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Utility scripts written for the lab
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README.md
bcsort_v5.pl
excelToSchema.py
ncbiTaxonomyMunger.py

README.md

##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.

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