gabaldonlab / crosslink-by-sequence

A tool to crosslink proteins between two proteomes from different sources using their sequences, aiming to avoid the inaccuracies associated with source-specific IDs.

crosslink-by-sequence

1. Setups on Unix systems

1.1 Install from Github

pip install https://github.com/Gabaldonlab/crosslink-by-sequence/archive/main.zip

1.2 Install from source

git clone https://github.com/gabaldonlab/crosslink-by-sequence
cd crosslink-by-sequence
make install

1.3 Install in a fresh virtual environment

git clone https://github.com/gabaldonlab/crosslink-by-sequence
cd crosslink-by-sequence
source scripts/install-with-fresh-env.sh

1.4 Uninstall

make uninstall

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2. Examples

2.1 Command xample

crosslink-by-sequence \
		--reference_species_fasta_gzip_file ./test_data/input_data/reference_proteomes/8.7165.faa.gz \
		--target_fasta_gzip_files ./test_data/input_data/target_proteomes/0.7165.fasta.gz \
		--output_directory ./test_data/output_data \
		--tmp_directory ./test_data/output_data/tmp \
		--max_threads 4 \
		--minimum_coverage 0.5 \
		--minimum_identity 0.5 \
        --verbose

2.2 Output example

reference_protein_id    target_protein_id       score
etc...
etc...
41948605        tr|B0F4F0|B0F4F0_ANOGA  0.7629310344827587
41951902        tr|D1MYR4|D1MYR4_ANOGA  0.9588148148148148
41946886        tr|F5HIZ5|F5HIZ5_ANOGA  0.9754098360655737
41953815        tr|F5HJI2|F5HJI2_ANOGA  0.897212543554007
41953900        tr|F5HJN2|F5HJN2_ANOGA  0.9845
etc...
etc...

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3. Singularity image

3.1. Build Singularity image for HPC cluster

NOTE: Inside the HPC you won't have sudo permissions to build the image. So you will have to build it locally on your working machine, then copy it to the remote one.

sudo make build-singularity-image

3.2. Run Singularity image example

singularity run --cleanenv crosslink_by_sequence_singularity.sif crosslink-by-sequence \
		--reference_species_fasta_gzip_file ./test_data/input_data/reference_proteomes/8.7165.faa.gz \
		--target_fasta_gzip_files ./test_data/input_data/target_proteomes/0.7165.fasta.gz \
		--output_directory ./test_data/output_data \
		--tmp_directory ./test_data/output_data/tmp \
		--max_threads 4 \
		--minimum_coverage 0.5 \
		--minimum_identity 0.5 \
		--verbose

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4. Acknowledgments

4.1. Diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen

This tool uses the Diamond software for sequence alignment. Please cite the following when using Diamond in your work:

• (Documentation, support and updates available at)[http://www.diamondsearch.org]
• Please cite: (Nature Methods (2021))[http://dx.doi.org/10.1038/s41592-021-01101-x]