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AG-1147/AG-1148/AG-1098: Add tests for rna seq data and rna distribution data #80

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Aug 1, 2023
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AG-1147/AG-1148/AG-1098: Add tests for rna seq data and rna distribution data #80

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f3edbbe
AG-1098: split rna_distribution.py into separate files for rna diff e…
jaclynbeck-sage Jun 29, 2023
9ef8c86
Added data-driven tests for rnaseq_differential_expression transform
jaclynbeck-sage Jun 29, 2023
e26e735
Added data-driven test for rna_distribution_data
jaclynbeck-sage Jun 29, 2023
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6 changes: 4 additions & 2 deletions src/agoradatatools/etl/transform/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,11 @@
from agoradatatools.etl.transform.proteomics_distribution import (
create_proteomics_distribution_data,
)
from agoradatatools.etl.transform.rnaseq_differential_expression import (
transform_rnaseq_differential_expression,
)
from agoradatatools.etl.transform.rna_distribution import (
transform_rna_distribution_data,
transform_rna_seq_data,
)
from agoradatatools.etl.transform.team_info import transform_team_info

Expand All @@ -30,6 +32,6 @@
"transform_overall_scores",
"create_proteomics_distribution_data",
"transform_rna_distribution_data",
"transform_rna_seq_data",
"transform_rnaseq_differential_expression",
"transform_team_info",
]
46 changes: 2 additions & 44 deletions src/agoradatatools/etl/transform/rna_distribution.py
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Original file line number Diff line number Diff line change
@@ -1,52 +1,10 @@
import numpy as np


def transform_rna_seq_data(datasets: dict):
diff_exp_data = datasets["diff_exp_data"]

diff_exp_data["study"].replace(
to_replace={"MAYO": "MayoRNAseq", "MSSM": "MSBB"}, regex=True, inplace=True
)
diff_exp_data["sex"].replace(
to_replace={
"ALL": "males and females",
"FEMALE": "females only",
"MALE": "males only",
},
regex=True,
inplace=True,
)
diff_exp_data["model"].replace(
to_replace="\\.", value=" x ", regex=True, inplace=True
)
diff_exp_data["model"].replace(
to_replace={"Diagnosis": "AD Diagnosis"}, regex=True, inplace=True
)
diff_exp_data["fc"] = 2 ** diff_exp_data["logfc"]
diff_exp_data["model"] = diff_exp_data["model"] + " (" + diff_exp_data["sex"] + ")"

diff_exp_data = diff_exp_data[
[
"ensembl_gene_id",
"hgnc_symbol",
"logfc",
"fc",
"ci_l",
"ci_r",
"adj_p_val",
"tissue",
"study",
"model",
]
]

return diff_exp_data

from agoradatatools.etl import transform

def transform_rna_distribution_data(datasets: dict):
# "datasets" contains the unprocessed RNA-seq data, which needs to go
# through the same processing as before in order to use it here.
rna_df = transform_rna_seq_data(datasets)
rna_df = transform.transform_rnaseq_differential_expression(datasets)
rna_df = rna_df[["tissue", "model", "logfc"]]

rna_df = (
Expand Down
40 changes: 40 additions & 0 deletions src/agoradatatools/etl/transform/rnaseq_differential_expression.py
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@@ -0,0 +1,40 @@
def transform_rnaseq_differential_expression(datasets: dict):
diff_exp_data = datasets["diff_exp_data"]

diff_exp_data["study"].replace(
to_replace={"MAYO": "MayoRNAseq", "MSSM": "MSBB"}, regex=True, inplace=True
)
diff_exp_data["sex"].replace(
to_replace={
"ALL": "males and females",
"FEMALE": "females only",
"MALE": "males only",
},
regex=True,
inplace=True,
)
diff_exp_data["model"].replace(
to_replace="\\.", value=" x ", regex=True, inplace=True
)
diff_exp_data["model"].replace(
to_replace={"Diagnosis": "AD Diagnosis"}, regex=True, inplace=True
)
diff_exp_data["fc"] = 2 ** diff_exp_data["logfc"]
diff_exp_data["model"] = diff_exp_data["model"] + " (" + diff_exp_data["sex"] + ")"

diff_exp_data = diff_exp_data[
[
"ensembl_gene_id",
"hgnc_symbol",
"logfc",
"fc",
"ci_l",
"ci_r",
"adj_p_val",
"tissue",
"study",
"model",
]
]

return diff_exp_data
2 changes: 1 addition & 1 deletion src/agoradatatools/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ def apply_custom_transformations(datasets: dict, dataset_name: str, dataset_obj:
if dataset_name == "team_info":
return transform.transform_team_info(datasets=datasets)
if dataset_name == "rnaseq_differential_expression":
return transform.transform_rna_seq_data(datasets=datasets)
return transform.transform_rnaseq_differential_expression(datasets=datasets)
if dataset_name == "gene_info":
return transform.transform_gene_info(
datasets=datasets,
Expand Down
7 changes: 7 additions & 0 deletions ...test_assets/rna_distribution_data/input/test_rna_distribution_data_bad_input_keyerror.csv
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@@ -0,0 +1,7 @@
model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
,CBE,AD-CONTROL,ENSG00000228521,1.646715414,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
,CBE,AD-CONTROL,ENSG00000286872,-0.181247795,-0.341187573,-0.021308017,0.032732484,-2.226401902,0.026439738,0.06693269,lncRNA,15,NONE,AC024270.5,46.5131873,13422,ALL,MAYO
,CBE,AD-CONTROL,ENSG00000144228,0.080531879,-0.016465937,0.177529695,4.913442808,1.63093857,0.10355023,0.193939662,protein_coding,2,NONE,SPOPL,36.67609796,71747,ALL,MAYO
Diagnosis.AOD,,AD-CONTROL,ENSG00000005339,0.074072272,0.042805132,0.105339413,7.626719604,4.656313999,4.15E-06,8.32E-05,protein_coding,16,NONE,CREBBP,45.00523533,155673,ALL,MAYO
Diagnosis.AOD,,AD-CONTROL,ENSG00000188994,0.03375383,-0.010318552,0.077826212,6.703806497,1.501322866,0.133920382,0.239511453,protein_coding,6,NONE,ZNF292,37.67626491,113111,ALL,MAYO
Diagnosis.AOD,,AD-CONTROL,ENSG00000261823,-0.008434191,-0.077650231,0.060781849,-0.970547902,-0.239149259,0.811089637,0.873760793,lncRNA,15,NONE,AC084782.2,42.13615023,1704,ALL,MAYO
2 changes: 2 additions & 0 deletions ...est_assets/rna_distribution_data/input/test_rna_distribution_data_bad_input_typeerror.csv
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@@ -0,0 +1,2 @@
model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
Diagnosis,CBE,AD-CONTROL,ENSG00000228521,No change,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
26 changes: 26 additions & 0 deletions tests/test_assets/rna_distribution_data/input/test_rna_distribution_data_good_input.csv
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@@ -0,0 +1,26 @@
model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
Diagnosis,CBE,AD-CONTROL,ENSG00000228521,1.646715414,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
Diagnosis,CBE,AD-CONTROL,ENSG00000286872,-0.181247795,-0.341187573,-0.021308017,0.032732484,-2.226401902,0.026439738,0.06693269,lncRNA,15,NONE,AC024270.5,46.5131873,13422,ALL,MAYO
Diagnosis,CBE,AD-CONTROL,ENSG00000144228,0.080531879,-0.016465937,0.177529695,4.913442808,1.63093857,0.10355023,0.193939662,protein_coding,2,NONE,SPOPL,36.67609796,71747,ALL,MAYO
Diagnosis,CBE,AD-CONTROL,ENSG00000285778,0.011774265,-0.225427841,0.248976371,-1.286000104,0.097352193,0.922486354,0.950960873,lncRNA,1,NONE,AL591463.1,36.23399051,127971,ALL,MAYO
Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000005339,0.074072272,0.042805132,0.105339413,7.626719604,4.656313999,4.15E-06,8.32E-05,protein_coding,16,NONE,CREBBP,45.00523533,155673,ALL,MAYO
Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000188994,0.03375383,-0.010318552,0.077826212,6.703806497,1.501322866,0.133920382,0.239511453,protein_coding,6,NONE,ZNF292,37.67626491,113111,ALL,MAYO
Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000261823,-0.008434191,-0.077650231,0.060781849,-0.970547902,-0.239149259,0.811089637,0.873760793,lncRNA,15,NONE,AC084782.2,42.13615023,1704,ALL,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000146733,0.245221101,0.088916757,0.401525444,3.6245628,3.081227128,0.002180227,0.025429476,protein_coding,7,NONE,PSPH,46.3530108,40554,FEMALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000164574,0.111683536,-0.075953728,0.299320799,4.556619644,1.16706539,0.24377083,0.459714102,protein_coding,5,NONE,GALNT10,44.28655187,230255,FEMALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000105127,0.036793733,-0.059745776,0.133333242,4.795637019,0.751265208,0.452857433,0.660329327,protein_coding,19,NONE,AKAP8,53.23691982,26414,FEMALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000205790,0.347641938,0.137145533,0.558138342,-0.677376322,3.255063005,0.001212908,0.010745247,lncRNA,19,UP,DPP9-AS1,59.2620369,6667,MALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000171469,-0.147816242,-0.269059529,-0.026572954,3.644836924,-2.399058545,0.016813764,0.066411124,protein_coding,19,NONE,ZNF561,44.45249743,16557,MALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000064703,-0.055752044,-0.165988677,0.054484588,3.592526425,-0.996676453,0.319418656,0.497558937,protein_coding,1,NONE,DDX20,40.26340546,12756,MALE,MAYO
Diagnosis,FP,AD-CONTROL,ENSG00000260751,-0.247109844,-0.416792039,-0.077427649,0.47017593,-2.856419551,0.004377501,0.037095362,lncRNA,16,NONE,AC008870.2,43.65234375,1024,ALL,MSSM
Diagnosis,FP,AD-CONTROL,ENSG00000170017,0.116124024,0.013752868,0.218495179,7.605164653,2.220609241,0.026685651,0.111182878,protein_coding,3,NONE,ALCAM,35.28991581,209992,ALL,MSSM
Diagnosis,FP,AD-CONTROL,ENSG00000235290,-0.057859204,-0.252212735,0.136494327,-0.16909436,-0.584873994,0.558811376,0.712709557,unprocessed_pseudogene,6,NONE,HLA-W,53.26582278,1975,ALL,MSSM
Diagnosis,FP,AD-CONTROL,ENSG00000177728,0.017353424,-0.086789821,0.12149667,6.788782124,0.32609337,0.744427926,0.845969576,protein_coding,17,NONE,TMEM94,52.00188889,59294,ALL,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000172780,-0.434385421,-0.717838177,-0.150932665,0.396064873,-3.00527216,0.00271497,0.065139157,protein_coding,3,NONE,RAB43,50.78477564,35233,MALE,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000269054,-0.155588882,-0.396743565,0.0855658,0.942597545,-1.265404041,0.206045462,0.491878373,lncRNA,19,NONE,AC012313.6,56.27619238,5011,MALE,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000197497,0.079706407,-0.081429533,0.240842348,2.881636183,0.973898187,0.33048948,0.611179707,protein_coding,19,NONE,ZNF665,45.25955405,34174,MALE,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000155827,0.02916353,-0.045914974,0.104242034,5.680912284,0.768042101,0.442712225,0.699692125,protein_coding,9,NONE,RNF20,38.16967313,29492,MALE,MSSM
Diagnosis,ACC,AD-CONTROL,ENSG00000125841,-0.181579939,-0.256616609,-0.10654327,6.725621038,-4.743548393,2.22E-06,6.90E-05,protein_coding,20,NONE,NRSN2,51.93726221,12879,ALL,ROSMAP
Diagnosis,ACC,AD-CONTROL,ENSG00000135898,-0.074241909,-0.471057434,0.322573617,0.222262803,-0.366638152,0.713920945,0.827016898,protein_coding,2,NONE,GPR55,48.82695492,53749,ALL,ROSMAP
Diagnosis,ACC,AD-CONTROL,ENSG00000151834,-0.027222811,-0.121567916,0.067122295,6.530023004,-0.56550242,0.571784411,0.72424515,protein_coding,4,NONE,GABRA2,35.62900125,226804,ALL,ROSMAP
Diagnosis.AOD,ACC,AD-CONTROL,ENSG00000099365,-0.093331151,-0.124320202,-0.0623421,8.150447477,-5.901609746,4.10E-09,4.84E-08,protein_coding,16,NONE,STX1B,55.21208437,21383,ALL,ROSMAP
26 changes: 26 additions & 0 deletions tests/test_assets/rna_distribution_data/input/test_rna_distribution_data_missing_values.csv
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@@ -0,0 +1,26 @@
model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
,CBE,AD-CONTROL,ENSG00000228521,1.646715414,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
Diagnosis,CBE,AD-CONTROL,ENSG00000286872,-0.181247795,-0.341187573,-0.021308017,0.032732484,-2.226401902,0.026439738,0.06693269,lncRNA,15,NONE,AC024270.5,46.5131873,13422,ALL,MAYO
Diagnosis,CBE,AD-CONTROL,ENSG00000144228,0.080531879,-0.016465937,0.177529695,4.913442808,1.63093857,0.10355023,0.193939662,protein_coding,2,NONE,SPOPL,36.67609796,71747,ALL,MAYO
Diagnosis,CBE,AD-CONTROL,ENSG00000285778,0.011774265,-0.225427841,0.248976371,-1.286000104,0.097352193,0.922486354,0.950960873,lncRNA,1,NONE,AL591463.1,36.23399051,127971,ALL,MAYO
Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000005339,0.074072272,0.042805132,0.105339413,7.626719604,4.656313999,4.15E-06,8.32E-05,protein_coding,16,NONE,CREBBP,45.00523533,155673,ALL,MAYO
Diagnosis.AOD,,AD-CONTROL,ENSG00000188994,0.03375383,-0.010318552,0.077826212,6.703806497,1.501322866,0.133920382,0.239511453,protein_coding,6,NONE,ZNF292,37.67626491,113111,ALL,MAYO
Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000261823,-0.008434191,-0.077650231,0.060781849,-0.970547902,-0.239149259,0.811089637,0.873760793,lncRNA,15,NONE,AC084782.2,42.13615023,1704,ALL,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000146733,0.245221101,0.088916757,0.401525444,3.6245628,3.081227128,0.002180227,0.025429476,protein_coding,7,NONE,PSPH,46.3530108,40554,FEMALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000164574,0.111683536,-0.075953728,0.299320799,4.556619644,1.16706539,0.24377083,0.459714102,protein_coding,5,NONE,GALNT10,44.28655187,230255,FEMALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000105127,0.036793733,-0.059745776,0.133333242,4.795637019,0.751265208,0.452857433,0.660329327,protein_coding,19,NONE,AKAP8,53.23691982,26414,FEMALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000205790,0.347641938,0.137145533,0.558138342,-0.677376322,3.255063005,0.001212908,0.010745247,lncRNA,19,UP,DPP9-AS1,59.2620369,6667,MALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000171469,-0.147816242,-0.269059529,-0.026572954,3.644836924,-2.399058545,0.016813764,0.066411124,protein_coding,19,NONE,ZNF561,44.45249743,16557,MALE,MAYO
Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000064703,-0.055752044,-0.165988677,0.054484588,3.592526425,-0.996676453,0.319418656,0.497558937,protein_coding,1,NONE,DDX20,40.26340546,12756,MALE,MAYO
Diagnosis,FP,AD-CONTROL,ENSG00000260751,-0.247109844,-0.416792039,-0.077427649,0.47017593,-2.856419551,0.004377501,0.037095362,lncRNA,16,NONE,AC008870.2,43.65234375,1024,ALL,MSSM
Diagnosis,FP,AD-CONTROL,ENSG00000170017,,0.013752868,0.218495179,7.605164653,2.220609241,0.026685651,0.111182878,protein_coding,3,NONE,ALCAM,35.28991581,209992,ALL,MSSM
Diagnosis,FP,AD-CONTROL,ENSG00000235290,-0.057859204,-0.252212735,0.136494327,-0.16909436,-0.584873994,0.558811376,0.712709557,unprocessed_pseudogene,6,NONE,HLA-W,53.26582278,1975,ALL,MSSM
Diagnosis,FP,AD-CONTROL,ENSG00000177728,0.017353424,-0.086789821,0.12149667,6.788782124,0.32609337,0.744427926,0.845969576,protein_coding,17,NONE,TMEM94,52.00188889,59294,ALL,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000172780,,-0.717838177,-0.150932665,0.396064873,-3.00527216,0.00271497,0.065139157,protein_coding,3,NONE,RAB43,50.78477564,35233,MALE,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000269054,,-0.396743565,0.0855658,0.942597545,-1.265404041,0.206045462,0.491878373,lncRNA,19,NONE,AC012313.6,56.27619238,5011,MALE,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000197497,,-0.081429533,0.240842348,2.881636183,0.973898187,0.33048948,0.611179707,protein_coding,19,NONE,ZNF665,45.25955405,34174,MALE,MSSM
Diagnosis.Sex,FP,AD-CONTROL,ENSG00000155827,,-0.045914974,0.104242034,5.680912284,0.768042101,0.442712225,0.699692125,protein_coding,9,NONE,RNF20,38.16967313,29492,MALE,MSSM
Diagnosis,ACC,AD-CONTROL,ENSG00000125841,-0.181579939,-0.256616609,-0.10654327,6.725621038,-4.743548393,2.22E-06,6.90E-05,protein_coding,20,NONE,NRSN2,51.93726221,12879,ALL,ROSMAP
Diagnosis,ACC,AD-CONTROL,ENSG00000135898,-0.074241909,-0.471057434,0.322573617,0.222262803,-0.366638152,0.713920945,0.827016898,protein_coding,2,NONE,GPR55,48.82695492,53749,ALL,ROSMAP
Diagnosis,ACC,AD-CONTROL,ENSG00000151834,-0.027222811,-0.121567916,0.067122295,6.530023004,-0.56550242,0.571784411,0.72424515,protein_coding,4,NONE,GABRA2,35.62900125,226804,ALL,ROSMAP
Diagnosis.AOD,ACC,AD-CONTROL,ENSG00000099365,-0.093331151,-0.124320202,-0.0623421,8.150447477,-5.901609746,4.10E-09,4.84E-08,protein_coding,16,NONE,STX1B,55.21208437,21383,ALL,ROSMAP
74 changes: 74 additions & 0 deletions tests/test_assets/rna_distribution_data/output/rna_distribution_data_good_output.json
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[
{
"model": "AD Diagnosis (males and females)",
"tissue": "ACC",
"min": -0.2437,
"max": 0.065,
"first_quartile": -0.1279,
"median": -0.0742,
"third_quartile": -0.0507
},
{
"model": "AD Diagnosis x AOD (males and females)",
"tissue": "ACC",
"min": -0.0933,
"max": -0.0933,
"first_quartile": -0.0933,
"median": -0.0933,
"third_quartile": -0.0933
},
{
"model": "AD Diagnosis (males and females)",
"tissue": "CBE",
"min": -0.7993,
"max": 1.2349,
"first_quartile": -0.0365,
"median": 0.0462,
"third_quartile": 0.4721
},
{
"model": "AD Diagnosis x AOD (males and females)",
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74 changes: 74 additions & 0 deletions ...s/test_assets/rna_distribution_data/output/rna_distribution_data_missing_data_output.json
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2 changes: 2 additions & 0 deletions ...ts/rnaseq_differential_expression/input/test_rnaseq_differential_expression_bad_input.csv
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