This is an backend, infrastructure project to prepare a mongo database. Project linked to .
Install Mongodb. Instructions available here [https://docs.mongodb.com/manual/tutorial/install-mongodb-on-windows/]
Clone this Repository:
git clone https://github.com/raymond301/CNVdb-Mongo-ETL.git
Configure your Python enviroment:
#Check Version (2.7.x):
python --version
#Install Dependancies:
pip install --upgrade -r Scripts/requirements.txt
python Scripts/DGV/load_DGV_all.py -h
Added a development user to database db.createUser( { user: "devUser", pwd: "etldev", roles: [ "readWrite", "dbAdmin" ] } )
Add Gene Refflat to Mongo
Navigate to: http://dgv.tcag.ca/dgv/app/downloads?ref=GRCh37/hg19 Download: Supporting Variants - 2016-05-15 or
wget http://dgv.tcag.ca/dgv/docs/GRCh37_hg19_supportingvariants_2016-05-15.txt
Navigate to: http://dgv.tcag.ca/dgv/app/search?ref=GRCh37/hg19#tabs-view_all_info_sample Inspect in browser, edit table show element to display all. Then download via CSV
Commandline example:
python Scripts/load_DGV_nonMergedVars.py -f Download/GRCh37_hg19_variants_2016-05-15.txt -m Download/Database\ of\ Genomic\ Variants.csv
| Original Column | Converted Field |
|---|---|
| study | studies |
| external sample id | external_ids |
| family id | bio_family_id |
| source | bio_source |
| sample description | bio_description |
| ethnicity | bio_ethnicity |
| gender | bio_gender |
| cohort name | bio_sample_cohort |
Commandline example:
python Python/Load/load_TCGA_all.py -g ../Data/TCGA/TCGA.hg19.June2011.gaf -s ../Data/TCGA/Job-30305677257777413408743051.csv -n /data2/bsi/staff_analysis/m092469/data/CNVdatabase/TCGA_PAN12_data/PANCAN12.Genome_Wide_SNP_6.cna.normal_whitelist -t /data2/bsi/staff_analysis/m092469/data/CNVdatabase/TCGA_PAN12_data/PANCAN12.Genome_Wide_SNP_6.cna.tumor_whitelist
This is a tool built and deployed by our department.
child_file<-"s_011-HLH-001_within_run.id/s_011-HLH-001_within_run.id_zoomout_BinCovg.txt" father_file<-"s_011-HLH-003_within_run.id/s_011-HLH-003_within_run.id_zoomout_BinCovg.txt" mother_file<-"s_011-HLH-004_within_run.id/s_011-HLH-004_within_run.id_zoomout_BinCovg.txt"
python Scripts/load_Wandy_Sample.py -i /Users/m088378/Desktop/ChenCNV/wandy/run.id_wandy_ver0p95/s_011-HLH-001_within_run.id/s_011-HLH-001_within_run.id_zoomout_BinCovg.txt -b 10000 -m s_011-HLH-001
python Scripts/load_Wandy_Sample.py -i /Users/m088378/Desktop/ChenCNV/wandy/run.id_wandy_ver0p95/s_011-HLH-003_within_run.id/s_011-HLH-003_within_run.id_zoomout_BinCovg.txt -b 10000 -m s_011-HLH-003
- Fork it!
- Create your feature branch:
git checkout -b my-new-feature - Commit your changes:
git commit -am 'Add some feature' - Push to the branch:
git push origin my-new-feature - Submit a pull request :D
- Need to add/fix Logging capabilities
Copyright © 2017 Raymond Moore
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.