peterjc
[blastxml_to_tabular] Add an option to print Header of file
Hello
I have modified the python script and its XML file in order to be able to print (or not) a header for the tabular file.
Is it possible to merge this within the current branch ?
Fred
blastxml_to_tabular.py-addPrintHeaderOption.patch.txt blastxml_to_tabular.xml-addPrintHeaderOption.patch.txt
I think the ideal fix is #84 (only filed today, but that's been a wish list for years now).
Unfortunately while your proposal should work nicely with Galaxy which (in places) understands the # header line convention, this does not match how the NCBI does its own (optional) headers. Does this bother you?
Regarding the proposed command line API:
parser.add_option('-p', '--print', dest='pheader', default=None, help='print header of file (default to None')
Rather than -p 1 and --print 1 (taking a meaningless argument), this should be a switch (i.e. -p only, or --print only). However, name wise, I'd probably go for --header instead.
Hello
Unfortunately while your proposal should work nicely with Galaxy which (in places) understands the # header line convention, this does not match how the NCBI does its own (optional) headers. Does this bother
not at all.
Regarding the proposed command line API your proposal is much better indeed . I'm not (yet) fluent in python (neither in english !) and I've done something quick based on a copy/paste of the other options defined in the file !
Thank you for this quick reply. Your wrappers are great, and this point is far from being an issue.
Fred