Select annotation lines in an ACNUC database
This function is called before using
modifylist with a
scan type operation to
select the annotation lines to be returned or scanned.
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the default "all" means that all annotation lines are selected. This can be more specific, see details.
this is used when
an object of class
logical, if TRUE mode verbose is on
The names of annotation lines in the opened ACNUC database is
countfreelists, they are forced to upper
case letters by
prepgetannots when supplied with the
For the EMBL/SWISSPROT format, keys are: ALL, AC, DT, KW, OS, OC, OG, OH, RN, RC, RP, RX, RA, RG, RT, RL, DR, AH, AS, CC, FH, FT, SQ, SEQ.
For GenBank: ALL, ACCESSION, VERSION, KEYWORDS, SOURCE, ORGANISM, REFERENCE, AUTHORS, CONSRTM, TITLE, JOURNAL, PUBMED, REMARK, COMMENT, FEATURES, ORIGIN, SEQUENCE.
For FT (embl, swissprot) and FEATURES (GenBank), one or more specific feature keys can be specified using lines with only uppercase and such as
Keys ALL and SEQ/SEQUENCE stand for all annotation and sequence lines, respectively. For the scan operation, key ALL stand for the DE/DEFINITION lines, and SEQ/SEQUENCE cannot be used (annotations but not sequence are scanned).
The function returns invisibly the annotation lines names.
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## Not run: # Need internet connection choosebank("genbank") mylist <- query("mylist","n=AQF16SRRN") pga() # We want to scan all annotations, including FEATURES mylist <- modifylist("mylist", operation = "strain", type = "scan") mylist$nelem # should be 1 ## End(Not run)