Dobby is the heroic house-elf that automates SampleSheet generation from Google Sheets
To get help on how to use dobby
, use the command dobby -h
:
$ dobby -h
Usage: dobby <command>
Hi! Dobby is the heroic house-elf that automates SampleSheet generation
from Google Sheets. And, of course, Dobby is free.
Options:
-h, --help Show this message and exit.
Commands:
cherrypick Convert concentrations --> ECHO pick list
Dobby outputs to the following folders:
cherrypicked/ # Tidy tables of samples with enough concentration
concentration/ # Heatmap of concentration data
flagged/
1stpass_regression/ # If regression R < 0.98
2ndpass_blanks/ # If mean blanks < 0
3rdpass_samples/ # If number of samples passing QC < 50
repeat_flags/ # Samples that got flagged with more than one criteria
fluorescence/ # Heatmap of fluorescence data
non-cherrypicked/ # Tidy tables of all samples
regression/ # Regression plots of standards
You can "cherrypick" the best samples out of a 384-well plate whose
fluorescence is high enough using dobby cherrypick
:
$ dobby cherrypick -h
Usage: dobby cherrypick [OPTIONS] FILENAME PLATE_NAME MOUSE_ID
Transform plate of cDNA fluorescence to ECHO pick list
Parameters
----------
filename : str
Name of the cDNA fluorescence 384 well QC output plate_name mouse_id filetype standards_col blanks_col
standards plot output_folder
Returns -------
Options:
--filetype TEXT
--standards-col INTEGER
--blanks_col INTEGER
--standards TEXT
--plot
--output-folder TEXT
-h, --help Show this message and exit.
Here is an example usage of it:
$ dobby cherrypick testing/MAA000154.txt MAA000154 30_2_M --plot --output-folder test_output
MAA000154: Wrote regression plot to test_output/regression/MAA000154_regression_lines.pdf
MAA000154: Wrote fluorescence heatmap to test_output/fluorescence/MAA000154_fluorescence_heatmap.pdf
MAA000154: Wrote concentrations heatmap to test_output/concentrations/MAA000154_concentrations_heatmap.pdf
MAA000154 (30_2_M) has 249 cells passing Concentration QC
MAA000154: Wrote concentrations_cherrypicked_no_standards_or_blanks heatmap to test_output/concentrations_cherrypicked_no_standards_or_blanks/MAA000154_concentrations_cherrypicked_no_standards_or_blanks_heatmap.pdf
Wrote cherrypicked ECHO pick list to test_output/cherrypicked/MAA000154_echo.csv
Wrote non_cherrypicked ECHO pick list to test_output/non_cherrypicked/MAA000154_echo.csv
dobby aggregate --desired-concentration 0.3 ~/Google\ Drive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3\ Month/cherrypicked/*.csv --output-folder ~/Google\ Drive/MACA/cDNA\ Pick\ Lists/3_month/
Advanced usage: sort files by date, then aggregate:
$ ls -Str ~/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/*.csv | xargs dobby aggregate --desired-concentration 0.3 --output-folder ~/googledrive/MACA/cDNA\ Pick\ Lists/3_month/
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000937_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D041912_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00000.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D041914_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00001.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042193_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042479_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00002.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000400_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00003.csv
Wrote 3 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000424_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000452_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000510_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00004.csv
Wrote 3 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000531_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000538_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000550_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00005.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000554_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000559_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00006.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000578_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00007.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000586_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000587_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00008.csv
Wrote 3 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000593_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000599_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000611_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00009.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000612_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000776_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00010.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000871_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00011.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000909_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00012.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000923_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000928_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00013.csv
Wrote 3 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000932_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000935_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000940_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00014.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D041911_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00015.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042044_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042180_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00016.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042253_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00017.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042467_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042474_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00018.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/D042475_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000377_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00019.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000385_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000398_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00020.csv
Wrote 3 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000409_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000439_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000441_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00021.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000487_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00022.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000560_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000564_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00023.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000571_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000572_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00024.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000573_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000577_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00025.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000583_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000592_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00026.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000595_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000596_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00027.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000603_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00028.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000604_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000605_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00029.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000609_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000617_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00030.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000652_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00031.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000752_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000844_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00032.csv
Wrote 1 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000848_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00033.csv
Wrote 3 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000870_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000873_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000891_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00034.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000899_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000901_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00035.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000908_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000914_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00036.csv
Wrote 4 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000918_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000919_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000922_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000925_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00037.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000927_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000930_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00038.csv
Wrote 2 files (/home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000938_echo.csv, /home/dobby/googledrive/MACA/384W_QC/plate_reader/raw_plate_reader_output/3_Month/cherrypicked/MAA000944_echo.csv) to /home/dobby/googledrive/MACA/cDNA Pick Lists/3_month/echo_picklist_00039.csv
(0) files () didn't make it into a pick list :(