/OrthologFinding

This repository is for Ortholog finding between two different species.

Primary LanguagePython

# OrthologFinding
This repository is for Ortholog finding between two different species by lastal.
usage: lftpip.v3.py [-h] -q QUERYGENOME -db DBDICT [-psl PSL] -t TARGETGENOME
                    -b ANOTATIONFILE [-sq SPLITQ] [-d OPTDIRECT] [-p PROCESS]
                    [-m RUNMEM]

To Run Liftover Program Automatically. Writen by Zhen Li at Jan, 4, 2020

optional arguments:
  -h, --help            show this help message and exit
  -q QUERYGENOME, --querygenome QUERYGENOME
                        The query genome sequence which should be fasta
                        format.
  -db DBDICT, --dbdict DBDICT
                        The db directory name.
  -psl PSL, --psl PSL   Whether use the psl format file directly.
  -t TARGETGENOME, --targetgenome TARGETGENOME
                        The target genome sequence which should be fasta
                        format.
  -b ANOTATIONFILE, --anotationfile ANOTATIONFILE
                        The anotation file which should be bed format.
  -sq SPLITQ, --splitq SPLITQ
                        The number that the query genome should be splited
                        into
  -d OPTDIRECT, --optdirect OPTDIRECT
                        The destinated directory in where all of your output
                        will be stored.
  -p PROCESS, --process PROCESS
                        The maximum process number that could run at the same
                        time.
  -m RUNMEM, --runmem RUNMEM
                        The memory size(gb) that each task will be used.