[Bioperl-l] Issue with HOWTO Beginners Examples from "Retrieving a sequence from a database" and beyond

Kevin Farquhar kevinfarq at gmail.com
Thu Jun 7 15:56:47 EDT 2012


Hi,

My Bioperl version is 1.6.1 and it runs on a Windows 7 64 bit Ultimate OS.
I'm trying to receive a sequence from the genbank database, but am having
no luck. What should I do?
Attached to this email is the pl I'm using
Here are the errors:

C:\Users\Kevin>perl C:\Perl64\lib\Perl\secondbioperl3.pl
Name "main::seq_obj" used only once: possible typo at
C:\Perl64\lib\Perl\secondb
ioperl3.pl line 7.
Replacement list is longer than search list at
C:/Perl64/site/lib/Bio/Range.pm l
ine 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at
C:/Perl6
4/site/lib/Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line
93, <
GEN1> line 22.
Subroutine start redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm
line 115
, <GEN1> line 22.
Subroutine end redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line
144,
<GEN1> line 22.
Subroutine length redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm
line 19
0, <GEN1> line 22.
Subroutine location_type redefined at
C:/Perl64/site/lib/Bio\Location\Simple.pm
line 281, <GEN1> line 22.
Subroutine to_FTstring redefined at
C:/Perl64/site/lib/Bio\Location\Simple.pm li
ne 328, <GEN1> line 22.
Subroutine trunc redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm
line 370
, <GEN1> line 22.

C:\Users\Kevin>
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