Overview of SoS Notebook

Step 0: Two separate scripts under command line



In [1]:

    
import pandas as pd
data = pd.read_excel('DEG_list.xlsx')
data.to_csv('DEG_list.csv')



In [2]:

    
data = read.csv('DEG_list.csv')
pdf('result.pdf')
plot(data$log2FoldChange, data$stat)
dev.off()









    




pdf: 2

Step 1: book keeping



In [3]:

    
%run

python:
import pandas as pd
data = pd.read_excel('DEG_list.xlsx')
data.to_csv('DEG_list.csv')

R:
data = read.csv('DEG_list.csv')
pdf('result.pdf')
plot(data$log2FoldChange, data$stat)
dev.off()









    



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Step 2: indentation



In [4]:

    
python:
    import pandas as pd
    data = pd.read_excel('DEG_list.xlsx')
    data.to_csv('DEG_list.csv')

R:
    data = read.csv('DEG_list.csv')
    pdf('result.pdf')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



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Step 3: Separate into two steps



In [5]:

    
%run
[1]
python:
    import pandas as pd
    data = pd.read_excel('DEG_list.xlsx')
    data.to_csv('DEG_list.csv')

[2]
R:
    data = read.csv('DEG_list.csv')
    pdf('result.pdf')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



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Step 4: Add some comments



In [6]:

    
%run
[1 (convert data)]
# convert data
python:
    import pandas as pd
    data = pd.read_excel('DEG_list.xlsx')
    data.to_csv('DEG_list.csv')

[2 (data analysis)]
# data analysis
R:
    data = read.csv('DEG_list.csv')
    pdf('result.pdf')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



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Step 5: Add parameter (use another file)



In [7]:

    
%run --deg-list DEG_list.xlsx

parameter: deg_list = 'DEG_list.xslx'

[proj_1 (convert data)]
# convert data
python: expand=True
    import pandas as pd
    data = pd.read_excel('{deg_list}')
    data.to_csv('DEG_list.csv')

[proj_2 (data analysis)]
# data analysis
R: 
    data = read.csv('DEG_list.csv')
    pdf('result.pdf')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



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Step 6: add input and output (rerun to skip step)



In [8]:

    
%run --deg-list DEG_list.xlsx

parameter: deg_list = 'DEG_list.xslx'

[proj_1 (convert data)]
input: deg_list
output: 'DEG_list.csv'
# convert data
python: expand=True
    import pandas as pd
    data = pd.read_excel('{_input}')
    data.to_csv('{_output}')

[proj_2 (data analysis)]
output: 'result.pdf'
# data analysis
R: expand=True
    data = read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



INFO: convert data (index=0) is ignored due to saved signature






    



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More on SoS Notebook

Step 7: make file style



In [9]:

    
%run --deg-list DEG_list.csv

parameter: deg_list = 'DEG_list.xslx'

[convert: provides='{FILENAME}.csv']
input: f"{FILENAME}.xlsx"
# convert data
python: expand=True
    import pandas as pd
    data = pd.read_excel('{_input}')
    data.to_csv('{_output}')

[analysis (data analysis)]
input: deg_list
output: 'result.pdf'
# data analysis
R: expand=True
    data = read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



INFO: data analysis (index=0) is ignored due to saved signature

Step 8: task (sos status)



In [10]:

    
%run -v3 --deg-list DEG_list.csv -s force

parameter: deg_list = 'DEG_list.xslx'

[convert: provides='{FILENAME}.csv']
input: f"{FILENAME}.xlsx"
# convert data
python: expand=True
    import pandas as pd
    data = pd.read_excel('{_input}')
    data.to_csv('{_output}')

[analysis (data analysis)]
input: deg_list
output: 'result.pdf'
# data analysis
task:
R: expand=True
    data = read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()









    



DEBUG: Workflow analysis created with 1 sections: analysis_0
DEBUG: Input of step convert_None is set to Undertermined: name 'FILENAME' is not defined
DEBUG: Executing analysis_0: 
DEBUG: input:    [file_target('DEG_list.csv')]






    





                        
                         
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                        52 sec

Step 9: Remote task



In [ ]:

    
## This step cannot be executed without
## proper host definition
%run --deg-list DEG_list.csv -s force 

parameter: deg_list = 'DEG_list.xslx'

[convert: provides='{FILENAME}.csv']
input: f"{FILENAME}.xlsx"
# convert data
python: expand=True
    import pandas as pd
    data = pd.read_excel('{input}')
    data.to_csv('{output}')

[analysis (data analysis)]
input: deg_list
output: 'result.pdf'
# data analysis
task:
R: expand=True
    data = read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()



In [ ]: