Processing of empty args with required parameters AND help=true for one of the declared parameters


If you are using JCommander to parse your commander, you may encounter the situations shown below:

You have an option that is required. For example:

@Parameter(names = { "-i", "--input-file"}, description = "Input file [.bed]", required = true)
private String input;
If you run your program without args (empty args) using SortBedErr.java, you will get the error message shown below:

Exception in thread "main" com.beust.jcommander.ParameterException: The following option is required: -i, --input-file 
 at com.beust.jcommander.JCommander.validateOptions(JCommander.java:321)
 at com.beust.jcommander.JCommander.parse(JCommander.java:283)
 at com.beust.jcommander.JCommander.parse(JCommander.java:265)
 at com.readbio.smRNACluster.bedtools.SortBed.main(SortBed.java:22)

To sovle this problem, you can catch ParameterException when the args is empty and print usage using usage() method. You can look into SortBed.java and get the detailed codes.
If there is no args, the output will be:
 The following option is required: -i, --input-file 

Usage: <main class> [options]
  Options:
    -h, -help, --help
       
       Default: false
  * -i, --input-file
       Input file [.bed]
    -o, --output
       Output file

References:
https://groups.google.com/forum/#!topic/jcommander/Um6Q8aaIrv8
https://github.com/cbeust/jcommander/issues/149
http://jcommander.org/


Comments

Post a Comment

Popular posts from this blog

gspread error:gspread.exceptions.SpreadsheetNotFound

Error message: Traceback (most recent call last):   File "read_google_sheet.py", line 20, in <module>     wks = gc.open_by_key("1jUJOlICOH6VnyuALdU2VAc_Ci_ZVwdW-xc5kr_qkJHY")   File "/usr/lib/python2.7/site-packages/gspread/client.py", line 113, in open_by_key     raise SpreadsheetNotFound gspread.exceptions.SpreadsheetNotFound Solved : In the json file, there is a "client_email". You need to share your file with this email. 
Read more

P and q values in RNA Seq

The q-value is an adjusted p-value, taking in to account the false discovery rate (FDR). Applying a FDR becomes necessary when we're measuring thousands of variables (e.g. gene expression levels) from a small sample set (e.g. a couple of individuals). A p-value of 0.05 implies that we are willing to accept that 5% of all tests will be false positives. An FDR-adjusted p-value (aka a q-value) of 0.05 implies that we are willing to accept that 5% of the tests found to be statistically significant (e.g. by p-value) will be false positives. Such an adjustment is necessary when we're making multiple tests on the same sample. See, for example, http://www.totallab.com/products/samespots/support/faq/pq-values.aspx. -HomeBrew What are p-values? The object of differential 2D expression analysis is to find those spots which show expression difference between groups, thereby signifying that they may be involved in some biological process of interest to the researcher. Due to chance, the...
Read more

Update the TOC (table of content) of MS Word .docx documents with Python

Here is a snippet to update the TOC of a word 2013 .docx document which includes only one table of content (e.g. just TOC of headings, no TOC of figures etc.). If the script  update_toc.py  is run from the command promt (windows 10, command promt not "running as admin") using  python update_toc.py  the system installation of python opens the file  doc_with_toc.docx  in the same directory, updates the TOC (in my case the headings) and saves the changes into the same file. The document may not be opened in another instance of Word 2013 and may not be write-protected. Be aware of that this script does  not the same as selecting the whole document content and pressing the F9 key . Content of  update_toc.py : import win32com . client import inspect , os def update_toc ( docx_file ): word = win32com . client . DispatchEx ( "Word.Application" ) doc = word . Documents . Open ( docx_file ) doc . TablesOfContents ( 1 ). Update () ...
Read more