Is your feature request related to a problem? Please describe.
It would be great if the option --prot-file could be used without the option --annot-parser.
Given that IntegronFinder can already read Prodigal output file, I think that it could read an input proteins file with the same structure.
Describe the solution you'd like
A solution can be to add a test to check if the input proteins file structure is similar to a Prodigal output file.
If this is the case, the step of proteins file creation can be skipped and the input proteins file can be used instead of.
Describe alternatives you've considered
An other solution can be to integrate a default function in the option --annot-parser if an input proteins file is provided.
For example, this function can be a lambda function which can parse headers of a Prodigal output file.
Please complete the following information):
OS:
[X] Linux
[ ] Windows
[ ] Mac
Integron_Finder Version:
integron_finder version 2.0.2
Using:
Python 3.8.11 (default, Aug 25 2021, 23:50:53) [GCC 9.2.0]
Is your feature request related to a problem? Please describe. It would be great if the option --prot-file could be used without the option --annot-parser. Given that IntegronFinder can already read Prodigal output file, I think that it could read an input proteins file with the same structure.
Describe the solution you'd like A solution can be to add a test to check if the input proteins file structure is similar to a Prodigal output file. If this is the case, the step of proteins file creation can be skipped and the input proteins file can be used instead of.
Describe alternatives you've considered An other solution can be to integrate a default function in the option --annot-parser if an input proteins file is provided. For example, this function can be a lambda function which can parse headers of a Prodigal output file.
Please complete the following information):
OS:
Integron_Finder Version: integron_finder version 2.0.2 Using:
Python 3.8.11 (default, Aug 25 2021, 23:50:53) [GCC 9.2.0]
numpy 1.22.1
pandas 1.4.0
matplolib 3.5.1
biopython 1.79
Prodigal V2.6.3: February, 2016
INFERNAL 1.1.4 (Dec 2020)
HMMER 3.3.2 (Nov 2020); http://hmmer.org/
Additional context