Can't locate BerkeleyDB.pm

[binlu1981]

Dear Dr.@MichaelHiller,

The perl module (BerkeleyDB.pm) missed and likely hard to install on my ubuntu 12. I plan to use fasta files of each CNEE rather than bdb file as input to calculate %id using your perl script (GetGlobalAndLocalPercentID.perl). Is it necessary to use BerkeleyDB.pm? Or there is another way to get %id value?

[MichaelHiller]

Dear Bin,

the module is here https://metacpan.org/pod/BerkeleyDB
If you don't want to install BDB and use individual fasta files that is totally OK. Then you don't need this module. Likely this requires some minor code changes.

Best
Michael

[binlu1981]

Thanks @MichaelHiller . I have installed BDB. However, it reported an error when run the GetGlobalAndLocalPercentID.perl.
sh: 1: set: Illegal option -o pipefail ERROR: set -o pipefail; ConvertTreeModToNewick.perl tree.mod /dev/shm/tree.nh.vNx6NbFK6 failed
Then I test the ConvertTreeModToNewick.perl and it likely worked well. What's the problem?
And what is ElementID when I used the fasta file as input?

[MichaelHiller]

Please remove
set -o pipefail;
from the command. It looks like sh cannot handle this. Alternatively, use bash.

BDB is nothing else then a file hash (dictionary). ElementID is the name given to the genomic element (CNE, exon etc) that was stored in the BDB.

[binlu1981]

Agree @MichaelHiller . One more question. For -allowedAncestralNodes, which nodes should be given here?

[MichaelHiller]

You should specify the node label that refers to the ancestor you would like to use.
E.g. if mouse is the reference species, you have 3 Afrotheria species in your alignment (say elephant, manatee, hyrax) and you want to specify the placental mammal ancestor (common ancestor of mouse and elephant),
then list
-allowedAncestralNodes mouse-elephant,mouse-manatee,mouse-hyrax

[binlu1981]

Thanks a lot for your reply. If I has a tree ((((a,b)a-b,c),d),e), a-b, a and b are the focused nodes, should I just set -allowedAncestralNodes a-b and ignore all the other ancestral nodes?

[MichaelHiller]

Yes, right.
If your tree is ((((a,b)a-b,(c,x)),d),e) and you want to specify the ancestor of abcx, then do
-allowedAncestralNodes a-c,a-x

I forgot to say that you need to have labeled ancestors. (tree_doctor -a from the Phast package does that)

[yuzhenpeng]

Dear hiller,
Sorry for disturbing you. When use your scripts, I meet some question.

As you say, I don't want to install BDB and I want use individual fasta files (the BDB is hard to install for me).
How should I to modify the code.
Could you help me.
Thank you.

[MichaelHiller]

Pls change the secureWriteBDB() fct in MyBDB.pm to output into a textfile instead of writing into a BDB.
The downstream scripts then need to be adapted to read from this textfile.

[yuzhenpeng]

Thanks for your reply.
I think I don‘t need MyBDB.pm module. right？

So, I just need remove use MyBDB in Maf2SpanningSeq_PRANK.perl. right?

[MichaelHiller]

Easiest is to simply replace the fct inside the module.

[yuzhenpeng]

So, I just need remove use MyBDB in Maf2SpanningSeq_PRANK.perl. right?