diff --git a/README.md b/README.md index 154df8298fab5ecf322016157858e08cd1bccbe1..04414f0e73658209a3791b6da9fe98bc9dd2737e 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,44 @@ ---- -license: apache-2.0 ---- +# Datasets + +Each folder contains either one benchmark or a set of benchmarks. See [docs/](../docs/) for code used to create these benchmarks. + +### Naming conventions + +* *dummy_...*: small datasets, used for testing purposes +* *demo_...*: middle size datasets, not necesarily biologically relevant or fully reproducible, used in demos + +### Versioning + +We recommend to check the version number when working with the dataset (i.e. not using default `None`). The version should be set to 0 when the dataset is proposed, after inicial curration it should be changed to 1 and then increased after every modification. + +### Data format + +Each benchmark should contain `metadata.yaml` file with its main folder with the specification in YAML format, namely + + * **the version** of the benchmark (0 = in development) + + * **the classes** of genomic sequences, for each class we further need to specify + + - *url* with the reference + - *type* of the reference (currently, only fa.gz implemented) + - *extra_processing*, a parameter helping to overcome some know issues with identifiers matching + +The main folder should also contain two folders, `train` and `test`. Both those folders should contain gzipped CSV files, one for each class (named `class_name.csv.gz`). + +The format of gzipped CSV files closely resemble BED format, the column names must be the following: + +* **id**: id of a sequence +* **region**: chromosome/transcript/... to be matched with the reference +* **start**, **end**: genomic interval specification (0-based, i.e. same as in Python) +* **strand**: either '+' or '-' + + +### To contribute a new datasets + +Create a new branch. Add the new subfolders to `datasets` and `docs`. The subfolder of `docs` should contain a description of the dataset in `README.md`. If the dataset comes with the paper, link the paper. If the dataset is not taken from the paper, make sure you have described and understand the biological process behind it. + +If you have access to `cloud_cache` folder on GDrive, upload your file there and update `CLOUD_CACHE` in [cloud_caching.py](https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks/blob/main/src/genomic_benchmarks/loc2seq/cloud_caching.py). + +### To review a new dataset + +Make sure you can run and reproduce the code. Check you can download the actual sequences and/or create a data loader. Do you understand what is behind these data? (either from the paper or the description) Ask for clarification if needed. diff --git a/demo_coding_vs_intergenomic_seqs/metadata.yaml b/demo_coding_vs_intergenomic_seqs/metadata.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b117bfa5a73eb39d01b093b602380b79783242e9 --- /dev/null +++ b/demo_coding_vs_intergenomic_seqs/metadata.yaml @@ -0,0 +1,10 @@ +classes: + coding_seqs: + extra_processing: ENSEMBL_HUMAN_TRANSCRIPTOME + type: fa.gz + url: http://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz + intergenomic_seqs: + extra_processing: ENSEMBL_HUMAN_GENOME + type: fa.gz + url: http://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz +version: 0 diff --git a/demo_coding_vs_intergenomic_seqs/test/coding_seqs.csv.gz b/demo_coding_vs_intergenomic_seqs/test/coding_seqs.csv.gz new file mode 100644 index 0000000000000000000000000000000000000000..9da462ddf762eb2a8417caa0f15840ab39e495df --- /dev/null +++ b/demo_coding_vs_intergenomic_seqs/test/coding_seqs.csv.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a691325db74c7a60667ec554180a4a0abae6698163590b3738076157ec8795e6 +size 132438 diff --git a/demo_coding_vs_intergenomic_seqs/test/intergenomic_seqs.csv.gz b/demo_coding_vs_intergenomic_seqs/test/intergenomic_seqs.csv.gz new file mode 100644 index 0000000000000000000000000000000000000000..4e76c3d10c2d1cee51e441330a0adce27fe90339 --- /dev/null +++ b/demo_coding_vs_intergenomic_seqs/test/intergenomic_seqs.csv.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d6c8adff76b78650c28272789539878a7b449fd810244e0e356095f5efe146f2 +size 156409 diff --git a/demo_coding_vs_intergenomic_seqs/train/coding_seqs.csv.gz b/demo_coding_vs_intergenomic_seqs/train/coding_seqs.csv.gz new file mode 100644 index 0000000000000000000000000000000000000000..c5a58162150b18b7365254027a39d44da649ae23 --- /dev/null +++ b/demo_coding_vs_intergenomic_seqs/train/coding_seqs.csv.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ad92694e4e4fedb8d7c65f40acc09846c813ab888306708716904768138199b5 +size 395239 diff --git a/demo_coding_vs_intergenomic_seqs/train/intergenomic_seqs.csv.gz b/demo_coding_vs_intergenomic_seqs/train/intergenomic_seqs.csv.gz new file mode 100644 index 0000000000000000000000000000000000000000..3ac4c460f7deee5a7050607887c301484f6daa0e --- /dev/null +++ b/demo_coding_vs_intergenomic_seqs/train/intergenomic_seqs.csv.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5fab0e675ed84de90891e76c7dbb62c0d5818dae6102dfed5f702d5727b1c70f +size 467863 diff --git a/demo_human_or_worm/metadata.yaml b/demo_human_or_worm/metadata.yaml new file mode 100644 index 0000000000000000000000000000000000000000..29cffb33062d6530e9f7a6dd02a1d709a7300df6 --- /dev/null +++ b/demo_human_or_worm/metadata.yaml @@ -0,0 +1,9 @@ +classes: + human: + extra_processing: ENSEMBL_HUMAN_GENOME + type: fa.gz + url: http://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz + worm: + type: fa.gz + url: http://ftp.ensembl.org/pub/release-104/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz +version: 0 diff --git a/demo_human_or_worm/test/human.csv.gz b/demo_human_or_worm/test/human.csv.gz new file mode 100644 index 0000000000000000000000000000000000000000..34347a5115ba11d8abe0236bb51fa4f5c5ffd4b5 --- /dev/null +++ b/demo_human_or_worm/test/human.csv.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:212ae29139f907d0e4a09eec70f68baf60247cd4cea70a169a9071c310b9b440 +size 158897 diff --git a/demo_human_or_worm/test/worm.csv.gz b/demo_human_or_worm/test/worm.csv.gz new file mode 100644 index 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