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 2.24.0 Index]