assemble_direct
-io io_handle:integer
-files filenames:strings
?-output_mode mode:integer(0)?
?-max_pmismatch percentage:float(-1)?
This performs the gap4 directed assembly function. It takes a list of
Experiment File filenames and processes these according to their content. The
Experiment Files should contain AP lines to govern their positions in the
assembly.
The function returns a list of failed files separated by newlines.
-io io_handle
-
The database IO handle returned from a previous
open_db call.
-files filenames
-
A Tcl list of Experiment File filenames.
-output_mode mode
-
Whether to display alignments when assembling sequences containing a
tolerance of zero or more. A mode of non-zero displays alignments, 0 does
not. This is an optional argument with the default as 0.
-max_pmismatch percentage
-
When aligning sequences (tolerance >= 0) the aligned sequences must match the
consensus sequence with <= percentage mismatch. A percentage of -1
implies no check should be made. The default for this option is -1.
This page is maintained by
staden-package.
Last generated on 1 March 2001.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/scripting_68.html