Test runs

InterProScan

Example run for interproscan to generate input for --interproscan_output. Please refer to the InterProScan documentation for full description of how to use it.

Download the interproscan datasets as described in the user documents:

singularity pull docker://interpro/interproscan:latest

# Beaware! If the sequences contain any non-alphabet characters, it will crash!
faa=path/to/faa/files
mkdir output temp

for FN in $faa/*.faa; do
N=$(basename $FN .faa)
singularity exec \
    -B $db:/opt/interproscan/data \
    -B $faa/output:/output \
    -B $faa/temp:/temp \
    -B $FN:$FN \
    interproscan_latest.sif \
    /opt/interproscan/interproscan.sh \
    --input $FN \
    --disable-precalc \
    --output-dir /output \
    --tempdir /temp \
    --cpu 16 \
    --applications PANTHER,ProSiteProfiles,ProSitePatterns,Pfam \
    --disable-residue-annot \
    --enable-tsv-residue-annot \
    --formats tsv; done

Full run

To test the functionality of AMPcombi, we provide test files for the required and optional inputs. Those can be found in the tests directory.

1. Download test files and untar

   git clone https://github.com/Darcy220606/AMPcombi.git
   
   tar -xzvf ./tests/test_faa.tar.gz
   tar -xzvf ./tests/test_gbk.tar.gz
   tar -xzvf ./tests/test_files.tar.gz
   tar -xzvf ./tests/test_optional_files.tar.gz
   

Tip

These input files can be generated in a streamlined approach using nf-core/funcscan - a pipeline for predicting functional genes in metagenomes.

2. Parse tables and filter recovered AMP hits

   ampcombi parse_tables \
   --amp_results ./tests/test_files/ \
   --faa ./tests/test_faa/ \
   --gbk ./tests/test_gbk/ \
   --interproscan_output ./tests/test_optional_files/interproscan_output/ \
   --sample_metadata ./tests/test_optional_files/sample_metadata.tsv \
   --contig_metadata ./tests/test_optional_files/contig_metadata.tsv \
   --sample_list sample_1 sample_2 \
   --amp_database 'DRAMP' \
   --aminoacid_length 100 --db_evalue 100 --amp_cutoff 0.7 \
   --ampir_file '.tsv' --amplify_file '.tsv' --macrel_file '.tsv' --neubi_file '.fasta' --hmmsearch_file '.txt' --ampgram_file '.tsv' --amptransformer_file '.txt' \
   --log --threads 16
   

3. Concatenate summary files

   mv sample_1 test_ampsummaries/
   mv sample_2 test_ampsummaries/
   
   ampcombi complete --summaries_directory ./test_ampsummaries --log
   

4. Cluster filtered AMPs into families

   ampcombi cluster --ampcombi_summary Ampcombi_summary.tsv --log --threads 16
   

5. Predict signal peptides

   ampcombi signal_peptide \
   --ampcombi_cluster Ampcombi_summary_cluster.tsv \
   --signalp_model ./signalpv6.0h-slowsequential/models --log