Closed zmertens closed 6 years ago
Can one of the admins verify this patch?
Look at dawg::residue_exchance
for code to covert between residues and strings.
Specifying rates will require some changes to the rate_model class to match supplied rates to nearest rate categories.
I think it's working now, I tested it and the output was more or less "A" with one or two SNPs sprinkled in (using the test file you sent me).
It is not working for me, have you pushed all of your changes?
I still cannot get your patch to work.
This input file produces correct output:
Tree.Tree = "(A:0.1,B:0.1);"
Root.Length = 10
This input file produces no output:
Tree.Tree = "(A:0.1,B:0.1);"
Root.Seq = "AAAAAAAAAAAA"
This input file produces corrupted output:
Tree.Tree = "(A:0.1,B:0.1);"
Root.Seq = "AAAAAAAAAAAA"
Root.Length = 10
Output:
CLUSTAL multiple sequence alignment (Created by dawg 2-current-rUnknown)
A !TAAAAAAGG
B !TTAAAAAAA
What are those !
doing there?
I'm pretty sure codon, RNA, and AA inputs are equally broken.
Also, do not overwrite your branch after you have created a pull request. It completely breaks the tracking and history of the pull request.
Wasn't sure why the original PR wasn't viewable so I recommitted everything and then force pushed it, hopefully won't have to do that again.
Should there be an error if the root length
is not present (or a check to set the root length to the root sequence's size)?
What if the user specifies a root sequence longer then the root length?
Okay, it seems like you are now making progress.
I made three comments on the patch you need to address next.
dawg::sequence residue_exchange::encode(const std::string &str)
root_model::create(unsigned int len, dawg:sequence seq)
dawg::matic::add_config_section
based on the new code.root_model::do_user_seq
to simply copy the stored sequence to the output seq.Still need to add codon parsing and error checking to encode
I tried changing the bit packing routine but I'm still getting invalid chars. I'm going to try and look closer how the develop
handles errors and generates the codons. I feel like since we know the end-value of a codon it should be easy to match the triplet to the codon.
Is there any reason for inserting an indel in the user defined root sequence?
The example file that I had been using may have been bad. I tested it on develop
branch and I got output that would suggest the input format was bad (wrong alphabet of letters). I'll attach the file and output for reference.
models_out_from_specify_root_sequence.txt models_out_from_develop.txt
I can confirm that the multiple_models
example is consistent when specifying a root sequence and on the develop and that uses a codon model.
Updated. Kind of forgot how long this PR has been open for, so I didn't need to reopen a new one.
Addresses #35
I wasn't sure what to do about converting the string and vector into the Boost 64 data type since all the existing examples use
mutt