Extract_seq

NAME

extract_seq -- extracts sequence from a trace or experiment file.

SYNOPSIS

extract_seq [-r] [-(abi|alf|scf|exp|pln)] [-good_only] [-clip_cosmid] [-fasta_out] [-output output_name] [input_name] ...

DESCRIPTION

extract_seq extracts the sequence information from binary trace files, Experiment files, or from the old Staden format plain files. The input can be read either from files or from standard input, and the output can be written to either a file or standard output. Multiple input files can be specified. The output contains the sequences split onto lines of at most 60 characters each.

OPTIONS

-r

Directs reading of experiment file to attempt extraction of sequence from the referenced (LN and LT line types) trace file. Without this option, or when the trace file cannot be found, the sequence output is that listed in the Experiment File. This option has no effect for other input format types.

-abi, -alf, -scf, -exp, -pln

Specify an input file format. This is not usually required as extract_seq 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).

-good_only

When reading an experiment file or SCF file containing clip marks, output only the good sequence which is contained within the boundaries marked by the QL, QR, SL, SR, CL, CR and CS line types.

-clip_cosmid

When the -good_only argument is specified this controls whether the cosmid sequence should be considered good data. Without this argument cosmid sequence is considered good.

-fasta_out

Specifies that the output should be in fasta format

-output file

The sequence will be written to file instead of standard output.

SEE ALSO

See section ExperimentFile(4).See section scf(4). Read(4)