!git clone https://github.com/evolu-tion/GenomeManagement.git

"""
Explanation: <a href="https://colab.research.google.com/github/evolu-tion/GenomeManagement/blob/master/example/get_protein_sequences.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
How to get protein sequence from whole protein sequence
1. Clone GenomeManagement package into your environment
End of explanation
"""


!wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/995/035/GCF_001995035.1_ASM199503v1/GCF_001995035.1_ASM199503v1_protein.faa.gz
!zcat GCF_001995035.1_ASM199503v1_protein.faa.gz | head

"""
Explanation: 2. Download whole protein sequence in FASTA format
End of explanation
"""


!python3 GenomeManagement/proteins_retrieve.py \
    --input GCF_001995035.1_ASM199503v1_protein.faa.gz \
    --list_of_interest list_of_protein_id.txt \
    --output output_file.fa

"""
Explanation: 3. Use proteins_retrieve.py to get your interested protein
3.1 Create a tab-delimited file of your protein and EC into list_of_protein_id.txt file and save on your working environment
XP_022136171.1  2.3.1.9
XP_022142541.1  2.3.1.9
XP_022152764.1  2.3.3.10
3.2 Use proteins_retrieve.py to get protein sequence using following command
python3 proteins_retrieve.py \
    --input &lt;input_fasta_file&gt; \
    --list_of_interest &lt;list_of_protein_id.txt&gt; \
    --output &lt;output_file.fa&gt;
3.3 Download an output of FASTA file output_file.fa on your working environment
End of explanation
"""


