Scripting save consensus

Simon Foote foote at nrcbsa.bio.nrc.ca
Tue Feb 20 19:13:23 EST 2001


I'm trying to write a small script to dump the consensus data from a Gap 
database into fasta format.
The part that seems to give me trouble is as follows:

set num_contigs [db_info num_contigs $io]
# Generate a string with contig #'s
set contigs ""
for {set i 1} {$i <= $num_contigs} {incr i} {
  append contigs "#$i "
# Get consensus
set cons [get_consensus  \
               -io $io \
               -contigs $contigs \
               -outfile "cons.fa" \
               -type normal \
               -format 2]

It gives a couldn't create consensus error -1. 
Is there an easy way to generate a list of contig identifiers for the 
-contigs option.

Simon Foote

Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-991-4342  [F] 613-952-9092


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