-
Notifications
You must be signed in to change notification settings - Fork 1
/
README.txt
executable file
·62 lines (52 loc) · 2.34 KB
/
README.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
20180820
Notes on using questionaire.py, goal is to quickly assess NMJ expression patterns
-modified list_figures.py script to only print 'zegami2' files
-questionaire.py script has sys arguments, path/to/questions, path/to/outputdir, and path/to/images/*.jpg
-modified question file in data/figures/question to have 3 questions
-so I get it to run, the GUI opens with the correct questions, but none of the buttons seem to work
Notes on OMERO_Figure scoring script
-environment is setup on ssh bioc1301@bioch2125
20181013
Using questionaire.py to quickly analyse glia expression
2111855/Lasp CPTI002905 appears to be not expressed in NMJ
Write MK's code to find disease associations in the collection
20181015
Cleaning up the code for generating Zegami databases
-list-figures.py find all of the figures in Omero labelled Zegami and parse the filenames into a .csv file
just as the figure2zegami.py script does
TO DO:
-write code to merge other datasets to the zegami text file
-Davis lab sequencing data
-Other sources
-flymine output
-smFISH screen annotations
KNOWN ISSUES:
-zegami.csv has to be cleaned up as follows
-remove Maria's data and others that are mis-labelled
-remove template data
-remove hyphens from CPTI ID numbers
-several typos in figure_name (CPTI numbers) that make it difficult to correlate
SUMMARY OF WORKFLOW TO BUILD ZEGAMI COLLECTION
-begin OMERO session
-make login from ../DavidGUI/ directory
-generate zegami.csv file from OMERO.Figure names that include Zegami
-list-figures.py
-download figures as json files
-download-figures.py
-requires arguments for outdir path and metadata(zegami.csv) path
-will have to delete first row because the code is looking integer values
-convert json files to jpg for the scoring app and png for Zegami
-figure-json2jpeg.py
-requires arguments for outdir path and metadata(zegami.csv) path
-convert jpg files to png
-expand zegami.csv file with other datasets
-run runFlymineQueries_zegami.py #needs Py2 because of some dictionary nonsense
-export PATH="/usr/people/bioc1301/miniconda3/bin:$PATH"
-source activate py27
SUMMARY OF WORKFLOW TO USE SCORING APP
-Generate image files (.jpgs) and ID table using the Zegami workflow above
-Run questionnaire.py script
-arguments
-questions path
-answers dir
-image path