Package: gfanno
GfannoGene Family Annoation Pipline______  ________    _     Gene Family Annotation Workflow                           
 .' ___  ||_   __  |  / \     Bioinformatics Lab of SCAU.            
/ .'   \_|  | |_ \_| / _ \     _ .--.   _ .--.   .--.   
| |   ____  |  _|   / ___ \   [ `.-. | [ `.-. |/ .'`\ \ 
\ `.___]  |_| |_  _/ /   \ \_  | | | |  | | | || \__. | 
 `._____.'|_____||____| |____|[___||__][___||__]'.__.'IntroductionThis software is used to identify candidate genes.
Here, we demonstrate the identification of the SCPLⅠA gene in Tieguanyin as an example,
based on parameter thresholds for gene filtering.InstallPreparation before usePlease ensure that you have installed BLAST and Hmmer software correctly before use.
You can execute the following two commands to test the software installation situation.# Test blastpblastp-version# Test Hmmsearchhmmsearch-hEnvironmentpython >= 3.5Install GfannoThere are several ways to run gfannoInstalling using pypipipinstallgfannoInstalling using source codegitclonehttps://github.com/qunjie-zhang/gfanno.gitcdgfanno
pythonsetup.pyinstallUsageGet Help InformationUse it as a terminal command. For all parameters, typegfanno -h.Program:gfanno(GeneFamilyAnnoationWorkflow)Version:1.00Useage:gfanno<command>[options]Commands:-f/--fastaInputfastafilepath.Thisoptionisrequired.-o/--outputOutputfilepath.-c/--configUsethespecifiedconfigurationfile.Thisparameterisoptional.Ifyoudonotsetthisparameter,theprogramwilluse'gfanno_config.ini'bydefault.-t/--targetSpecifiestheparametercategoryusedintheconfigurationfile.Thisoptionisrequired.-g/--generateGeneratethedefaultconfigurationfile(gfanno_config.ini)underthecurrentpath.Usedtoinitializethesoftwareoperatingenvironmentorresetdamagedconfigurationfiles--/--dataReleasebuilt-indatasetsinthecurrentdirectory.-h/--helpDisplaythishelpmessage.-v/--versionDetailedversioninformation-fis the input fasta file path,is a required parameter.-ois the data output path. If the path does not exist, the program will automatically create it. The default isoutput-cThis parameter is used to specify the path of the configuration file. By default, the configuration file is located in the current directory and is namedgfanno_config.ini. In this case, you do not need to specify this parameter, as the program will use this file by default. If your configuration file has a different name or path, or if you want to use a specific configuration file, please use this parameter to inform the program about the configuration file you want to use.-tThis is an optional parameter used to specify the parameter schemes used during software runtime. In the configuration file, you can define multiple runtime schemes. You can use this parameter to specify the names of the runtime schemes, allowing you to input multiple names separated by commas. If this parameter is not specified, all the schemes provided in the configuration file will be used by default.-gThis parameter is used to generate the default configuration file in the current directory. The default name of this file isgfanno_config.ini. You can use this parameter to create a new configuration file for modification when the configuration file template is missing or when the file is corrupt.--dataThis is used to extract the built-in default dataset in the current path. It includes seed files and HMM models.Configuration fileBefore starting, you need to prepare a configuration file to obtain relevant parameters when the software is running.
You can directly use thegfanno -gcommand to create the default configuration content configuration filegfanno_config.iniin the current path.
When special attention is required, you may create multiple sets of configuration files. Be careful to avoid accidental overwriting of files and loss of content.You can create multiple configuration files to use with the software by using the -c parameter, or you can maintain a set of configuration files for use with the -t parameter to specify which ones will be run. It's important to note that the software has a configuration file validation feature. When the software is run, it will first check whether the configuration files being used are all valid. Data that doesn't meet the requirements will be flagged and the program will terminateThis is a demonstration scenario from the default configuration file:# PPO[PPO]blastp_seed=seed/PPO.seed.fastahmm=hmm/PPO1_DWL.hmm,hmm/PPO1_KFDV.hmmhmm_coverage=70,70domain=PPO1_KFDV,PPO1_DWLblastp_identity=50blastp_qcovs=50In the configuration file, the hmm parameter, hmm_coverage parameter, and domain parameter can have multiple values separated by commas. However, it is important to note that the number of values they carry must be equal.The configuration file supports comment text information starting with ‘;’ or ‘#’LICENSECopyright [2023] [Bioinformatics Laboratory of South China Agricultural University]Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.ContactIf any questions, please create an issue on this repo, we will deal with it as soon as possible.