##Liston/Cronn Lab utility scripts## These are all scripts done for the the Liston or Cronn labs that I've either written entirely (ncbiTaxonomyMunger.py and excelToSchema.py) or contributed heavily to (bcsort_v5.pl).
###bcsort_v5.pl###
A perl program to partition barcoded fasta or fastq files.
###excelToSchema.py###
A python script for converting an Excel template to an executable SQL table creation script. Used for the redevelopment of the wildstrawberry website and still a work in progress.
Dependency: python xlrd module
Obvious next steps:
- support more field types
- support more types of foreign key constraints
- add validation to ensure that each table has a primary key
- tighten up whether boolean fields are considered True or not. Currently entering 'False' into the spreadsheet could be interpreted as True just because it is not null
- add tabs that have been ignored to the ignore list
- add a check to make sure fields with a foreign key ref have the same field type as the referenced field
###ncbiTaxonomyMunger.py### Accepts tabular input (usually BLAST output) and adds columns for taxonomic identifiers. Taxonomomy information is derived from an NCBI Taxonomy Database.