Clone the repository using the following command:
https://github.com/Genome3d/codes3d.git
cd codes3d/
(The following guide has been tested on Ubuntu 14.04+.)
Install required apt packages:
sudo apt update
sudo apt install -y libz-dev libxslt1-dev libpq-dev python3-pip python3-dev python3-virtualenv bedtools
pip3 install --upgrade pip virtualenv setuptools
Ensure that you have conda installed. Then create a conda environment from the root directory. In this example, the environment is created in the envs directory and has all the required dependencies. (Size of environment ~1.8GB.)
conda env create --prefix ./codes3d_env --file environment.yaml
Then activate the environment with
conda activate codes3d_env/
To deactivate,
conda deactivate
You will also need to install Hi-C libraries and data necessary to calculate eQTLs. You can find detailed instructions and helper scripts in the download_data directory's README file.
The CoDeS3D interface is heavily inspired by the Qiime interface (J Gregory Caporaso et al., Nature Methods, 2010; doi:10.1038/nmeth.f.303). Running the CoDeS3D script in the codes3d directory will drop the user into the CoDeS3D shell, in which all CoDeS3D scripts are accessible from anywhere in the system, e.g.
(/mnt/projects/codes3d/codes3d_env) /m/p/codes3d$ python codes3d/codes3d.py -h
usage: codes3d.py [-h] [-s SNP_INPUT [SNP_INPUT ...]] [-g GENE_INPUT [GENE_INPUT ...]] [--snps-within-gene SNPS_WITHIN_GENE [SNPS_WITHIN_GENE ...]] [-o OUTPUT_DIR] [--multi-test MULTI_TEST] [--pval-threshold PVAL_THRESHOLD]
[-f FDR_THRESHOLD] [--maf-threshold MAF_THRESHOLD] [-p NUM_PROCESSES] [--no-afc] [--afc-bootstrap AFC_BOOTSTRAP] [-n INCLUDE_CELL_LINES [INCLUDE_CELL_LINES ...]] [-x EXCLUDE_CELL_LINES [EXCLUDE_CELL_LINES ...]]
[--list-hic-libraries] [--match-tissues ...] [--list-tissue-tags] [-t TISSUES [TISSUES ...]] [--eqtl-project EQTL_PROJECT] [--list-eqtl-db] [-r RESTRICTION_ENZYMES [RESTRICTION_ENZYMES ...]] [--list-enzymes]
[--list-eqtl-tissues] [-c CONFIG] [--output-format OUTPUT_FORMAT] [--do-not-produce-summary] [--suppress-intermediate-files] [--non-spatial] [--gene-list GENE_LIST [GENE_LIST ...]] [--gtex-cis]
CoDeS3D maps gene regulatory landscape using chromatin
interaction and eQTL data.
optional arguments:
-h, --help show this help message and exit
-s SNP_INPUT [SNP_INPUT ...], --snp-input SNP_INPUT [SNP_INPUT ...]
The dbSNP IDs or loci of SNPs of interest in the format 'chr<x>:<locus>'. Use this flag to identify eGenes associated with the SNPs of interest.
-g GENE_INPUT [GENE_INPUT ...], --gene-input GENE_INPUT [GENE_INPUT ...]
The symbols, Ensembl IDs or loci of genes interest in the format 'chr<x>:<start>-<end>'. Use this flag to identify eQTLs associated with the gene of interest.
--snps-within-gene SNPS_WITHIN_GENE [SNPS_WITHIN_GENE ...]
A gene symbol, Ensembl ID or location in the format 'chr<x>:<start>-<end>'. Use this flag to identify eGenes associated with the SNPs located within the gene of interest.
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
The directory in which to output results.
--multi-test MULTI_TEST
Options for BH multiple-testing: ['snp', 'tissue', 'multi']. 'snp': corrects for genes associated with a given SNP in a given tissue. 'tissue': corrects for all associations in a given tissue. 'multi': corrects
for all associations across all tissues tested.
--pval-threshold PVAL_THRESHOLD
Maximum p value for mapping eQTLs. Default: 1.
-f FDR_THRESHOLD, --fdr-threshold FDR_THRESHOLD
The FDR threshold to consider an eQTL statistically significant (default: 0.05).
--maf-threshold MAF_THRESHOLD
Minimum MAF for variants to include. Default: 0.1.
-p NUM_PROCESSES, --num-processes NUM_PROCESSES
Number of CPUs to use (default: half the number of CPUs).
--no-afc Do not calculate allelic fold change (aFC). If true, eQTL beta (normalised effect size) is calculated instead. (default: False).
--afc-bootstrap AFC_BOOTSTRAP
Number of bootstrap for aFC calculation (default: 1000).
-n INCLUDE_CELL_LINES [INCLUDE_CELL_LINES ...], --include-cell-lines INCLUDE_CELL_LINES [INCLUDE_CELL_LINES ...]
Space-separated list of cell lines to include (others will be ignored). NOTE: Mutually exclusive with EXCLUDE_CELL_LINES. --match-tissues takes precedence.
-x EXCLUDE_CELL_LINES [EXCLUDE_CELL_LINES ...], --exclude-cell-lines EXCLUDE_CELL_LINES [EXCLUDE_CELL_LINES ...]
Space-separated list of cell lines to exclude (others will be included). NOTE: Mutually exclusive with INCLUDE_CELL_LINES. --match-tissues and -n take precedence.
--list-hic-libraries List available Hi-C libraries.
--match-tissues ... Try to match eQTL and Hi-C tissue types using space-separated tags. When using this, make sure that it is the last tag. Note that tags are combined with the AND logic. Prepend "-" to a tag if you want it to be
excluded. Use `--list-tissues-tags' for possible tags.
--list-tissue-tags List tags to be used with `--match-tissues'.
-t TISSUES [TISSUES ...], --tissues TISSUES [TISSUES ...]
Space-separated list of eQTL tissues to query. Note that tissues are case-sensitive and must be from the same eQTL projects. Default is all tissues from the GTEx project. Use 'codes3d.py --list-eqtl-tissues'
for a list of installed tissues.
--eqtl-project EQTL_PROJECT
The eQTL project to query. Default: GTEx. 'use 'codes3d.py --list-eqtl-db' to list available databases.
--list-eqtl-db List available eQTL projects to query.
-r RESTRICTION_ENZYMES [RESTRICTION_ENZYMES ...], --restriction-enzymes RESTRICTION_ENZYMES [RESTRICTION_ENZYMES ...]
Space-separated list of restriction enzymes used in Hi-C data.' Use 'list-enzymes' to see available enzymes.
--list-enzymes List restriction enzymes used to prepare installed Hi-C libraries.
--list-eqtl-tissues List available eQTL tissues to query.
-c CONFIG, --config CONFIG
The configuration file to use (default: docs/codes3d.conf).
--output-format OUTPUT_FORMAT
Determines columns of output. 'short': snp|gencode_id|gene|tissue|adj_pval| [log2_aFC|log2_aFC_lower|log2_aFC_upper] or [beta|beta_se]| maf|interaction_type|hic_score. 'medium' adds:
eqtl_pval|snp_chr|snp_locus|ref|alt|gene_chr| gene_start|gene_end|distance. 'long' adds:cell_lines|cell_line_hic_scores| expression|max_expressed_tissue|max_expression| min_expressed_tissue|min_expression.
(default: long).
--do-not-produce-summary
Do not produce final summary file, stop process after mapping eQTLs. Helpful if running batches (default: False).
--suppress-intermediate-files
Do not produce intermediate files. These can be used to run the pipeline from an intermediate stage in the event of interruption (default: False).
--non-spatial Map non-spatial eQTLs.
--gene-list GENE_LIST [GENE_LIST ...]
List of genes for non-spatial eQTL mapping.
--gtex-cis Retrieve spatially unconstrained cis-eQTLs as calculated in GTEx. To be used in combination with 'non-spatial'.
If you want to make CoDeS3D accessible from anywhere in your system, you can add the codes3d directory to your PATH by appending this line to the bottom of your .bash_profile/.bashrc file in your home directory:
export PATH=$PATH:/path/to/CoDeS3D # Replace "/path/to" with the path where the CoDeS3D program is stored
Alternatively, you can make a link to the program in a directory which is already in your path (e.g. /usr/local/bin) using the following commands:
cd /usr/local/bin
sudo ln -s /path/to/CoDeS3D CoDeS3D # Replace "/path/to" with the path where the CoDeS3D program is stored
For details on the expected inputs of any CoDeS3D script, simply run the script with the -h argument, as in the example above.
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