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media_compiler.py
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media_compiler.py
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import pandas as pd
from IPython.display import display
import matplotlib.pyplot as plt
import numpy as np
from pyDOE import lhs
import math
#Magic Numbers
min_volume = 5 #uL per well
max_volume = 1200 #uL per well
#Transfer Volume (Property of the Pipette)
#Might want to make a Pipette Class
min_transfer = 5 #uL
max_transfer = 180 #uL
#Plate Limits
#This should probably be cleaned up
dead_volume = 50 #uL
safety_factor = 2
DILUTION_SAFETY_FACTOR = 2
ideal_transfer_volume = 8 #uL
dilution_volume = ideal_transfer_volume
#Biomek Robot Object, Stores the State of the Robot and All plates that are on it.
class BioMek(object):
def __init__(self,deck_df):
self.deck_df = deck_df.loc[~deck_df['Target'],deck_df.columns != 'Target']
self.goal_df = deck_df.loc[ deck_df['Target'],deck_df.columns != 'Target']
#self.water_wells =
transfer_columns = ['srcpos','srcwell','destpos','destwell','vol']
self.transfer_df = pd.DataFrame(columns=transfer_columns)
def transfer(self, source_plate, source_well, dest_plate, dest_well, transfer_volume):
total_transfered = 0 #uL
#Check to see if there is enough volume for the transfer!
if transfer_volume > (self.deck_df.loc[(source_plate,source_well)]['Volume'] + dead_volume):
raise('Transfer Pulling Too Much Volume! {}'.format(transfer_volume))
#Add Transfer To Ledger
while total_transfered < transfer_volume:
if transfer_volume - total_transfered > max_transfer:
values = [source_plate,source_well,dest_plate,dest_well,max_transfer]
total_transfered += max_transfer
else:
values = [source_plate,source_well,dest_plate,dest_well,transfer_volume-total_transfered]
total_transfered += transfer_volume-total_transfered
self.transfer_df = self.transfer_df.append(dict(zip(self.transfer_df.columns,values)),ignore_index=True)
#Update Deck State
source_composition = self.deck_df.xs((source_plate,source_well))
transfer = source_composition*(transfer_volume/source_composition['Volume'])
self.deck_df.loc[(source_plate,source_well)] -= transfer
try:
self.deck_df.loc[(dest_plate ,dest_well )] += transfer
except:
columns = self.deck_df.reset_index().columns
data = [dest_plate,dest_well] + [0]*(len(columns) - 2)
new_well = pd.DataFrame(dict(zip(columns,data)),index=[0]).set_index(['Plate','Well']) + transfer
self.deck_df = self.deck_df.append(new_well)
def get_well_state(self,plate,well):
try:
return self.deck_df.loc[(dest_plate,dest_well)]
except:
columns = self.deck_df.reset_index().columns
data = [dest_plate,dest_well] + [0]*(len(columns) - 2)
new_well = pd.DataFrame(dict(zip(columns,data)),index=[0]).set_index(['Plate','Well'])
self.deck_df = self.deck_df.append(new_well)
return self.deck_df.loc[(dest_plate,dest_well)]
def transfer_water(self,dest_plate,dest_well,transfer_volume):
total_transfered = 0
while total_transfered < transfer_volume:
if transfer_volume - total_transfered > max_transfer:
water_plate, water_well = self.find_water(max_transfer)
self.transfer(water_plate,water_well,dest_plate,dest_well,max_transfer)
total_transfered += max_transfer
else:
water_plate, water_well = self.find_water(transfer_volume - total_transfered)
self.transfer(water_plate,water_well,dest_plate,dest_well,transfer_volume - total_transfered)
total_transfered += transfer_volume - total_transfered
def dilute(self,reagent_wells,solute,moles_needed,transfer_volume=ideal_transfer_volume):
'''Creates a Diluted Version of the Source Plate'''
#Find The Right Well
ENOUGH_VOLUME = reagent_wells['Volume'] > min_volume * safety_factor + transfer_volume
reagent_wells = reagent_wells.loc[ENOUGH_VOLUME]
reagent_wells['dilution_factor'] = reagent_wells[solute]/reagent_wells['Volume']
#Calculate Required transfer volume
#source = reagent_wells['dilution_factor'].idxmin()
#source = self.deck_df.loc[(source_plate,source_well)]
#source_well_moles = source[solute]
reagent_wells['dilution_volume'] = moles_needed*max_volume*reagent_wells['Volume']/(transfer_volume*reagent_wells[solute])
#display(reagent_wells)
reagent_wells = reagent_wells.loc[reagent_wells['dilution_volume'] < (reagent_wells['Volume'] - dead_volume)]
#display('after',reagent_wells)
if len(reagent_wells) == 0:
reagent=solute
print(solute)
REAGENT_WELL = (self.deck_df.loc[:,~biomek.deck_df.columns.isin([reagent,'Volume'])] == 0).all(1)
CONTAINS_REAGENT = (biomek.deck_df.loc[:,biomek.deck_df.columns == reagent] > 0).any(1)
reagent_wells = self.deck_df.loc[REAGENT_WELL & CONTAINS_REAGENT]
display(reagent_wells)
raise('Not Enough {}! Add More To Reagent Plate.'.format(solute))
source = reagent_wells['dilution_factor'].idxmin()
dilution_volume = max(min_volume,reagent_wells.loc[source]['dilution_volume'])
#display(reagent_wells)
#print('Dilution Performed!, Volume: {}'.format(dilution_volume))
#Check to see if dilution volume is above minimum volume
#if dilution_volume < min_volume:
# dilution_volume = min_volume
#Transfer into New Well
dilution_plate, dilution_well = self.allocate_well()
self.transfer(*source,dilution_plate,dilution_well,dilution_volume)
#Fill With Water
self.transfer_water(dilution_plate,dilution_well,max_volume - dilution_volume)
def allocate_well(self):
'''Allocate a New Well'''
plate = 'mixing_plate'
try:
well = len(self.deck_df.loc[plate])+1
except:
well = 1
if well > 96:
display(biomek.deck_df)
display(self.transfer_df)
raise('Too Many Wells: Implement New Plate Method')
return (plate,well)
def find_water(self,transfer_volume):
WATER_WELL = (self.deck_df.loc[:,~self.deck_df.columns.isin(['Volume'])] == 0).all(1) & (self.deck_df.loc[:,self.deck_df.columns == 'Volume'] > (transfer_volume+dead_volume)).any(1)
source = self.deck_df[WATER_WELL].iloc[0]
return source.name
def concentration_to_moles(df):
#Convert NaNs to Zeros
df = df.fillna(value=0)
#Convert Molar Concentrion to Moles
for column in df.loc[:,~df.columns.isin(['Volume','Target'])].columns:
df.loc[:,column] = df[column]*df['Volume']*1e-6
return df
def read_deckfile(deck_file):
deck_df = pd.read_csv(deck_file)
deck_df = deck_df.set_index(['Plate','Well'])
deck_df = concentration_to_moles(deck_df)
return deck_df
def generate_biomek_csvs(biomek):
#Generate 5 CSVs for BIOMEK
water_mix_df = biomek.transfer_df.loc[(biomek.transfer_df['destpos']=='mixing_plate') & (biomek.transfer_df['srcpos']=='water_plate')]
water_dest_df = biomek.transfer_df.loc[(biomek.transfer_df['destpos']=='dest_plate') & (biomek.transfer_df['srcpos']=='water_plate')]
mix_df = biomek.transfer_df.loc[(biomek.transfer_df['destpos']=='mixing_plate') & (biomek.transfer_df['srcpos']!='water_plate')]
src_df = biomek.transfer_df.loc[(biomek.transfer_df['destpos']=='dest_plate') & (biomek.transfer_df['srcpos']=='src_plate')]
dest_df = biomek.transfer_df.loc[(biomek.transfer_df['destpos']=='dest_plate') & (biomek.transfer_df['srcpos']=='mixing_plate')]
#line terminator required for csvs to be read by biomek software properly...
water_mix_df.to_csv('biomek_files/water_mix.csv',index=False,line_terminator='\r\n')
water_dest_df.to_csv('biomek_files/water_dest.csv',index=False,line_terminator='\r\n')
mix_df.to_csv('biomek_files/mix.csv',index=False,line_terminator='\r\n')
src_df.to_csv('biomek_files/src.csv',index=False,line_terminator='\r\n')
dest_df.to_csv('biomek_files/dest.csv',index=False,line_terminator='\r\n')
#Generate Tip Report
import math
print('')
print('Tips Needed By Subrutine')
operations = ['Adding Water To Mixing Plate (Done with 8 tips in method)','Adding Water to Destination Plate (Done with 8 Tips)','Diluting Stock Solutions','Adding Undilute Media To Dest','Mixing Final Media']
for df,op in zip([water_mix_df,water_dest_df,mix_df,src_df,dest_df],operations):
boxes = math.ceil(len(df)/96)
print('{}: {} Tips, {} Plates'.format(op,len(df),boxes))
total_tips = 16 + len(mix_df) + len(dest_df)
total_tips = len(biomek.transfer_df)
print('')
print('Overall Experiment Need')
print('Total Tips Needed:',total_tips)
print('Tip Plates Consumed:',math.ceil(total_tips/96))
def compile_media(deck_df):
biomek = BioMek(deck_df)
#display(biomek.goal_df)
#Iterate Through Destination Wells
for (dest_plate,dest_well),solution in biomek.goal_df.iterrows():
#print(dest_plate,dest_well)
#Find Solute & Moles Needed
for i,(reagent,moles) in enumerate(solution.loc[solution.index != 'Volume'].iteritems()):
while moles > 0:
#Get All Reagent Wells
REAGENT_WELL = (biomek.deck_df.loc[:,~biomek.deck_df.columns.isin([reagent,'Volume'])] == 0).all(1)
CONTAINS_REAGENT = (biomek.deck_df.loc[:,biomek.deck_df.columns == reagent] > 0).any(1)
reagent_wells = biomek.deck_df.loc[REAGENT_WELL & CONTAINS_REAGENT]
#See There Are Enough Moles in The Reagent Wells ON Deck from any Well
reagent_wells = reagent_wells.loc[reagent_wells[reagent] > moles]
if len(reagent_wells):
#Find Wells require above the minimum pipette volume
reagent_wells['volume_needed'] = reagent_wells['Volume']*(moles/reagent_wells[reagent])
ENOUGH_VOLUME = (reagent_wells['Volume'] - dead_volume > reagent_wells['volume_needed'])
source_wells = reagent_wells.loc[(reagent_wells['volume_needed'] > min_volume) & (reagent_wells[reagent] > moles) & ENOUGH_VOLUME]
#Find Wells With Enough Volume For Transfer
source_wells = source_wells.loc[source_wells['volume_needed'] < (source_wells['Volume'] - dead_volume)]
if len(source_wells):
#Get Least Dilute Well
source = source_wells['volume_needed'].idxmin()
transfer_volume = source_wells.loc[source]['volume_needed']
#Perform Transfer
biomek.transfer(*source,dest_plate,dest_well,transfer_volume)
break
else:
biomek.dilute(reagent_wells,reagent,moles,transfer_volume=ideal_transfer_volume)
else:
print(solute,moles)
display(reagent_wells)
display(biomek.transfer_df)
display(biomek.deck_df.loc['src_plate'])
raise('No Valid Well')
#Fill Remaining Volume with Water
transfer_volume = biomek.goal_df.loc[(dest_plate,dest_well)]['Volume'] - biomek.deck_df.loc[(dest_plate,dest_well)]['Volume']
biomek.transfer_water(dest_plate,dest_well,transfer_volume)
#Create CSVs Needed
generate_biomek_csvs(biomek)
def generate_initial_media(media_component_file,NUM_MEDIA=16,OVERLAY_VOLUME = 200,REAGENT_VOLUME = 1000,WELL_VOLUME = 1100,WATER_VOLUME = 1600,EXTRA_WELLS = {},OUTFILE='data/media.csv',DECKFILE='data/wells.csv',WATER_WELLS=96):
media_df = pd.read_csv(media_component_file)
#Create Source Plate
columns = ['Plate','Well'] + [c for c in media_df['Media Components']] + ['Volume','Target']
df = pd.DataFrame(columns=columns)
#Work in mM concentrations
well = 1
for i,component in media_df.iterrows():
if component['Media Components'] in EXTRA_WELLS:
for _ in range(EXTRA_WELLS[component['Media Components']]):
row = {'Plate':'src_plate',
'Well':well,
'Volume':REAGENT_VOLUME,
'Target':False,
component['Media Components']:component['Master Solution Concentration [M]']*1e3,
}
df = df.append(row, ignore_index=True)
well +=1
else:
row = {'Plate':'src_plate',
'Well':well,
'Volume':REAGENT_VOLUME,
'Target':False,
component['Media Components']:component['Master Solution Concentration [M]']*1e3,
}
df = df.append(row, ignore_index=True)
well +=1
df = df.fillna(0)
# Create DataFrame to Help Make Reagent Plate By Hand!
letters = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
well_df = df.loc[:,~df.columns.isin(['Target','Volume'])].melt(id_vars=['Plate','Well'])
well_df = well_df.loc[well_df['value']!=0].rename(columns={'variable':'Reagent'})#.set_index(['Plate','Well'])['Reagent'].to_frame()
well_df = well_df.rename(columns={'Well':'Well Number'})
#
well = lambda x: '{}{}'.format(letters[int((x-1)/12)],(x-1)%12 + 1)
well_df['Well'] = well_df['Well Number'].apply(well)
well_df = well_df[['Plate','Well','Well Number','Reagent']]
#display(well_df)
#Create Water Plate
for i in range(WATER_WELLS):
row = {'Plate':'water_plate',
'Well':i+1,
'Volume':WATER_VOLUME,
'Target':False,
}
df = df.append(row, ignore_index=True)
df = df.fillna(0)
n=len(media_df)
media_array = lhs(n,NUM_MEDIA).tolist()
m_df = media_df
media_molarity = [((m_df['Max Concentration [mM]'] - m_df['Min Concentration [mM]'])* m + m_df['Min Concentration [mM]']).tolist() for m in media_array]
#print(media_molarity)
media_data = media_molarity
#Create Robolector Plate
for i,media in enumerate(media_data):
base_well = (math.floor((i)/8)*24 + (i) % 8) + 1
for j in range(3):
row = ['dest_plate',base_well + 8*j] + media_data[i] + [WELL_VOLUME,True]
df = df.append(dict(zip(columns,row)),ignore_index=True)
#Sort DF Columns By Concentration
#sorted_components = media_df.sort_values('Min_Dilution_Factor')['Media Components']
sorted_components = media_df['Media Components']
column_reorder = ['Plate','Well'] + sorted_components.tolist() + ['Volume','Target']
df = df[column_reorder]
#Write out Initial Media Configuration
df.to_csv(OUTFILE,index=False)
well_df.to_csv(DECKFILE,index=False)
df = df.set_index(['Plate','Well'])
df = concentration_to_moles(df)
return df