| readfirstrec {seqinr} | R Documentation |
Low level function to get the record count of the specified ACNUC
index file
Description
Called without arguments, the list of available values for argument type is
returned.
Usage
readfirstrec(socket = autosocket(), type)
Arguments
socket |
an object of class sockconn connecting to a remote ACNUC
database (default is a socket to the last opened database). |
type |
the ACNUC index file |
Details
Available index files are:
- AUT
- AUTHOR one record for each author name (last name only, no initials)
- BIB
- BIBLIO one record for each reference
- ACC
- ACCESS one record for each accession number
- SMJ
- SMJYT one record for each status, molecule, journal, year, type,
organelle, division, and db structure information
- SUB
- SUBSEQ one record for each parent or sub-sequence
- LOC
- LOCUS one record for each parent sequence
- KEY
- KEYWORDS one record for each keyword
- SPEC
- SPECIES one record for each taxon
- SHRT
- SHORTL mostly, one record for each element of a short list
- LNG
- LONGL one record for each group of SUBINLNG elements of a long list
- EXT
- EXTRACT (for nucleotide databases only) one record for each exon of each subsequence
- TXT
- TEXT one lrtxt-character record for each label of a species, keyword, or SMJYT
Value
The record count of ACNUC index file, or NA if missing (typically when
asking for type = EXT on a protein database).
Author(s)
J.R. Lobry
References
See ACNUC physical structure at
http://pbil.univ-lyon1.fr/databases/acnuc/structure.html.
citation("seqinr")
See Also
choosebank
Examples
## Not run:
# Need internet connection
choosebank("genbank")
allowedtype <- readfirstrec()
sapply(allowedtype, function(x) readfirstrec(type = x))
## End(Not run)
Worked out examples