Code

Incorporating SNP data#40

Code

Merged

rnmitchell merged 32 commits intomasterbioforensics/lusSTR:masterfrom snpsbioforensics/lusSTR:snpsCopy head branch name to clipboardJan 27, 2021

+23,156-681

Commits

Commits on Jan 12, 2021

• Inital commit

  

  Rebecca Mitchell

  committed
  00fa8ed

• Added safeguard to exclude non-STRait Razor .txt files in provided directory

  

  Rebecca Mitchell

  committed
  3f4069e

Commits on Jan 13, 2021

• Added script for formatting SNP data from STRait Razor output

  

  Rebecca Mitchell

  committed
  203b5a1

• updated SNP .json file

  

  Rebecca Mitchell

  committed
  d983685

Commits on Jan 14, 2021

• Added formatting for UAS output files

  

  Rebecca Mitchell

  committed
  701b9a0

• Bypass any .xlsx file in a UAS specified directory that is not a Sample Details or Phenotype Report

  

  Rebecca Mitchell

  committed
  edd785b

• Updated UAS bulk code in format.py and UAS bulk test datasets

  

  Rebecca Mitchell

  committed
  dd7ebce

• Updated UAS bulk test data files

  

  Rebecca Mitchell

  committed
  bf55323

• upated snp_data.json file

  

  Rebecca Mitchell

  committed
  f79e183

Commits on Jan 15, 2021

• Handling multiple SNPs within one reported sequence in STRait Razor data; refactored code into different functions

  

  Rebecca Mitchell

  committed
  e5f6252

Commits on Jan 19, 2021

• Added combine reads fuction for strait razor data; fixed other bugs

  

  Rebecca Mitchell

  committed
  48043d5

• Fixed bugs in UAS file processing

  

  Rebecca Mitchell

  committed
  96f2200

Commits on Jan 20, 2021

• Added reads for total reads in sr data

  

  Rebecca Mitchell

  committed
  af77715

• Updated error in snp dict

  

  Rebecca Mitchell

  committed
  d4400d4

• changed cli command from "format_snps" to "snps"

  

  Rebecca Mitchell

  committed
  6fbdad2

• changed name of command to "snps"; removed option of "a" SNPs (both "p" and "a" SNPs included when "p" is specified on CLI)

  

  Rebecca Mitchell

  committed
  54dcd9c

Commits on Jan 21, 2021

• Reformatted UAS code processing to process p/a snps together

  

  Rebecca Mitchell

  committed
  8ecc28d

• Rearranged final output tables

  

  Rebecca Mitchell

  committed
  4ebaa79

• Updated README

  

  Rebecca Mitchell

  committed
  04480fa

• updated setup.py

  

  Rebecca Mitchell

  committed
  72dd9ae

Commits on Jan 22, 2021

• added expected length exception for rs2402130

  

  Rebecca Mitchell

  committed
  16ca20d

• added exception for rs1821380

  

  Rebecca Mitchell

  committed
  0d1b397

• fixed bug in uas processing

  

  Rebecca Mitchell

  committed
  abeb248

• Added flags for unexpected alleles in main reports

  

  Rebecca Mitchell

  committed
  c0cbaf3

• Updated README

  

  Rebecca Mitchell

  committed
  646af0b

Commits on Jan 25, 2021

• Added test for UAS SNP output

  

  Rebecca Mitchell

  committed
  de67414

• Added test for SR data for all SNPs

  

  Rebecca Mitchell

  committed
  2e7e1e3

• Updated docstrings for functions

  

  Rebecca Mitchell

  committed
  0da89bd

Commits on Jan 26, 2021

• fixed bug with dropping index from subsetted dataframe

  

  Rebecca Mitchell

  committed
  e13692b

• Added tests to check # of lines for type specified output

  

  Rebecca Mitchell

  committed
  7942886

• Reorganized code

  

  Rebecca Mitchell

  committed
  3effb20

• Updated README

  

  Rebecca Mitchell

  committed
  9f51c6b