makeIndex {GeneR} | R Documentation |
Makes an index for a bank file (if there wasn't).
makeIndex(file, type="E", index="ix")
file |
string/scalar, file name of bank file |
type |
Sequence format ("E" for Embl, "G", for Genebank, "F" for Fasta) |
index |
Suffix for the index file (usually: ix) |
Checks if index file exists and is newer than bank file. If not, calls one of indexFasta, indexEmbl, indexGbk functions.
1 |
Index already exists (and no changes) |
0 |
Index successfully created |
-1 |
Error |
Index files are in the form:
Accno deb_feature deb_sequence length_sequence
with one line by sequence. Number of char must be
the same for each line (it is used to search
a specific access number) but size used for accno is
of 40 char by default. This can be change by setting
variable MAX\_LEN\_ACCNO
in GeneR\_globals.h file and
recompile the library.
Antoine Lucas
indexFasta
,indexEmbl
,
indexGbk
seqNcbi("BY608190",file="BY608190.fa") # Write index file BY608190.fa.ix ... indexFasta("BY608190.fa")