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olp-cs/README.md

Created July 27, 2024 16:06
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[GEOParse] Non-breaking change compatible with pandas 1.3.0 and 2.2.2
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README.md

The notebooks in this Gist compare the following operations and demonstrate their equivalent outputs:

For pandas 1.3.0:

input_data.groupby(group_by_column).mean()[[expression_column]]

For pandas 1.3.0 and 2.2.2:

input_data.groupby(group_by_column).mean(numeric_only=True)[[expression_column]]

input_data.groupby(group_by_column)[[expression_column]].mean()
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check_pandas_1.3.0.ipynb
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check_pandas_2.2.2.ipynb
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pandas2_compatibility_input.csv
ID_REF VALUE LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal ID GB_ACC Gene_Desc Gene_Sym SPOT_ID SEQUENCE
0 1 -1.627476 0.1360 6.410000e-33 9130.0 215.00 1 U02079 nuclear factor of activated T-cells, cytoplasmic 2 Nfatc2 NaN ACCTGGATGACGCAGCCACTTCAGAAAGCTGGGTTGGGACAGAAAGGTATATAGAGAGAAAATTTTGGAA
1 2 0.141225 1.3400 1.000000e+00 41.4 57.20 2 NM_008154 G-protein coupled receptor 3 Gpr3 NaN CTGTACAATGCTCTCACTTACTACTCAGAGACAACGGTAACTCGGACTTATGTGATGCTGGCCTTGGTGT
2 3 0.182768 0.0519 4.330000e-04 5130.0 7810.00 3 AK015719 tropomodulin 2 Tmod2 NaN CACCAGGCTCAGTGCCTAGTATCGGCTTCACCTAGTGTGGTTACTCAGGGCACGCAGAGCTACAGAACAC
3 4 -0.393227 0.0608 1.020000e-10 4650.0 1880.00 4 AK003367 mitochondrial ribosomal protein L15 Mrpl15 NaN CAAGAAGTCTAGAAATTCTGTGCAAGCCTATTCCATTCTTTCTGCGGGGACAACCAATTCCGAAAAGAAT
4 5 -0.986599 0.1050 6.320000e-21 2910.0 301.00 5 BC003333 RIKEN cDNA 0610033I05 gene 0610033I05Rik NaN AGAACTGGGTGGCAGATATCCTAGAGTTTTGACCAACGTTCACAGCACACATATTGATCTTATAGGACCT
5 6 0.023881 0.1020 8.150000e-01 708.0 748.00 6 NM_008462 killer cell lectin-like receptor, subfamily A, member 2 Klra2 NaN TGAATTGAAGTTCCTTAAATCCCAACTTCAAAGAAACACATACTGGATTTCACTGACACATCATAAAAGC
6 7 -1.484182 0.1250 1.420000e-32 10200.0 336.00 7 NM_008029 FMS-like tyrosine kinase 4 Flt4 NaN GAGGTGCTGTGGGATGACCGCCGGGGCATGCGGGTGCCCACTCAACTGTTGCGCGATGCCCTGTACCTGC
7 8 -1.826136 0.4150 1.100000e-05 719.0 10.70 8 NM_054088 adiponutrin Adpn NaN GTCTGAGTTCCATTCCAAAGACGAAGTCGTGGATGCCCTGGTGTGTTCCTGCTTCATTCCCCTCTTCTCT
8 9 -1.034478 1.7800 1.000000e+00 96.2 8.89 9 NM_009750 nerve growth factor receptor (TNFRSF16) associated protein 1 Ngfrap1 NaN TACAGCTGAGAAATTGTCTACGCATCCTTATGGGGGAGCTGTCTAACCACCACGATCACCATGATGAATT
9 10 0.240589 0.3090 4.360000e-01 161.0 280.00 10 AB045323 DNA segment, Chr 8, ERATO Doi 594, expressed D8Ertd594e NaN GATTCAGACTCGGGAGGAGCATCCCAACCTCTCCTTGAGGATAAAGGCCTGAGCGATTGCCCTGGGGAGC
10 11 0.320937 0.3590 3.710000e-01 125.0 261.00 11 AK005789 dynein, cytoplasmic, light chain 2B Dncl2b NaN TGCAGAAGGCATTCCAATCCGAACAACCCTGGACAACTCCACAACGGTTCAGTATGCGGGTCTTCTCCAC
11 12 0.358304 2.0600 1.000000e+00 20.4 46.60 12 NM_010517 insulin-like growth factor binding protein 4 Igfbp4 NaN GGAGAAGCTGGCGCGCTGCCGCCCCCCCGTGGGTTGCGAGGAGTTGGTGCGGGAGCCAGGCTGCGGTTGT
12 13 -0.012207 0.3640 9.730000e-01 184.0 179.00 13 AK010722 RIKEN cDNA 2410075D05 gene 2410075D05Rik NaN GGAGCATCTGGAGTTCCGCTTACCGGAAATAAAGTCTTTACTATCGGTGATTGGAGGGCAGTTCACTAAC
13 14 -1.548040 0.1300 7.210000e-33 10200.0 290.00 14 AK003755 DNA segment, Chr 4, ERATO Doi 421, expressed D4Ertd421e NaN AGCAAAGAGATCTCCCTCAGTGTGCCCATAGGTGGCGGTGCGAGCTTGCGGTTATTGGCCAGTGACTTGC
14 15 0.007342 0.2980 9.800000e-01 221.0 225.00 15 BC003241 cleavage stimulation factor, 3\' pre-RNA, subunit 3 Cstf3 NaN AAATTAGAAGAAAATCCATATGACCTTGATGCTTGGAGCATTCTCATTCGAGAGGCACAGAATCAACCTA
15 16 -0.226702 0.9440 8.100000e-01 89.0 52.80 16 AK004937 RIKEN cDNA 1300007O09 gene 1300007O09Rik NaN CAGACACAAACCCTAGGTTGTATTGTAGACCGGAGTTTAAGCAGGCACTACCTGTCTGTCTTTTCTTCAT
16 17 -0.148402 0.8010 8.530000e-01 96.5 68.60 17 AK004524 unnamed protein product; hypothetical SOCS domain NaN NaN CGGAGCCCTGCGCGCCCAGAGCCCCCTCCCACCCGCTTCCACCAAGTGCATGGAGCCAACATCCGCATGG
17 18 -0.612220 0.1280 1.690000e-06 1120.0 273.00 18 NM_025999 RIKEN cDNA 2610110L04 gene 2610110L04Rik NaN TGCATTGATAAATGGAGTGATCGACACAGGAACTGCCCCATTTGTCGCCTACAGATGACTGGAGCAAATG
18 19 0.079690 0.0878 3.640000e-01 821.0 987.00 19 NaN NaN NaN -- CONTROL NaN
19 20 -0.084895 0.9380 9.280000e-01 76.8 63.20 20 NM_023120 guanine nucleotide binding protein (G protein), beta polypeptide 1-like Gnb1l NaN ACCGCCTGGTCCCAGATTTGTCCTCCGAGGCACACAGTCGGCTGTGAACACGCTCCATTTCTGCCCACCA
Raw
pandas2_compatibility_output.csv
GB_ACC VALUE
AB045323 0.240589
AK003367 -0.393227
AK003755 -1.54804
AK004524 -0.148402
AK004937 -0.226702
AK005789 0.320937
AK010722 -0.012207
AK015719 0.182768
BC003241 0.007342
BC003333 -0.986599
NM_008029 -1.484182
NM_008154 0.141225
NM_008462 0.023881
NM_009750 -1.034478
NM_010517 0.358304
NM_023120 -0.084895
NM_025999 -0.61222
NM_054088 -1.826136
U02079 -1.627476
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