makeIndex {GeneR}R Documentation

Index file creation for a bank file (internal function)

Description

Makes an index for a bank file (if there wasn't).

Usage

makeIndex(file, type="E", index="ix")

Arguments

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)

Details

Checks if index file exists and is newer than bank file. If not, calls one of indexFasta, indexEmbl, indexGbk functions.

Value

1 Index already exists (and no changes)
0 Index successfully created
-1 Error

Note

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.

Author(s)

Antoine Lucas

See Also

indexFasta,indexEmbl, indexGbk

Examples

  seqNcbi("BY608190",file="BY608190.fa")

  # Write index file BY608190.fa.ix ...
  indexFasta("BY608190.fa")

  

[Package GeneR version 2.13.1 Index]