GenomeRunner web

Command line module

GenomeRunner can be run from command line by using the hypergeom4 module. As with the server module, first create a database and define at least one custom background.

There are 3 mandatory arguments:

  • fois.txt - a text file containing paths to the sets of SNPs of interest. This file should contain at least one path. Example:
    /home/testuser/db_4.10_05.12.2014/custom_data/fois/hg19/GWASmore15new/bone_mineral_density.bed
/home/testuser/db_4.10_05.12.2014/custom_data/fois/hg19/GWASmore15new/endometriosis.bed
/home/testuser/db_4.10_05.12.2014/custom_data/fois/hg19/GWASmore15new/intelligence.bed
/home/testuser/db_4.10_05.12.2014/custom_data/fois/hg19/GWASmore15new/colorectal_cancer.bed
  • gfs.txt - a text file with paths to the genomic features to be used for the analysis. Again, provide at least one path. Example:
    /home/testuser/db_4.10_05.12.2014/grsnp_db/hg19/ENCODE/BroadHistone/Tier1/Gm12878/wgEncodeBroadHistoneGm12878H3k4me3StdPk.bed.gz
/home/testuser/db_4.10_05.12.2014/grsnp_db/hg19/ENCODE/BroadHistone/Tier1/Gm12878/wgEncodeBroadHistoneGm12878H3k27acStdPk.bed.gz
/home/testuser/db_4.10_05.12.2014/grsnp_db/hg19/ENCODE/BroadHistone/Tier1/Gm12878/wgEncodeBroadHistoneGm12878H3k4me1StdPk.bed.gz
  • a path to the background file. Example:
    /home/testuser/db_4.10_05.12.2014/custom_data/backgrounds/hg19/1snp138Common.bed.gz

Execute the hypergeom4 module like:

python -m grsnp.hypergeom4 fois.txt gfs.txt /home/testuser/db_4.10_05.12.2014/custom_data/backgrounds/hg19/1snp138Common.bed.gz

Use the following arguments to tweak the analysis:

  • --run_files_dir, or -r - a path to a folder where the results will be outputted. Default: current folder
  • --pv_adjust, or -v - a method for p-value adjustment. Default: fdr. Possible values (case sensitive): bonferroni, holm, hochberg, hommel, BH, BY, fdr, None.
  • --run_annotation, or -a - for each set of SNPs, run annotation analysis, i.e., annotate each SNP in a set by the number of co-localization with the regulatory datasets from the gfs.txt file.

Use the aforementioned arguments as follows:

python -m grsnp.hypergeom4 fois.txt gfs.txt /home/testuser/db_4.10_05.12.2014/custom_data/backgrounds/hg19/1snp138Common.bed.gz --run_files_dir test --pv_adjust fdr --run_annotation

The hypergeom4 modules creates a log file (gr_log.txt) in the output folder with the other results.