Re: [Treesoft-treefam] TreeFam API fails to returns some nucleotide sequences

[Sebastien M. <seb...@un...>]

Hi,

It is the same for this family also: TF101053.

It seems that some leaf sequences are not returned, and some cigar 
sequences also. But they are in the tree !
No cigar and aa sequences return for cr01.sctg9.wum.65.1 id.
cr01.sctg9.wum.65.1 is missing from aa_full_align table.


Something missing in TreeFam-7 database ?
Or a problem with stop codon in sequences (*) upstream ?



Here is the error message I got (for Treefam-7/Treefam/Tree.pm):

Use of uninitialized value in length at Treefam/Tree.pm line 1000 (#1)
     (W uninitialized) An undefined value was used as if it were already
     defined.  It was interpreted as a "" or a 0, but maybe it was a 
mistake.
     To suppress this warning assign a defined value to your variables.

     To help you figure out what was undefined, perl tells you what 
operation
     you used the undefined value in.  Note, however, that perl 
optimizes your
     program and the operation displayed in the warning may not necessarily
     appear literally in your program.  For example, "that $foo" is
     usually optimized into "that " . $foo, and the warning will refer to
     the concatenation (.) operator, even though there is no . in your
     program.

Use of uninitialized value in substitution (s///) at Treefam/Tree.pm 
line 1006 (#1)
Use of uninitialized value in substitution (s///) at Treefam/Tree.pm 
line 1007 (#1)
Use of uninitialized value in concatenation (.) or string at Treefam/Tree.pm
     line 960 (#1)
Use of uninitialized value in length at Treefam/Tree.pm line 1027 (#1)
Use of uninitialized value in concatenation (.) or string at Treefam/Tree.pm
     line 961 (#1)
Use of uninitialized value in substitution (s///) at Treefam/Tree.pm 
line 1002 (#1)
Use of uninitialized value in substitution (s///) at Treefam/Tree.pm 
line 1003 (#1)
Use of uninitialized value in concatenation (.) or string at Treefam/Tree.pm
     line 969 (#1)
Use of uninitialized value in concatenation (.) or string at Treefam/Tree.pm
     line 970 (#1)


Thanks

> Hi,
> 
> Have you been able to solve this problem ?
> I have other families with, it seems, this kind of problem.
> 
> Regards
> Sébastien
> 
>> Hi Sebastien,
>>
>> I am away this week but I'll have a look when I am back, unless 
>> someone comes up
>> with an answer before.
>>
>> Cheers
>>
>> J-K
>>
>> Quoting Sebastien MORETTI <seb...@un...>:
>>
>>> Hi,
>>>
>>> It seems that TreeFam API fails to return some genes for this family: =
>>>
>>> TF105900.
>>>
>>> Both from the web site and in command line, the API returns
>>> 58 protein sequences for the 'clean' protein alignment,
>>> 58 external branches for the 'clean' tree
>>> BUT 56 nucleotides sequences for the 'clean' nucleotide alignment.
>>>
>>> BGIOSIFCE019517.1_ORYSA & BGIBMGA012703_BOMMO are not in the 'clean' =
>>>
>>> nucleotide alignment.
>>>
>>> Do you have an idea why it happens ?
>>> Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4056
http://bioinfo.unil.ch/