python toolkit to analyse, view and modify (mix) idat files.
Installation with python 3.6 did not work, installation through python 3.9 did, probably caused by some legacy stuff in the beartype library.
git clone https://github.com/yhoogstrate/idat-tools.git
virtualenv -p python3 .venv
source .venv/bin/activate
pip install .
idat-tools --version
Usage [idat-tools view]:
idat-tools view GSM6379997_203927450093_R01C01_Grn.idat
Results in:
# manifest: ''
# manifest (old style): ''
# unknown #1: [1][0][0][0]
# sample id: ''
# description: ''
# plate: ''
# well: ''
# unknown #2: ''
# run info:
# 1. [8/21/2019 3:16:12 PM] [Decoding] [CallsToUsed=2798107|CallsToUnused=1889|CallsToInvalid=49292] [AutoDecode] [2.6.2]
# 2. [6/5/2020 2:44:03 PM] [Scan] [sherlockID=N1065|ScannerID=N1065|Username=Illumina|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.4.8] [iScan Control Software] [3.4.8]
# 3. [6/5/2020 2:44:03 PM] [Register] [Algorithm=StandardGeneric] [iScan Control Software] [3.4.8]
# 4. [6/5/2020 2:44:03 PM] [Extract] [Algorithm=StandardWithBackground] [iScan Control Software] [3.4.8]
# 5. [8/21/2019 3:16:26 PM] [Decoding] [CallsToUsed=2860469|CallsToUnused=1764|CallsToInvalid=60031] [AutoDecode] [2.6.2]
# 6. [6/5/2020 2:44:24 PM] [Scan] [sherlockID=N1065|ScannerID=N1065|Username=Illumina|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.4.8] [iScan Control Software] [3.4.8]
# 7. [6/5/2020 2:44:24 PM] [Register] [Algorithm=StandardGeneric] [iScan Control Software] [3.4.8]
# 8. [6/5/2020 2:44:24 PM] [Extract] [Algorithm=StandardWithBackground] [iScan Control Software] [3.4.8]
# 9. [8/21/2019 3:16:18 PM] [Decoding] [CallsToUsed=2867167|CallsToUnused=1847|CallsToInvalid=65541] [AutoDecode] [2.6.2]
# 10. [6/5/2020 2:44:44 PM] [Scan] [sherlockID=N1065|ScannerID=N1065|Username=Illumina|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.4.8] [iScan Control Software] [3.4.8]
# 11. [6/5/2020 2:44:44 PM] [Register] [Algorithm=StandardGeneric] [iScan Control Software] [3.4.8]
# 12. [6/5/2020 2:44:44 PM] [Extract] [Algorithm=StandardWithBackground] [iScan Control Software] [3.4.8]
# 13. [8/21/2019 3:16:10 PM] [Decoding] [CallsToUsed=2862808|CallsToUnused=1695|CallsToInvalid=53309] [AutoDecode] [2.6.2]
# 14. [6/5/2020 2:45:05 PM] [Scan] [sherlockID=N1065|ScannerID=N1065|Username=Illumina|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.4.8] [iScan Control Software] [3.4.8]
# 15. [6/5/2020 2:45:05 PM] [Register] [Algorithm=StandardGeneric] [iScan Control Software] [3.4.8]
# 16. [6/5/2020 2:45:05 PM] [Extract] [Algorithm=StandardWithBackground] [iScan Control Software] [3.4.8]
# 17. [8/21/2019 3:16:45 PM] [Decoding] [CallsToUsed=2886279|CallsToUnused=1866|CallsToInvalid=65578] [AutoDecode] [2.6.2]
# 18. [6/5/2020 2:45:24 PM] [Scan] [sherlockID=N1065|ScannerID=N1065|Username=Illumina|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.4.8] [iScan Control Software] [3.4.8]
# 19. [6/5/2020 2:45:24 PM] [Register] [Algorithm=StandardGeneric] [iScan Control Software] [3.4.8]
# 20. [6/5/2020 2:45:24 PM] [Extract] [Algorithm=StandardWithBackground] [iScan Control Software] [3.4.8]
IDAT v3: 203927450093_R01C01 (R/G: 0, BeadChip 8x5)
probe_ids probe_std_devs probe_mean_intensities probe_n_beads probe_mid_block
0 1600101 436 7582 9 1600101
1 1600111 523 4757 14 1600111
2 1600115 554 4851 18 1600115
3 1600123 299 3165 9 1600123
4 1600131 152 173 15 1600131
... ... ... ... ... ...
1051810 99810958 504 2401 12 99810958
1051811 99810970 74 97 10 99810970
1051812 99810978 1030 7236 14 99810978
1051813 99810990 331 4191 8 99810990
1051814 99810992 585 4213 17 99810992
[1051815 rows x 5 columns]
Usage [idat-tools mix]:
idat-tools mix --help
Usage: idat-tools mix [OPTIONS] IDAT_FILE_REFERENCE IDAT_FILE_MIXED_IN
IDAT_FILE_OUTPUT
Options:
-r, --mix-ratio FLOAT RANGE Fraction of mixed-in file values to be mixed
into reference file. E.g. 0.25 results in 75%
of reference and 25% of mixed-in file.
[default: 0.5; 0<=x<=1]
--help Show this message and exit.