diff options
| author | Muriithi Frederick Muriuki | 2021-08-30 07:00:38 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-30 07:00:38 +0300 |
| commit | 983acfdfc523677b4d7501287a000b7fd52a2c39 (patch) | |
| tree | 92547cd368fd0f024d4aedf92b1c3dc62417e65d /qtlfilesexport.py | |
| parent | c045122908d36bba4ca197f3f67e89d80958f38f (diff) | |
| download | genenetwork3-983acfdfc523677b4d7501287a000b7fd52a2c39.tar.gz | |
Implement module for interfacing with rust-qtlreaper
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: move `generate_traits_file` function to new
module
* gn3/computations/qtlreaper.py: new module to interface with the
`rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
use functions in new module.
Provide a module with functions to be used to interface with
`rust-qtlreaper`. This module essentially contains all the functions that
are needed to build the files needed for, and to run the qtlreaper utility.
Diffstat (limited to 'qtlfilesexport.py')
| -rw-r--r-- | qtlfilesexport.py | 10 |
1 files changed, 1 insertions, 9 deletions
diff --git a/qtlfilesexport.py b/qtlfilesexport.py index 2e7c9c2..0543dc9 100644 --- a/qtlfilesexport.py +++ b/qtlfilesexport.py @@ -7,16 +7,14 @@ Run with: replacing the variables in the angled brackets with the appropriate values """ -import random -import string from gn3.computations.slink import slink from gn3.db_utils import database_connector from gn3.computations.heatmap import export_trait_data from gn3.db.traits import retrieve_trait_data, retrieve_trait_info +from gn3.computations.qtlreaper import random_string, generate_traits_file from gn3.computations.heatmap import ( cluster_traits, compute_heatmap_order, - generate_traits_file, retrieve_strains_and_values) TMPDIR = "tmp/qtltests" @@ -35,11 +33,6 @@ def trait_fullnames(): "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064", "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"] -def random_string(length): - return "".join( - random.choices( - string.ascii_letters + string.digits, k=length)) - def main(): """entrypoint function""" conn = database_connector()[0] @@ -56,7 +49,6 @@ def main(): strains_and_values = retrieve_strains_and_values( orders, strains, exported_traits_data_list) strains_values = strains_and_values[0][1] - strains_values2 = strains_and_values[1][1] trait_values = [t[2] for t in strains_and_values] traits_filename = "{}/traits_test_file_{}.txt".format( TMPDIR, random_string(10)) |