Init_exp

NAME

init_exp -- create and initialise an Experiment File

SYNOPSIS

init_exp [-(abi|alf|scf|pln)] [-output file] [-name entry_name] [-conf] file

DESCRIPTION

init_exp initiates an Experiment File for a binary trace file or a plain sequence file. The Experiment File created contains the ID, EN, LN, LT and SQ lines.

The experiment file is, by default, sent to standard output, unless an output file is specified using the -output option. The default entry name for the Experiment File is derived from the filenames used. If an output file has been specified, then this is taken as the EN field. Otherwise the input file name is used. The user can override the default by using the -name option.

OPTIONS

-abi, -alf, -scf, -pln

Specify an input file format. This is not usually required as init_exp will automatically determine the correct input file type. This option is supplied incase the automatic determination is incorrect (which is possible, but has never been observed).

-output file

The experiment file will be written to file instead of standard output. Additionally the value of the EN and ID fields, assuming -name has not been specified, will be file.

-name name

Sets the ID and EN fields to name, regardless of the output filename used.

-conf

Fills out the AV field with the quality values found in the SCF file.

NOTES

This program was formerly known as expGetSeq.

SEE ALSO

See section ExperimentFile(4). Read(4)