Confidence Score Reading using io_read_data...

major major at genome.wi.mit.edu
Tue Jul 10 12:46:36 EST 2001


Hello-

I'm having some troubles getting to the confidence scores contained in
the io_read_readings structure.  I need to be able to access the
sequence, and confidence/quality data in each base call of a reading,
and manipulate them.  I can fairly easily do this for the sequence, but
am having some difficulty using the io_read_data proc.  When I issue
this command:
set conf_vals [io_read_data $io [keylget r confidence] [keylget r
length] 1];

I get what appears to be a setid, or pointer:
puts $conf_vals =
%*.27;@DDIIJJHGFFFFGHGGHGGFEFHGGGHGGHHIIHHIHGGGHIIIHHFGHGFB=94/)% 

  But i can't manage to resolve the scores from this.  And once I do, I
need to be able to modify the scores, and re-write them.

I'm using Staden2000.0 gap4sh, and below is a full piece of code
attempting to get the quality scores(of which there should be one per
base...)

Any help would be greatly appreciated.

Cheers-
John

++++++++++++++++++++++++++++++++++++++++++++++++

set a [lindex $argv 0];
if {[set dot [string last . $a]] == -1} {
    puts "ERROR: Invalid database name '$a'";
    exit 1;
}

set db_name [string range $a 0 [expr $dot-1]];
set version_num [string range $a [expr $dot+1] [expr $dot+1]];
set specdir 0;

load_package gap;
#SetDefaults gaprc gap_defs;
set io [open_db -name $db_name -version $version_num -access rw];

puts $io;
set read_db [io_read_database $io];
puts "$read_db \n\n";

set r [io_read_reading $io 2];

puts " -- $r \n";

set vals [keylget r sequence];
puts "_ $vals _\n";

set seq_vals [io_read_text $io [keylget r sequence]];
puts "Sequence:\n $seq_vals\n\nQuality:\n";

set conf_vals [io_read_data $io [keylget r confidence] [keylget r
length] 1];
puts "$conf_vals \n\n";

close_db -io $io
exit 0;
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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