first previous next last contents

GetABIfield

NAME

getABIfield -- extract arbitrary components from an ABI file

SYNOPSIS

getABIfield [OPTIONS] filename [Field-ID [ Count]] ...

DESCRIPTION

The getABIfield command extracts specified blocks from an ABI file and displays them in a variety of formats. The ABI file may be considered as a directory structure with files (data blocks) contained within it. Supply just the ABI filename as an argument will give a listing of the blocks.

To extract specific data one or more "name count" pairs need to be specified.

OPTIONS

-a
Dump all blocks.
-D separator
Sets the output field separator for elements within a date and time format. Dates default to "yyyy/mm/dd" format and times default to "hh:mm:ss.xx".
-F separator
Sets the output field separator to be a specified character. This defaults to space.
-f format
Reformat the data to a specific style. By default the data is listed in the format specified within the ABI file. format should be chosen of 1(1-byte integer), 4(2-byte integer), 5(4-byte integer), 7(4-byte real), 8(8-byte real), 10(date), 11(time), 18(Pascal-string), 19(C-string).
-h
Displays data in hex format. By default the output format will be chosen based on the data type (eg string, integer, floating point).
-I fofn
Instead of reading the single file specified on the argument list this reads a list of filenames from fofn. If fofn is "-" then the file of filenames is read from 'stdin'.
-L separator
Sets the line separator between multiple blocks listed within a single file. Defaults to newline.
-l
Sets the output field separator to be a newline. Query mode. Here no output is displayed, but it simply returns true or false depending on whether any of requested comments were found.
-r
Displays data in raw byte format.
-t
Enable tagged output format. Each name/count pair are listed on a single line in the format "filename name count data...".

EXAMPLES

To extract the run dates in a tagged format for all the ab1 files in the current working directory:

ls *.ab1 | getABIfield -t -I - RUND

To see the order of the processed data channels (e.g. "GATC") on a single file:

getABIfield 3150.ab1 FWO_

To see the processed trace data for the first channel (e.g. "G") with one sample point per line:

getABIfield -l 3150.ab1 DATA 9

To obtain the version numbers of the various trace processing steps:

getABIfield -t 3150.ab1 SVER 1 SVER 2 SVER 3

SEE ALSO

See section get_comment(1).

See section scf(4).


first previous next last contents
Last generated on 25 November 2011.