diff --git a/README.md b/README.md index 6f0038523f0524a6ff9bf34f7d0ec8d9b58c4983..54bfd785727088a900e96abfddae7b870380b126 100644 --- a/README.md +++ b/README.md @@ -69,6 +69,35 @@ TACCATGAGGTAGTAGGTTGTATAGTT..................................................... .........................................................TATACAATCTACTGTCTTTCCT. 1 ``` +## Example + +There is a set of test files available in directory `tests/`. If you are in +the repository root directory, and all dependencies are installed and +available, you can use the following command to run a test: + +```bash +ascii_alignment_pileup.R \ + --verbose \ + --annotations="tests/test_files/test.gff" \ + --output-directory="$PWD" \ + "tests/test_files/test.bed" \ + "tests/test_files/test.bam" +``` + +Note that if you build a Docker image from the provided `Dockerfile` or pull +one of the prebuilt images (see section [Requirements](#requirements)), the +test files are included in those images. Therefore, you can also run the tests +in a container. To do that, start a container with: + +```bash +docker run --rm -it <IMAGE_ID> /bin/bash +``` + +Then run the test command above. + +In both cases, a successful test will create a file +`test.hsa-let-7a-1.min.1.pileup.tab` in the current working directory. + ## Options ```console diff --git a/ascii_alignment_pileup.R b/ascii_alignment_pileup.R old mode 100644 new mode 100755 diff --git a/tests/test_files/test.bam b/tests/test_files/test.bam new file mode 100644 index 0000000000000000000000000000000000000000..22d87f0ceb2ede21cb6bea4c9a693dc2c88a537b Binary files /dev/null and b/tests/test_files/test.bam differ diff --git a/tests/test_files/test.bam.bai b/tests/test_files/test.bam.bai new file mode 100644 index 0000000000000000000000000000000000000000..9ac006efd3ce5851200a72d391f018eb8ad9735d Binary files /dev/null and b/tests/test_files/test.bam.bai differ diff --git a/tests/test_files/test.bed b/tests/test_files/test.bed new file mode 100644 index 0000000000000000000000000000000000000000..b75f3526e2a97b5db935e5984b3828f7c155b4cc --- /dev/null +++ b/tests/test_files/test.bed @@ -0,0 +1 @@ +9 94175956 94176036 hsa-let-7a-1 0 + diff --git a/tests/test_files/test.gff b/tests/test_files/test.gff new file mode 100644 index 0000000000000000000000000000000000000000..00e05f02347173d012ce93db78bb4318435c4b8d --- /dev/null +++ b/tests/test_files/test.gff @@ -0,0 +1,3 @@ +9 . miRNA_primary_transcript 94175957 94176036 . + . ID=MI0000060;Alias=MI0000060;Name=hsa-let-7a-1 +9 . miRNA 94175962 94175983 . + . ID=MIMAT0000062_2;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000060 +9 . miRNA 94176013 94176033 . + . ID=MIMAT0004481_1;Alias=MIMAT0004481;Name=hsa-let-7a-3p;Derives_from=MI0000060