Beginner using a downloaded script

TattieSoup has asked for the wisdom of the Perl Monks concerning the following question:

Hello,

I have never used perl before but would like to analyse some data using a publically available perl script called ProxyGeneLD. (http://ki.se/ki/jsp/polopoly.jsp?d=26072&l=en)

The main command line in the software is this:

Usage: >Perl proxyGeneLD (qry) (rs) (P) (d) r2 5' 3' (qry)- file name that includes SNP list, output of genome-wide association study.

(rs) - column number containing rs numbers of SNPs (P) - column number of P-values

(d) - delimiter used in the (qry) file (Possible options are 'space', 'tab' and 'comma'.)

r2 - threshold of r2 that classifies two SNPs are so highly correlated to join proxy cluster (default is 0.8)

5' - 5' promoter region length that is included as the genic region (default is 1000bp)

3' - possible 3'UTR extension from reference transcript (default is 0bp)

As a complete beginner, I would appreciate it if someone could give me some guidance as to how to format the arguments in the command line - should they be inside the brackets as shown? Do they need to be separated by commas or spaces or something else? Should they be inside quotes?

If someone could give me some guidance on what this command line should look like with realistic example arguments I would really appreciate it.

Thanks.

Comment on Beginner using a downloaded script

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Re: Beginner using a downloaded script (argument notation shell invocation) by Anonymous Monk on Nov 14, 2013 at 14:21 UTC
should they be inside the brackets as shown? No, brackets mean optional, see Optional Arguments Notation ( Backus–Naur Form ), its one of the dumber conventions adopted for help documentation, I prefer actual to include actual examples of usage Do they need to be separated by commas or spaces or something else? Should they be inside quotes? If they contain spaces or other weird characters, then quoting should be done (easier than escaping), it all depends on your shell on windows under cmd.exe this might look like `perl preprocess2_LDfiles.pl "i am snpF file" iamgffile "i am path inc +luding pth file" pS-population-symbol perl preprocess2_LDfiles.pl "i am snpF file" iamgffile "i am path inc +luding pth file" pS-population-symbol th=.8` [download] I know nothing of this program, and I'm assuming that (snpF) means mandatory argument (href:/http://ki.se/ki/jsp/polopoly.jsp?d=26072&l=en explains that `[th=.8]` is optional argument) More tutorials/explanation/examples on shells Read more... (1209 Bytes)	[reply] [d/l] [select]
Re^2: Beginner using a downloaded script (argument notation shell invocation) by TattieSoup (Initiate) on Nov 14, 2013 at 19:12 UTC
Thanks, I have now got this working	[reply]