extract_readings quality function not working....

major major at genome.wi.mit.edu
Thu Aug 9 12:42:27 EST 2001


Hello,

I've been attempting to build a new set of experiment files from a
gapDB. I can get an exp file with very minimal info(ie sequence and some
descriptive info) However, I really need to get the quality info and
original position info as well....

The extract_readings call has a flag '-quality', which when set to
non-zero values should provide all this info in the generated exp; And
this flag should default to true.
However, when I run extract_readings without the flag, I dont get any of
the quality data, and when I specify '-quality 1' I get the following
error message(even though the docs say this is a valid option!):
_________________________________________
Thu 09 Aug 12:59:41 2001 parse_args: Unknown option '-quality'

Thu 09 Aug 12:59:41 2001 parse_args: Unknown option '1'
    while executing
"extract_readings -io $io -readings $all_reads -quality 1 -directory
$dirname"
__________________________________________

When I runthis under Staden.02_97.beta gap4sh, I DO get the quality
info, BUT there is an enforced limit of 16 char exp filenames(!) which
we exceed in many cases....  In no other version can I coax out the
quality info, but in later versions this char limit has been removed. 
Does anyone have a suggestion on how to extract this data using a more
recent Staden gap4sh (ie 2000)?

Thanks In Advance,
John


Here is the piece of code(which works spledidly with Staden.02_97.beta,
except for the filename char limit...)

++++++++++++++++++++++++++++++++++++++++++++
set dbn [lindex $argv 0]
set extract_dir [lindex $argv 1];
if {[set dot [string last . $dbn]] == -1} {
    puts "ERROR: Invalid database name '$bdn'"
    exit 1
}
set db_name [string range $dbn 0 [expr $dot-1]]
set version_num [string range $dbn [expr $dot+1] [expr $dot+1]]
set specdir 1
set dirname $extract_dir;


load_package gap

set io [open_db -name $db_name -version $version_num]

global maxseq
set maxseq [expr [db_info t_contig_length $io] * 2]

set num_reads [db_info num_readings $io]
for {set i 1} {$i <= $num_reads} {incr i 1} {
    lappend all_reads [get_read_names -io $io "\#$i"]
}
if {$specdir} {
    extract_readings -io $io -readings $all_reads -quality 1 -directory
$dirname

} else {
    puts "ERROR!\n";
    exit 0;
}

close_db -io $io
exit 0

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