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| author | Muriithi Frederick Muriuki | 2021-08-27 15:49:53 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-27 15:49:53 +0300 |
| commit | 1a3901b174d00af8fa7f5ae78b810de66024b5ab (patch) | |
| tree | 2a3412075ba36a49f6137b4cd0fb7d5446aa905a | |
| parent | 557e482c88ba3d44ae7d278b7222f37fa043b4d0 (diff) | |
| download | genenetwork3-1a3901b174d00af8fa7f5ae78b810de66024b5ab.tar.gz | |
Export trait data to file
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide a function to export the given strains and traits data into a traits
file for use with `rust-qtlreaper`.
| -rw-r--r-- | gn3/computations/heatmap.py | 8 |
1 files changed, 8 insertions, 0 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py index da13ceb..2f92048 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/computations/heatmap.py @@ -229,3 +229,11 @@ def retrieve_strains_and_values(orders, strainlist, traits_data_list): values = [] return rets + +def generate_traits_file(strains, trait_values, traits_filename): + header = "Traits\t{}\n".format("\t".join(strains)) + data = [header] + [ + "T{}\t{}\n".format(i+1, "\t".join([str(i) for i in t])) + for i,t in enumerate(trait_values)] + with open(traits_filename, "w") as outfile: + outfile.writelines(data) |