From 14c8c67cb84dedff115660ea1c7ef4dd7e66de86 Mon Sep 17 00:00:00 2001 From: "A. Murat Eren" Date: Thu, 3 Aug 2023 12:29:57 -0400 Subject: [PATCH] make anvi-self-test --suite workflow-contigs work --- anvio/tests/run_workflow_tests_for_contigs.sh | 19 ++++++++++++++++--- .../tests/sandbox/workflows/contigs/fasta.txt | 6 +++--- 2 files changed, 19 insertions(+), 6 deletions(-) diff --git a/anvio/tests/run_workflow_tests_for_contigs.sh b/anvio/tests/run_workflow_tests_for_contigs.sh index fbcef91940..e60ed64ff7 100755 --- a/anvio/tests/run_workflow_tests_for_contigs.sh +++ b/anvio/tests/run_workflow_tests_for_contigs.sh @@ -7,12 +7,25 @@ SETUP_WITH_OUTPUT_DIR $1 $2 INFO "Setting up the pan analysis directory" mkdir $output_dir/workflow_test -cp $files/mock_data_for_pangenomics/*.fa $output_dir/workflow_test/ +cp $files/mock_data_for_pangenomics/*.db $output_dir/workflow_test/ cp $files/workflows/contigs/* $output_dir/workflow_test/ cd $output_dir/workflow_test -INFO "compressing sample 1" -gzip 01.fa +# all we need a FASTA file here to get things to work, so we +# will start by migrating the anvi'o contigs-db files +anvi-migrate *.db --migrate-quickly --quiet + +# then generate some files as expected by the test: +anvi-export-contigs -c E_faecalis_6240.db -o E_faecalis_6240.fa +anvi-export-contigs -c E_faecalis_6255.db -o E_faecalis_6255.fa +anvi-export-contigs -c E_faecalis_6512.db -o E_faecalis_6512.fa + +# compressing one of the FASTA files to match the `fasta.txt` coming +# from `$files/workflows/contigs/fasta.txt` +gzip E_faecalis_6240.fa + +# and get rid of the contigs-db files, and resume normal operations +rm -rf E_fa*.db INFO "Creating a default config for contigs workflow" anvi-run-workflow -w contigs --get-default-config default-config.json diff --git a/anvio/tests/sandbox/workflows/contigs/fasta.txt b/anvio/tests/sandbox/workflows/contigs/fasta.txt index d44c1452b6..fa45185bb3 100644 --- a/anvio/tests/sandbox/workflows/contigs/fasta.txt +++ b/anvio/tests/sandbox/workflows/contigs/fasta.txt @@ -1,4 +1,4 @@ name path -s01 01.fa.gz -s02 02.fa -s03 03.fa +E_faecalis_6240 E_faecalis_6240.fa.gz +E_faecalis_6255 E_faecalis_6255.fa +E_faecalis_6512 E_faecalis_6512.fa