diff --git a/anvio/tests/run_component_tests_for_metagenomics.sh b/anvio/tests/run_component_tests_for_metagenomics.sh index 80beadd3b7..cdf763f1a2 100755 --- a/anvio/tests/run_component_tests_for_metagenomics.sh +++ b/anvio/tests/run_component_tests_for_metagenomics.sh @@ -643,10 +643,18 @@ anvi-get-codon-frequencies -c $output_dir/CONTIGS.db \ --no-progress SHOW_FILE $output_dir/CODON_frequencies_for_the_contigs_db.txt -INFO "Getting back the sequence for gene call 3" +INFO "Learning about the available defline variables" anvi-get-sequences-for-gene-calls -c $output_dir/CONTIGS.db \ --gene-caller-ids 3 \ -o $output_dir/Sequence_for_gene_caller_id_3.fa \ + --list-defline-variables \ + --no-progress + +INFO "Getting back the sequence for gene call 3 with a specific defline template" +anvi-get-sequences-for-gene-calls -c $output_dir/CONTIGS.db \ + --gene-caller-ids 3 \ + -o $output_dir/Sequence_for_gene_caller_id_3.fa \ + --defline-format "{contigs_db_project_name}_{contig_name}_{gene_caller_id}" \ --no-progress INFO "Getting back the AA sequence for gene call 3" @@ -697,12 +705,13 @@ anvi-get-sequences-for-hmm-hits -c $output_dir/CONTIGS.db \ -L \ --no-progress -INFO "Get DNA sequences for HMM hits for a bin in a collection" +INFO "Get DNA sequences for HMM hits for a bin in a collection with a defline format" anvi-get-sequences-for-hmm-hits -p $output_dir/SAMPLES-MERGED/PROFILE.db \ -c $output_dir/CONTIGS.db \ -C CONCOCT \ -b Bin_1 \ -o $output_dir/hmm_hits_sequences_in_Bin_1.txt \ + --defline-format "{contig_name}_{gene_callers_id}" --no-progress INFO "Get DNA sequences for all ABC transporter hits defined in an HMM source"