[Bioperl-l] Re: Trace coordinates from scf files

[Chad Matsalla]

> Please does anyone have experience with using the
> Bio::Seq::SequenceTrace and Bio::SeqIO::scf modules to extract peak
> values for the different traces (G,A,T and C) which can then be
> plotted using a graphics module along with the bases themselves at the
> appropriate positions. I'm a little unclear as to how the trace, peak
> indices, peak_index_at, base_at etc methods work.

Hi All,

You can do that very easily.

Check the method Bio::Seq::SequenceTrace->scf_dump(). It demonstrates
how this can be done. There is a line in t/sequencetrace that calls that
method but in the interest of brevity iof output it is commented out.

<clickety click>

Remove the pound for line 119 and you will get output like this.[1]

See also the internal method Bio::Seq::SequenceTrace->_dump_traces($transformed):

'     - if a scalar is included as an argument (any scalar), this
     procedure will dump the _delta'd trace. If you don't know what
     that means you should not be using this.'

Note that scf_dump calls _dump_traces to produce output like this.[1]

Hope that helps,

Chad Matsalla

[1]
$ make test_sequencetrace TEST_VERBOSE=1
<snip>
Count   a       c       g       t
0       0       0       0       0
1       0       0       7       0
2       0       0       28      0
3       0       0       91      0
4       0       0       203     0
5       0       0       357     0
6       0       0       525     0
7       0       0       560     0
8       0       0       525     0
9       0       0       357     0
10      0       0       203     0
11      0       0       91      0
12      0       0       28      0
13      7       0       7       0
14      28      0       0       0
15      91      0       0       0
16      203     0       0       0
17      357     0       0       0
18      525     0       0       0
19      560     0       0       0
20      525     0       0       0
21      357     0       0       0
22      203     0       0       0
23      91      0       0       0
24      28      0       0       0
25      7       0       0       7
26      0       0       0       28
27      0       0       0       91
28      0       0       0       203
29      0       0       0       357
30      0       0       0       525
31      0       0       0       560
32      0       0       0       525
33      0       0       0       357
34      0       0       0       203
35      0       0       0       91
36      0       0       0       28
...