diff options
| author | Lan Hui <lanhui@zjnu.edu.cn> | 2025-10-05 18:56:22 +0800 |
|---|---|---|
| committer | Lan Hui <lanhui@zjnu.edu.cn> | 2025-10-05 18:56:22 +0800 |
| commit | fbdf9e5c31fb360476beca2657d2696f5103b145 (patch) | |
| tree | 2801be015dd2c4042821de1f59292818a25c308c | |
| parent | 466dde75d1f16ac72ee47295fdea45d0389fb55c (diff) | |
Write a bash script for updating json files in Data/history/expr/json/
| -rw-r--r-- | Code/mergeTPM.py | 2 | ||||
| -rw-r--r-- | Code/update_gene_expression_json.sh | 5 |
2 files changed, 6 insertions, 1 deletions
diff --git a/Code/mergeTPM.py b/Code/mergeTPM.py index f37f438..ba1f0c4 100644 --- a/Code/mergeTPM.py +++ b/Code/mergeTPM.py @@ -78,7 +78,7 @@ run_ids_sorted = sorted(list(run_ids)) assemble_dir = os.path.join(PATH_TO_TPM, 'assemble') if not os.path.exists(assemble_dir): os.mkdir(assemble_dir) -fname = os.path.join(assemble_dir, 'assemble.%d.txt' % (len(run_ids))) +fname = os.path.join(assemble_dir, 'TPM.assembled.txt') print(f'Write to {fname}') with open(fname, 'w') as f: # write first line diff --git a/Code/update_gene_expression_json.sh b/Code/update_gene_expression_json.sh new file mode 100644 index 0000000..631f999 --- /dev/null +++ b/Code/update_gene_expression_json.sh @@ -0,0 +1,5 @@ +# Included the newly mapped RNA-seq data. May take several hours. +python3 make_parameter_rnaseq.py > ../Data/parameter/parameter_for_buildRmatrix.txt +python3 buildRmatrix.py ../Data/parameter/parameter_for_buildRmatrix.txt +python3 mergeTPM.py +python3 slice_TPM_to_JSON.py ../Data/parameter/parameter_for_net.txt |