gbnc.py

New cli script to generate BIOSAMPLEs and CALLSETs. Usage is very similar to gvnc.py except two destination collections are needed instead of one:

• '-dstb, --collection_dst_biosamples TEXT The collection to write into, default is "biosamples"'
• '-dstc, --collection_dst_callsets TEXT The collection to write into, default is "callsets"'

Not all relevent attributes in sample are copied to biosample, just have some for deomstration.

gvnc.py:

New cli script gvnc.py is added.

This script checks through the given source db collection, generate new VARIANTs containing CALLs, and put them in the destination db collection.

NOTE: Please manually create the destination collection to avoid accidental overwritting of existing collection.

WARNING: This script will overwrite the destination db collection, check before running.

Example: python3 gvnc.py --demo 1000 --dnw --log log.txt This will run for 1000 valid samples, the result wont be written to the database, and any error or warning messages will be shown in log.txt.

Options:

• -db, --dbname TEXT The name of the database, default is "arraymap"
• -src, --collection_src TEXT The collection to read from, default is "samples"
• -dst, --collection_dst TEXT The collection to write into, default is "variants"
• --demo INTEGER RANGE Only process a limited number of entries
• --dnw Do Not Write to the db
• --log FILENAME Output errors and warnings to a log file
• --help Show this message and exit.

Pre-requiremnt:

• sudo pip3 install pymongo
• sudo pip3 install click

generate.py:

The old script version:

USAGE:

• python generate.py

Pre-requirement:

• sudo pip install pymongo

This script will scan the "samples", find all the "HG18 segment"s and put ones with identical type and locaation in one variant.