Turns sep-separated TALE sequences — RVD strings, or repeat-code
strings — into a tales object, taking sequence order as
position_in_array and sequence names as array_id.
Usage
as_tales(x, ...)
# S3 method for class 'data.frame'
as_tales(x, ...)
# Default S3 method
as_tales(x, sep = "-", residue_col = c("rvd", "dom_code"), ...)Arguments
- x
A path to a fasta file, a
BStringSet/AAStringSet, a list of strings, or a data frame (which is passed totales, including atales_msa, which is demoted).- ...
Passed to methods.
- sep
Separator between elements of a sequence. Use
"-"for RVD sequences and" "for repeat-code strings.- residue_col
Which residue column the parsed elements become:
"rvd"(default) or"dom_code". It is never guessed from the values.
Details
The result is deliberately column-poor: a bare sequence file carries no
domain types, amino acid sequences or source contigs, so only
array_id, position_in_array and the chosen residue column are
produced. That is a valid tales: seqnames and the other
columns are optional.
A tales_msa passed to as_tales() is demoted to a plain
tales: alignment_position stays as an ordinary column, and
the alignment width is dropped (tales_msa_width returns
NULL).
See also
Other tales objects:
[.tales(),
format.tales(),
format.tales_msa(),
is_tales(),
new_tales(),
print.tales(),
print.tales_msa(),
summary.tales(),
summary.tales_msa(),
tales(),
tales_anchor_codes(),
tales_anomalies(),
tales_assert_complete(),
tales_bind(),
tales_names(),
tales_namespace(),
tales_requirements(),
validate_tales()
Examples
rvd_fasta <- system.file("extdata", "TalA_RVDSeqs_AnnoTALE.fasta",
package = "tantale")
as_tales(rvd_fasta, sep = "-")
#> <tales> 11 arrays, 258 parts
#> layers: rvd
#> rvd
#> TalA_BAI3 NN NG NN HD HD NI N* NG HD NI NG NN HD NI NG NI NG NN NG ...
#> TalA_CFBP1947 NN NG NN HD HD NI N* NG HD NI NG NN HD NI NG NI NG NN NG ...
#> ... ...
#> TalA_MAI95 NN N* NN HD HD NI NG NN HD NS NG NI N* NN NG HD NI NI NG ...
#> TalA_MAI99 NN N* NN HD HD NI NG NN HD NS NG NI N* NN NG HD NI NI NG ...