[Bioperl-l] Alignment->slice() issue?

Kevin Brown Kevin.M.Brown at asu.edu
Wed Jan 17 11:16:48 EST 2007


Bioperl: 1.5.2_100
Perl: perl -v
This is perl, v5.8.5 built for i386-linux-thread-multi

I'm hoping this is just me, but I've created a huge alignment of a set
of primers on a chromosome and then I'm trying to slice up that one
large alignment into smaller alignments based around the CDS features of
the chromosome (taken from a Genbank file that the script read in
previously that gives me both the features and the chromosome sequence).
The error occurs when I request the slice.  I get the following:

------------- EXCEPTION  -------------
MSG: Bad start,end parameters. Start [1088] has to be less than end
[850]
STACK Bio::PrimarySeq::subseq
/usr/lib/perl5/site_perl/5.8.5/Bio/PrimarySeq.pm:354
STACK Bio::SimpleAlign::slice
/usr/lib/perl5/site_perl/5.8.5/Bio/SimpleAlign.pm:929
STACK toplevel ./PrimerAnalysis.pl:376

--------------------------------------

But, based on output I've put into my script that isn't the range I
requested from the alignment.  What I've requested is
$align = $alignments{$key}->slice($start, $stop);
$start is 1088 and $stop is 2377 (from the printout below)
"Forward strand with start(1088) and stop(2377) at ./PrimerAnalysis.pl
line 358, <$primer> line 657."

The feature I'm initally after is BMAA0001 start:1139 stop:2326 with
some upstream and downstream sequence.

I noticed that slice does "foreach my $seq ( $self->each_seq() )", so I
copied that to printout all the sequences held by the alignment and
their start and stop locations and get the following:
NC_006349       1       2325379
BurkM_0005_a-f..BurkM_0005_a-r  80686   81516
BurkM_0005_a-f..BurkM_0005_a-r  268747  269577
BurkM_0005_a-f..BurkM_0005_a-r  329852  330682
BurkM_0005_a-f..BurkM_0005_a-r  560818  561648
BurkM_0005_a-f..BurkM_0005_a-r  592443  593273
BurkM_0005_a-f..BurkM_0005_a-r  908245  909075
BurkM_0005_a-f..BurkM_0005_a-r  935390  936220
BurkM_0005_a-f..BurkM_0005_a-r  1014714 1015544
BurkM_0005_a-f..BurkM_0005_a-r  1034315 1035145
BurkM_0005_a-f..BurkM_0005_a-r  1225934 1226764
BurkM_0005_a-f..BurkM_0005_a-r  1324779 1325609
BurkM_0005_a-f..BurkM_0005_a-r  1413075 1413905
BurkM_0005_a-f..BurkM_0005_a-r  1480717 1481547
BurkM_0005_a-f..BurkM_0005_a-r  1517965 1518795
BurkM_0005_a-f..BurkM_0005_a-r  1900786 1901616
BurkM_0005_a-f..BurkM_0005_a-r  1921906 1922736
BurkM_0005_a-f..BurkM_0005_a-r  1957979 1958809
BurkM_0005_a-f..BurkM_0005_a-r  2136301 2137131
BurkM_0005_a-r..BurkM_0005_a-f  103238  104068
BurkM_0005_a-r..BurkM_0005_a-f  170641  171471
BurkM_0005_a-r..BurkM_0005_a-f  408755  409585
BurkM_0005_a-r..BurkM_0005_a-f  432906  433736
BurkM_0005_a-r..BurkM_0005_a-f  509458  510288
BurkM_0005_a-r..BurkM_0005_a-f  565194  566024
BurkM_0005_a-r..BurkM_0005_a-f  656754  657584
BurkM_0005_a-r..BurkM_0005_a-f  733927  734757
BurkM_0005_a-r..BurkM_0005_a-f  838705  839535
BurkM_0005_a-r..BurkM_0005_a-f  869777  870607
BurkM_0005_a-r..BurkM_0005_a-f  892021  892851
BurkM_0005_a-r..BurkM_0005_a-f  909903  910733
BurkM_0005_a-r..BurkM_0005_a-f  1061801 1062631
BurkM_0005_a-r..BurkM_0005_a-f  1096777 1097607
BurkM_0005_a-r..BurkM_0005_a-f  1636356 1637186
BurkM_0005_a-r..BurkM_0005_a-f  1636356 1643935
BurkM_0005_a-r..BurkM_0005_a-f  1643105 1643935
BurkM_0005_a-r..BurkM_0005_a-f  1790703 1791533
BurkM_0005_a-r..BurkM_0005_a-f  2267109 2267939
BurkM_0005_a-f..BurkM_0005_a-f  560818  566024
BurkM_0005_a-f..BurkM_0005_a-f  908245  910733
BMA_0006_a-r..BMA_0006_a-r      561646  565196
BMA_0006_a-r..BMA_0006_a-r      909073  909905
BMA_0046_a-f..BMA_0046_a-r      437921  438661
BurkM_0092_a-f..BurkM_0092_a-f  561670  565172
BurkM_0092_a-f..BurkM_0092_a-f  909097  909881
BMA_0113_a-f..BMA_0113_a-r      1310782 1311536
BMA_0113_a-r..BMA_0113_a-f      172284  173038
BMA_0113_a-r..BMA_0113_a-f      2266197 2266951
BMA_0146_a-f..BMA_0146_a-r      1172194 1173065
BMA_0146_a-f..BMA_0146_a-r      2267012 2269123
BMA_0146_a-r..BMA_0146_a-f      167410  168281
BMA_0146_a-r..BMA_0146_a-f      320180  321051
BMA_0146_a-r..BMA_0146_a-f      894226  895097
BMA_0146_a-r..BMA_0146_a-f      894226  900207
BMA_0146_a-r..BMA_0146_a-f      899335  900207
BMA_0146_a-r..BMA_0146_a-f      1638747 1639622
BMA_0146_a-r..BMA_0146_a-f      1972415 1973286
BMA_0146_a-r..BMA_0146_a-f      2157899 2158770
BMA_0146_a-r..BMA_0146_a-f      2321169 2322040

So, I can see that all the sequences held in the alignment have Start <
Stop as expected.  What I can't figure is where the end value is coming
from that is messing this up.

Any help is greatly appreciated.



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