It seems I spoke too soon about my Staden2000 scripts working under
2001.
I have a script which automatically assembles sequences from a
pregap.passed file, and then generates a consensus from them. I now
find that this script only enters one sequence (the first one) and then
rejects all the rest. The errors it spits out as shown below.
Automatic sequence assembler
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Processing 1 in batch
File name G10P608084RC10.T0.exp
Reading length 650
New reading does not overlap: start a new contig
This gel reading has been given the number 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Processing 2 in batch
File name G10P630536FE3.T0.exp
Reading length 587
Thu 17 Jan 13:44:30 2002 Error: Error in FNDCON: illegal consensus
header
Total matches found 3
Contig -1 position 182 matches strand 1 at position 2
Contig -1 position 305 matches strand 1 at position 125
Contig -1 position 380 matches strand 1 at position 199
Thu 17 Jan 13:44:30 2002 Error: Failed file G10P630536FE3.T0.exp written
to error file
Failed file G10P630536FE3.T0.exp written to error file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Processing 3 in batch
File name G10P651784RC11.T0.exp
Reading length 634
Thu 17 Jan 13:44:31 2002 Error: Error in FNDCON: illegal consensus
header
Total matches found 1
Contig -1 position 426 matches strand 1 at position 31
Thu 17 Jan 13:44:31 2002 Error: Failed file G10P651784RC11.T0.exp
written to error file
Failed file G10P651784RC11.T0.exp written to error file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
All the remaining files fail with the message about an error in FNDCON.
I include the script below. Can anyone point out what I can change to
get this working under the new version of Staden? It still works find
under Staden 2000.
Many thanks
Simon.
###### Staden Script ########
#!/usr/bin/sh
# \
exec stash -f "$0" ${@+"$@"} || exit 1
load_package gap
error_bell 0
set dbname [lindex $argv 0]
set fofn pregap.passed
set oldnew [lindex $argv 1]
set io [open_db -name $dbname -version 0 -access rq -create $oldnew]
assemble_shotgun \
-io $io \
-files [ListLoad $fofn files] \
-min_match 24 \
-max_pads 25 \
-max_pmismatch 7
set num_contigs [db_info num_contigs $io]
if {$num_contigs > 1} {
puts "CONSENSUS MULTICONTIG $num_contigs"
close_db -io $io
exit
}
set consensus_cutoff 0.01
set quality_cutoff 0
set consensus_mode 2
set seq [calc_consensus -io $io -contigs #1 ]
puts "CONSENSUS $seq"
close_db -io $io
exit
