parses text using pmcText and tables using pmcTable and extracts tags using findTags. Also adds captions to collapsed table rows and writes mentions to output file

None. Mentions are saved to output file

Chris Stubben

## Not run: 
org <- "Yersinia_pestis_CO92_uid57621"
ypgff <- read.ncbi.ftp( org, "NC_003143.gff")
yp <- ncbiPMC( "(YPO0* OR YPO1* OR YPO2* OR YPO3* OR YPO4*) AND (Yersinia[ABSTRACT] OR Yersinia[TITLE]) AND open access[FILTER]" )
pmcLoop(yp, ypgff, "YPO", "a", "YPO.tab" )

## End(Not run)