Add automated LA State parsing solution (#4)

* allow for user-defined alt delimter

* add tsv_to_newline executable

* adding gisaid_multifasta.parser.py

* Added comments

* change shebang and allow write to existing dir

* update shebang

* added gisaid_metadata_cleanser

* Update gisaid_metadata_cleanser.py

* added column rename schema

* fixed shebang line

* added comments into data cleaning dection, swapped in shebang line that can be used in cloud env

* Swapped out old shebang line

* swapped out old shebang line

* swapped out old shebang line

* Jeanne Calment is the oldest human ever recorded at 122 years

* create la-state-dashboarding automated solution; print individual executables only

* set variables

* write to automation log dir at initiation

* read in tsv instead of csv

* replace all commas with spaces instead of underscores

* Remove duplicat samplenames

* tweaking automation scripts

* fix variables

* fix typo

* dat tagging json file

* remove redundant file extention

* Append data table rather than replace

* export full table before pushing to gcp

* fix variables

* ignore qoutes in echo statement

* fix script print statement

* fix gcp cp paths

* execute automation scripts with bash

* remove -it flag from docker commands

* Fixed output headers

* run without interactive mode

* clarify automation log

* Added required positional arg to ns3 metadata cleanser to define name of terra data table

* Read in age col as strings and switch to ints at line 66

* changing pangolin_lineage col header to pango_lineage

* Adding LA Parish ZipCodes

* Update bq schema

* replace all value > 122, not 151, with unknowns in the age col

Co-authored-by: frankambrosio3 <[email protected]>

Author: kevinlibuit