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Extract_seq

NAME

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

SYNOPSIS

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

DESCRIPTION

extract_seq extracts the sequence only information from a binary trace file, an Experiment File, or from the old Staden format plain files. The input can be read from either a file or standard input, and the output can be written to either a file or standard output. The output contains the sequence 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 outputted is that listed in the Experiment File. This option has no effect for other input format types.
-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.
-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).
-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)


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/manpages_4.html