Fixes and enhancements #22

saramonzon · 2024-05-01T19:57:53Z

Now distance matrix computes pairwise filtering all non INF or EXC values
Distance matrix modules outputes two matrices one without filters and one alfter results alleles fileting.
Results allele filtered table is also outputted
Added two scripts as assets showing benchmarking data and mash/blast correlation
Some renaming and cleaning

…trix is printed as well as two distance matrices

…istance matrix fil

saramonzon added 21 commits April 27, 2024 11:41

added mash blast correlation script

7878b04

adapted mash blast correlation script

8f8a80f

added requiremens for assets

b92e13f

a couple of fixes in mash_blast_correlation script

0656976

fix result df creation in mash blat correlation script

385897c

linting mash blast correlation script

4b06a60

fix typo in requirements.txt

4abdcad

renaming and cleaning main

77f3e47

rewriten hamming distance, tested and fixed bugs

0469523

renaming def in utils

0067084

rewritten filter_df function, now filtering both rows and columns, ma…

554e255

…trix is printed as well as two distance matrices

rename variable for clarity, add dtype to read_csv

25d07e7

clarified help messages, fixed default value for keeping a locus in d…

e465cfa

…istance matrix fil

removed missing pdb

e2e2416

fixed big fingers typo

a70d500

variable renaming and fixed bounds for condition

2d8af1e

minor modifications in graph for mash blast corr script

4816242

added filter with regex

c666e1d

added notebook for benchmarking analysis

4ba230d

added masking after filtering per row in df_filter

5edcc6d

black linting

b47351c

luissian approved these changes May 2, 2024

View reviewed changes

luissian merged commit 7e381ca into BU-ISCIII:develop May 2, 2024
3 checks passed

Provide feedback