add intiial code for making annotations object

preetisi committed Jun 16, 2022

get intron to splice site annotations from gene model

preetisi committed Jun 28, 2022

find unique exon-exon junctions from all sample files

preetisi committed Jun 30, 2022

full exon matches

preetisi committed Jun 30, 2022

sparse matrix initial code

preetisi committed Jul 6, 2022

updated gitignore, get the unique junctions from all the exon junctio… …

…n files

preetisi committed Jul 6, 2022

get all unique junctions of all samples and add them to a single data… …

…frame

calculate total junction counts by parsing sample files

divide the input sample files in chunk and multiprocess them in chunk… …

…s of 50

Merge branch 'master' of https://github.com/SalomonisLab/altanalyze3 … …

…into ps-merging_annotating_genecounts

intermittent code for sparse matrix

working sparse matrix from two samples

sparse matrix function

sparse matrix using dictionary of keys

dok_matrix to csr matrix

read multiple files from a directory

working version of multiprocessing

new main file

parse each file and make a sparse matrix

remove the chromosome guard

ignore the test data folder

read files using pandaframes

created a giant dictionary where key is junction coordinate and it's … …

…value is an object defining it's sample id and number of spliceevents

check if the junction already exists in the dictionary

get junction annotations from gene model

working version - got splice site annotations from gene model

imported the junctions from bam derived text file

get junction annotations

getting splice annotation from junction file and gene model file

add log statement

sparse matrix from giant dictionary

working version of making dok_matrix

indexing of dok_matrix fixed

sparse matrix printed as dense matrix for testing

old main

fix the way we are storing exon annotations, fix the if statements in… …

…side splice site annotations function

fix - junction coordinates should be added for all junction files

check if coordinate is in range for both positive and negative strand

ignore the tsv files

make a separate class for collecting the data

remove the dead code

added classes

memory efficent way for reading the junctions from gene model and cre… …

…ating annotations for junctions which exist in sample bed files

remove dead code

add print statements

initial commits for splice annotation

check if start and stop annotations are not None and then find the sp… …

…lice annotations resepectively

get all the exons for a given gene id

got the exons for candidate gene

working version of getting the start and stop annotations

splice annotations working

working version of splice site annotations

annotations writing to a txt file

correct annotations when both start and stop coordinates of a junctio… …

…n exists in gene model

working if else statements for checking if junction exists in the gen… …

…e model

fix if statement

short circuiting in if else fixed

start annotation getting annotated correctly when stop target tuple d… …

…oesn't exist in gene model

working annotations

negative and positive both strand working

exon id of stop coordinate should be first when strand is nrgative

U_ annotations coorected

getting coorect annotation whene splice sites are not in same gene

all annotations working correctly

remove unnecessary print statements

refactoring #1 - removing variables which are not needed

bug -fix - fixed the infinite loop while finding the annotation, refa… …

…ctoring#2'

benchmark with timeit without indexing junction files"

refactoring #3 - add logging statements, cleaner way of string concat… …

…enation,separate function for writing to annotation file to add async multiprocessing in future

benchmarking and adding multiprocessing

optimised gene model file reading - removed pandas, instead using pyt… …

…hon file system

normalize data types of junction file and gene model

fix data type issues

optimised when both start and stop are present - refactoring #4

refactoring #5 - reduced the number of if else statements

refatored splice site annotation function

reading junctions using pandas - for some reason it was faster than p… …

…ython file reading system

refactored the annotation function

sorting function

removed the old main.py, added output annotations file to docs folder

resolve conflict

preliminary attempt to sort junctions

remove dead code

close the pool processes