TAD_pathways #19
TAD_pathways #19
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Thank you for your interest and contributions to this project @Colin-Cheng ! Many of these changes are exciting. I have made several in line comments that must be addressed before the changes are merged in.
One thing that is not mentioned in the in line comments: Please add *.pyc to the .gitignore file and remove all .pyc files from this Pull Request.
| @@ -33,7 +33,7 @@ experimental validation at | |||
| First, clone the repository and navigate into the top directory: | |||
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| ```bash | |||
| git clone git@github.com:greenelab/tad_pathways_pipeline.git | |||
| git clone https://github.com/marislab/tad_pathways_pipeline.git | |||
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this is not an acceptable change to the master pipeline. This change can live in the marislab fork.
| #-s, --SNP_File path to the snp file | ||
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| # process arguments | ||
| function usage() |
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I love the resourcefulness here and am a big fan of the essence of these modifications.
However, can you port this logic into a python script with arguments defined by argparse? I would much prefer to keep run_pipeline.sh unchanged since it will impact the original analysis.
scripts/build_custom_tad_genelist.py
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| @@ -16,6 +16,7 @@ | |||
| --snp_data_file The file name of where SNP data is stored. SNP data is | |||
| generated by `scripts/build_snp_list.R` | |||
| --output_file The name of the results file to build | |||
| --TAD-Boundary The name of tad cell to use | |||
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Can we make this argument lowercase and add a suffix: --tad-boundary-file
scripts/build_custom_tad_genelist.py
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| @@ -30,6 +31,7 @@ | |||
| parser = argparse.ArgumentParser() | |||
| parser.add_argument("-s", "--snp_data_file", help="Location of SNP data") | |||
| parser.add_argument("-o", "--output_file", help="Name of the output file") | |||
| parser.add_argument("-t", "--TAD-Boundary", help="Name of the tad cell") | |||
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see above comment regarding the name of the argument. Lets also add a default.
parser.add_argument("-t", "--tad-boundary-file", help="Name of the tad cell",
default='data/GENE_index_hg19_hESC.tsv.bz2')
scripts/build_custom_tad_genelist.py
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| @@ -59,12 +61,13 @@ def assign_custom_snp_to_tad(snp_signal, tad_boundary): | |||
| # Load Constants | |||
| snp_data_file = args.snp_data_file | |||
| output_file = args.output_file | |||
| tad_cell = args.TAD_Boundary | |||
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Great! (except it now needs to be updated to lowercase)
tad_boundary_file = args.tad-boundary-file| @@ -0,0 +1,677 @@ | |||
| """ | |||
| @@ -0,0 +1,234 @@ | |||
| """ | |||
| @@ -0,0 +1,313 @@ | |||
| """ | |||
| @@ -0,0 +1,2819 @@ | |||
| chromosome db type start stop strand gene_type gene_name | |||
| @@ -0,0 +1,46 @@ | |||
| gene_type gene_class hg19 mm9 | |||
This version of TAD_pathways enable users to just input the TAD domain file and SNPs file into the pipeline. And the program will go through the tad pathways analysis.