Hi,
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.
Thanks,
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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