qianfeng2/detrec_program

A Program to Detect Recombinants From Unaligned Sequences

detrec_program's Issues

Not being able to run for large number of sequences (>10000 sequences)

Hi,

I am trying to make the "Mosaic Program to Detect Partial Alignments From Large Unaligned Sequences" work, but I am pretty sure that all the paths are incorrect in all the files and are directed towards your account etc (especially the moaic_est_par.sh scripts.
When I try to run estimate_transition_probs_frn_viterbi_qian.py, it gives the following error: Typerror: 'NonType' object has no attribute 'getitem'. This code is also in python2 while the rest of your code is python3, which is confusing.

I have 16000 proteins so this step is pretty necessary, if I use the normal route, it kills itself at the "Computing alignment paths for each sequence" step.

Can you help me with running your tool?

With kind regards,
Daan

cannot execute binary file: Exec format error

hello ！
Doctor qian
When I ran the mosaic script, it got the following error “cannot execute binary file: Exec format error”. How can I solve this problem?

purpose of the -group and -target flags

Hello Dr. Qian Feng,

I'm investigating recombination in a large gene family and I think detREC is a good approach, but I'm still struggling to implement the parallelization pipeline you and Dr. Gerry Tonkin-Hill used in your two papers. Could you tell me how the -group and -target flags work in mosaic? I can't find any documentation on them. I'm trying to understand the "-group 2 db target -target target" part of the mosaic command used both in 1nd_mosaic_est_par.sh and in Gerry's supplemental scripts. When I include this in a mosaic command I just get the error, "Could not assign sequence to group". It seems to run without that part but I don't want to exclude that part of the command without understanding what its doing.

Also, in order to replicate the pipeline of Dr. Gerry Tonkin-Hill, when estimating the recombination rate parameter I'll ultimately want to perform some 1000-vs-all runs like he did, where one set of sequences (a subset with 1000 sequences) are aligned to another set of sequences (all of the sequences). However I don't know how to get mosaic to use two sets of sequences like that. I suspect it involves the -group and -target flags, but that's just me guessing.

I'd appreciate any insight you can offer.

Best,
Derek Conkle-Gutierrez