Skip to content

Commit

Permalink
added
Browse files Browse the repository at this point in the history
  • Loading branch information
@maxozo
maxozo committed Nov 17, 2023
1 parent aa30bb8 commit d77379c
Showing 1 changed file with 45 additions and 5 deletions.
50 changes: 45 additions & 5 deletions bin/concordance_calculations.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -702,9 +702,10 @@ def concordance_table_production(self,expected_vars_norm,cell_vars,cell1,donor_g
donors_contributing_to_Whithin_Cohort=[]

for donor in set(donor_assignments_table['donor_gt']):

expected_vars_norm_of_other_donor = all_donor_data[donor]

try:
expected_vars_norm_of_other_donor = all_donor_data[donor]
except:
continue
try:
donor_cohort = donor_cohorts[donor]
donor_vars = vars_per_donor_gt[donor]
Expand Down Expand Up @@ -767,6 +768,11 @@ def concordance_table_production(self,expected_vars_norm,cell_vars,cell1,donor_g

if not donor == donor_gt_match:
# We want to kow how many of these discordant site
if 'U937' in donor:
continue
if 'THP1' in donor:
continue

if donor_gt_match_cohort == donor_cohort:
coh = 'Whithin_Cohort'
if len(DonorDiscordant_Sites_that_are_atributed_to_other_donor)>0:
Expand Down Expand Up @@ -839,20 +845,41 @@ def concordance_table_production(self,expected_vars_norm,cell_vars,cell1,donor_g
cohort_specific_read_quant_string=""

Whithin_Cohort__total_number_of_potential_contaminent_reads=0
Whithin_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool=0
Out_of_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool=0
try:
Whithin_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool = len(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'].keys())
for k1 in total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'].keys():
Whithin_Cohort__total_number_of_potential_contaminent_reads+= max(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'][k1])
except:
_='Doesnt Exist'

Out_of_Cohort__total_number_of_potential_contaminent_reads=0
try:
Out_of_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool = len(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Out_of_Cohort'].keys())
for k1 in total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Out_of_Cohort'].keys():
Out_of_Cohort__total_number_of_potential_contaminent_reads+= max(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Out_of_Cohort'][k1])
except:
_='Doesnt Exist'


try:
Out_of_Cohort__sites = set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Out_of_Cohort'].keys())
Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool = set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Out_of_Cohort'].keys()) - set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'].keys())
except:
Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool = set()
Out_of_Cohort__sites = set()

Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool = total_reads_for_site,_,_ = self.read_extraction(Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool,expected_vars_norm,cell_vars_norm)

try:
Whithin_Cohort__sites = set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'].keys())
Whithin_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool = set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'].keys()) - set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Out_of_Cohort'].keys())
except:
Whithin_Cohort__sites = set()
Whithin_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool = set()

Total__discordant_sites_that_are_concordant_with_other_donors_in_pool = Whithin_Cohort__sites.union(Out_of_Cohort__sites)
# total_reads_for_site,discordant_reads_for_site,concordant_for_site = self.read_extraction(set(total_discordant_sites_that_are_concordant_with_other_donors_in_pool__cohortBreakdown['Whithin_Cohort'].keys()),expected_vars_norm_of_other_donor,cell_vars_norm_otherDonor)

# discordant_vars_in_pool_str = (";").join(discordant_vars_in_pool)
Expand Down Expand Up @@ -907,7 +934,14 @@ def concordance_table_production(self,expected_vars_norm,cell_vars,cell1,donor_g
'Whithin_Cohort__total_number_of_potential_contaminent_reads':Whithin_Cohort__total_number_of_potential_contaminent_reads, \
'Out_of_Cohort__total_number_of_potential_contaminent_reads':Out_of_Cohort__total_number_of_potential_contaminent_reads, \
'NrDonors_contributing_to_out_of_cohort':len(set(donors_contributing_to_out_of_cohort)), \
'NrDonors_contributing_to_Whithin_Cohort':len(set(donors_contributing_to_Whithin_Cohort))
'NrDonors_contributing_to_Whithin_Cohort':len(set(donors_contributing_to_Whithin_Cohort)), \

'Out_of_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool':Out_of_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool, \
'Whithin_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool':Whithin_Cohort__discordant_sites_that_are_concordant_with_other_donors_in_pool, \
'Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool':len(Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool), \
'Whithin_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool':len(Whithin_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool), \
'Total_Reads_for_Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool':Out_of_Cohort__unique_sites_discordant_sites_that_are_concordant_with_other_donors_in_pool, \
'Total__discordant_sites_that_are_concordant_with_other_donors_in_pool':len(Total__discordant_sites_that_are_concordant_with_other_donors_in_pool)
}, donor_table_of_concordances]


Expand Down Expand Up @@ -1294,12 +1328,18 @@ def donor_exclusive_sites(exclusive_don_variants2):


result = pd.DataFrame(cell_concordance_table).T

try:
site_identities = result[['Concordant_Site_Identities','Discordant_Site_Identities']]
result.drop(columns=['Concordant_Site_Identities','Discordant_Site_Identities'],inplace=True)
result.drop(columns=['Concordant_Site_Identities'],inplace=True)
site_identities.to_csv(f"site_identities_{outfile}",sep='\t')
except:
_='sample_hasnt_matched_any_gt --- most likely too little cells assigned'
try:
result.drop(columns=['Discordant_Site_Identities'],inplace=True)
except:
_='sample_hasnt_matched_any_gt --- most likely too little cells assigned'

result.to_csv(outfile,sep='\t')

print('Processing Done')

0 comments on commit d77379c

Please sign in to comment.