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Merge pull request #108 from EdinburghGenomics/107_fix_generate_hamil…
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…ton_input_cst

Updated to make the csv dictoinary key the output well location and n…
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Timothee Cezard committed Oct 31, 2019
2 parents b672173 + 8153649 commit aac6e7b
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83 changes: 41 additions & 42 deletions scripts/generate_hamilton_input_make_cst.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ def get_reagent_barcodes(self):
for lot in reagent_lots:
reagent_barcodes[lot.reagent_kit.name] = lot.lot_number

#generate error if user has forgotten to assign the barcode in the step
# generate error if user has forgotten to assign the barcode in the step
for expected_reagent_name in expected_reagent_names:
if expected_reagent_name not in reagent_barcodes:
raise InvalidStepError(
Expand All @@ -77,14 +77,14 @@ def _generate_csv_dict(self):
output = outputs[0]

# LIMS outputs CST strip locations as numbers, convert to well positions used by Hamilton
hamilton_well_locations={'1:1':'A1',
'2:1':'B1',
'3:1':'C1',
'4:1':'D1',
'5:1':'E1',
'6:1':'F1',
'7:1':'G1',
'8:1':'H1'}
hamilton_well_locations = {'1:1': 'A1',
'2:1': 'B1',
'3:1': 'C1',
'4:1': 'D1',
'5:1': 'E1',
'6:1': 'F1',
'7:1': 'G1',
'8:1': 'H1'}

output_location = hamilton_well_locations[output.location[1]]
# obtain the list of artifacts that were used to make the pool
Expand All @@ -98,37 +98,37 @@ def _generate_csv_dict(self):

self.parent_container_set.add(parent_input_container)

# assemble each line of the Hamilton input file in the correct structure for the Hamilton
csv_line = [
parent_input_container,
parent_input_location,
self.process.udf['Library Volume (uL)'],
output.location[0].name,
output_location,
reagent_barcodes['EPX1'],
self.process.udf['EPX 1 (uL)'],
reagent_barcodes['EPX2'],
self.process.udf['EPX 2 (uL)'],
reagent_barcodes['EPX3'],
self.process.udf['EPX 3 (uL)'],
self.process.udf['EPX Master Mix (uL)'],
reagent_barcodes['NaOH'],
self.process.udf['NaOH (uL)'],
reagent_barcodes['TrisHCL'],
self.process.udf['TrisHCL (uL)'],
reagent_barcodes['PhiX'],
self.process.udf['PhiX (uL)']
]
# build a dictionary of the lines for the Hamilton input file with a key that facilitates
# the lines being by input container then column then row
csv_dict[parent_input_container + parent_artifact.location[1]] = csv_line
# assemble each line of the Hamilton input file in the correct structure for the Hamilton
csv_line = [
parent_input_container,
parent_input_location,
self.process.udf['Library Volume (uL)'],
output.location[0].name,
output_location,
reagent_barcodes['EPX1'],
self.process.udf['EPX 1 (uL)'],
reagent_barcodes['EPX2'],
self.process.udf['EPX 2 (uL)'],
reagent_barcodes['EPX3'],
self.process.udf['EPX 3 (uL)'],
self.process.udf['EPX Master Mix (uL)'],
reagent_barcodes['NaOH'],
self.process.udf['NaOH (uL)'],
reagent_barcodes['TrisHCL'],
self.process.udf['TrisHCL (uL)'],
reagent_barcodes['PhiX'],
self.process.udf['PhiX (uL)']
]
# build a dictionary of the lines for the Hamilton input file with the output well as the key
# cst strips have eight wells and are always loaded from A1 to H1
csv_dict[output_location] = csv_line

return csv_dict

def generate_csv_array(self):
"""
Generate the csv array from the implemented csv dictionary.
It sorts the csv lines by column (self.plate_columns) then row (self.plate_rows)
CST strips only have eight wells so the array is sorted by the well name i.e. A1,B1,C1,D1,E1,F1,G1,H1.
"""
csv_dict = self._generate_csv_dict()

Expand All @@ -139,17 +139,16 @@ def generate_csv_array(self):

counter = 0

# create list of parent containers
for column in self.plate_columns:
for row in self.plate_rows:

for container in sorted(self.parent_container_set):
for column in self.plate_columns:
for row in self.plate_rows:
if container + row + ":" + column in csv_dict.keys():
csv_rows.append(csv_dict[container + row + ":" + column])
counter += 1
if row + column in csv_dict.keys():
csv_rows.append(csv_dict[row + column])
counter += 1

if counter == 0:
raise InvalidStepError("No valid keys present in csv_dict. Key format must be container+row:column e.g. T1999P001A:1.")
raise InvalidStepError(
"No valid keys present in csv_dict. Key format must be container+row:column e.g. T1999P001A:1.")

return csv_rows

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12 changes: 6 additions & 6 deletions tests/test_generate_hamilton_input_make_cst.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,17 +49,17 @@ def test_generate_hamilton_input_make_cst(self):
expected_file = ['Input Container,Input Well,Library,Output Container,Output Well,EPX1 Barcode,EPX1,'
'EPX2 Barcode,EPX2,EPX3 Barcode,EPX3,EPX Master Mix,NaOH Barcode,NaOH,TrisHCL Barcode,'
'TrisHCL,PhiX Barcode,PhiX',
'container1,A1,10,container3,A1,LP9999999-EPX1,231,LP9999999-EPX2,33,LP9999999-EPX3,121,'
'35,LP9999999-NAOH,2.5,LP9999999-THCL,2.5,LP9999999-PHIX,1',
'container2,A1,10,container3,A1,LP9999999-EPX1,231,LP9999999-EPX2,33,LP9999999-EPX3,121,'
'35,LP9999999-NAOH,2.5,LP9999999-THCL,2.5,LP9999999-PHIX,1',
'container2,B1,10,container3,A1,LP9999999-EPX1,231,LP9999999-EPX2,33,LP9999999-EPX3,121,'
'35,LP9999999-NAOH,2.5,LP9999999-THCL,2.5,LP9999999-PHIX,1']
'35,LP9999999-NAOH,2.5,LP9999999-THCL,2.5,LP9999999-PHIX,1'
]

expected_md5s = "02e9ab963b32da5dbf1dee315eebc5cd"

expected_md5s = "7c4ca08a0aa89afc9ab8d093436d01aa"

actual_file = self.file_content('a_file_location-hamilton_input.csv')

actual_lims_md5s = self.stripped_md5('a_file_location-hamilton_input.csv')
print(actual_lims_md5s)
actual_shared_drive_md5s = self.stripped_md5(self.epp.shared_drive_file_path)

assert actual_file == expected_file
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