Description Usage Arguments Details Value Author(s) Examples
Loops through PMC search results and downloads and extracts locus tags in text and tables
1 |
pmcresults |
PMC search results from |
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
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