LGT is a python package that suggests candidate accession numbers for a given orthogroup and a user-defined list of species. LGT uses pickled data frames created by the user from blast results. These data frames contain three columns of 'qseqid', 'sseqid', and 'evalue'. For each query sequence id found in the orthogroup file provided by the user, the pickled data frames are searched to retreive the subject sequences hit by the query sequence together with their e-values. Next, the proportion of hits among all query sequence ids and the average e-values are calculated for each subject sequence id. For each subject sequence id, the taxonomics ranks are obtained and searched for the user-defined list of species. Finally, for each species, the three best and two random subject sequence ids are suggested to the user for the creation of phylogenetic trees.
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Author: Fardokhtsadat Mohammadi
E-Mail: [email protected]
LGT makes use of several python packages. Here we provide a list of used python packages:
- pandas
- numpy
- math
- glob
- mysql.connector
- os
Beside the aforementioned python packages, ypou will need a database to be able to retreive the taxomomic rank for the subject sequence ids. You can find the scripts to create this database for you accession numbers in this github repository.
The ZIP-File of the package can be downloaded via "Clone or download" as well as the command line:
git clone https://github.com/fardokhtsadat/LGT.gitFirst specify all the parameters in a config file. You can find an example config file in you LGT repository. Next call the config_reader.py:
python3 config_reader.py <name_of_the_config_file>