tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

changed aa_prop_water to 3 categ according to KD, updated ref dict

Browse source
This commit is contained in:
Tanushree Tunstall 2021-06-14 13:22:56 +01:00
parent 81ab3fe5ba
commit 57e4d8cd1e
2 changed files with 11 additions and 7 deletions
Download patch file Download diff file Expand all files Collapse all files

8
scripts/mut_electrostatic_changes.py
View file

@ -5,13 +5,15 @@ Created on Tue Aug 6 12:56:03 2019
@author: tanu @author: tanu
''' '''
# FIXME: import dirs.py to get the basic dir paths available # FIXME: import dirs.py to get the basic dir paths available
#======================================================================= #=======================================================================
# TASK: calculate how many mutations result in # TASK: calculate how many mutations result in
# electrostatic changes wrt wt # electrostatic changes wrt wt
# Input: merged_df3 # Input: mCSM-normalised file or any file containing one-letter aa code
# of wt and mut
# Note: this can be easily modified into 3-letter code
# TODO: turn to a function
# Output: mut_elec_changes_results.txt # Output: mut_elec_changes_results.txt
#======================================================================= #=======================================================================
@ -215,4 +217,4 @@ print('Total no. of mutations: ', total_muts
, '\nTotal no. of unchanged muts: ', no_change_muts.mut_count.sum() , '\nTotal no. of unchanged muts: ', no_change_muts.mut_count.sum()
, '\n=======================================================') , '\n=======================================================')
#%% end of script #%% end of script
#======================================================================= #=======================================================================

10
scripts/reference_dict.py
View file

@ -132,9 +132,11 @@ qualities_taylor = { ('R', 'H', 'K'): 'Basic'
, ('C', 'G', 'P'): 'Special' , ('C', 'G', 'P'): 'Special'
} }
# binary classification: hydrophilic or hydrophobic # ternary classification: hydrophobic --> neutral --> hydrophilic (KD scale)
qualities_water = { ('D', 'E', 'N', 'P', 'Q', 'R', 'S'): 'hydrophilic' #http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html
, ('A', 'C', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'T', 'V', 'W', 'X', 'Y'): 'hydrophobic' qualities_water = { ('I','V','L','F','C','M','A','W'): 'hydrophobic'
, ('G','T','S','Y','P','H'): 'neutral'
, ('N','D','Q','E','K','R'): 'hydrophilic'
} }
# polarity: no overlap # polarity: no overlap
@ -232,4 +234,4 @@ for k, v in oneletter_aa_dict.items():
# COMMENT:VOILA! two different keytypes set for dicts containinga all # COMMENT:VOILA! two different keytypes set for dicts containinga all
# associated aa properties # associated aa properties
#============================================================================== #==============================================================================
#%% end of script #%% end of script