Fix unlocalized peptide mods not adding

See merge request s184069/abundanceparser!1

# Conflicts:
#   main.py

Vishruth Mullapudi authored 5 years ago and Vishruth Mullapudi committed 5 years ago

fixed unlocalized modifications not being counted in fragment modification analysis by adding a field in the data indicating that the fragment posesses a modification

Vishruth Mullapudi authored 5 years ago and Vishruth Mullapudi committed 5 years ago

added test for multiple abundance columns
removed printing for debugging

added test for multiple abundance columns
removed printing for debugging

residue modification calculation completed

Vishruth Mullapudi authored 5 years ago and Vishruth Mullapudi committed 5 years ago

fized bug where localized data was getting extended with the ocntents of filetuple isntead of ahving the filetuple added to it

Vishruth Mullapudi authored 5 years ago and Vishruth Mullapudi committed 5 years ago

updated parse amster to work better with format of non-master parsing
progress on residue modification calculations

non-master protein alignment working with multiple files, stored localization column titles in dict instead of pointless list of dicts

cleaned up masterlocalization parsing to remove unnecessary insertion of tuples to the localization list instead of simply appending them

Vishruth Mullapudi authored 5 years ago and Vishruth Mullapudi committed 5 years ago

fixed a bug where the only the last protein sequence fie's sequences were contained in the list of the protein sequences due to the list being overwritten and not being appended to upon the ingestion of each fasta file

Vishruth Mullapudi authored 5 years ago and Vishruth Mullapudi committed 5 years ago

cleaned up csv input and protein sequence input

started master protein localization parsing

Signed-off-by: Vishruth Mullapudi <vmullapudi1@gmail.com>

Signed-off-by: Vishruth Mullapudi <vmullapudi1@gmail.com>

Signed-off-by: Vishruth Mullapudi <vmullapudi1@gmail.com>