Staden scripting

Simon Andrews simon.andrews at bbsrc.ac.uk
Thu Jun 28 10:05:10 EST 2001

Hopefully someone still reads this group despite the low level of

I'm trying to automate the assembly of a number of SCF files using
Staden.  The whole process is quite complex involving multiple rounds of
searches to find SCF files to extend a contig.  Having found new files I
then enter them into a database through pregap/gap.

I can get the pregap bit working by building a custom pregap.config file
and adding other command line options.  This gets me to a list of .exp
files and a pregap.passed fofn.  

The problem comes when I try to automate Gap.  I've found the TCL
scripting information and I'm afraid I can't manage to put all of the
parts into a working script.

The functionality I need is quite basic.  All I need to do is;

1) open a database of a given name

2) add in exp files from pregap.passed using normal shotgun assembly

3) count how many contigs are in the database

4) halt if there is more than one contig (return an error or something)

5) if there is one contig extract its consensus (with all gaps removed)

... and that's it.  This will then be wrapped in a larger iterative Perl
script which will do all sorts of fancy stuff around it - but the whole
thing relies on being able to get this simple Staden script working.

Can anyone help me out on this one?  Even examples of working Staden
scripts would be useful so I can sort out the information in James'
scripting manual.

	Many thanks


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