Running rpsblast on all files in directory, using perl

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

I am having a issue trying to run a local rpsblast on all the files in a specified directory. I believe it's a syntax issue. Here's what I have below.
system'rpsblast -i NC_017249.faa –d PFAM2/pfam -o file.out';
I have tried it with and out the 's, with "s and (). Still no luck, But if I copy/paste just the command into a command prompt it works no problem. Here is the error message below
rpsblast 2.2.24 ERROR: Arguments must start with '-' (the offending argument #3 was: 'ûd')

Comment on Running rpsblast on all files in directory, using perl

Replies are listed 'Best First'.
Re: Running rpsblast on all files in directory, using perl by erix (Prior) on Dec 20, 2012 at 17:44 UTC
Looks you managed to insert a strange character (that only looks like a dash) before the 'd' instead of a simple dash '-'. So this has really nothing to do with perl; it's just a copy-and-paste error. Try to make rpsblast run without perl first.	[reply]
Re^2: Running rpsblast on all files in directory, using perl by runrig (Abbot) on Dec 20, 2012 at 17:50 UTC
That's what happens when you copy from some auto-correcting MS app like Outlook, it changes a plain dash into an 'en dash'. E.g., according to the Unicode Sliderule, '–d PF' is: `Char 08211 \| U+2013 \| en dash Char 00100 \| U+64 \| small d Char 00032 \| U+20 \| space Char 00080 \| U+50 \| capital p Char 00070 \| U+46 \| capital f` [download]	[reply] [d/l]
Re: Running rpsblast on all files in directory, using perl by frozenwithjoy (Priest) on Dec 20, 2012 at 17:53 UTC
Given that your error msg mentions arguments starting with a dash and you precede argument `d` with an endash or emdash, I'd start by replacing it with a regular dash. Compare the following (not sure how they will turn out on your screen, but here are dash/endash/emdash): -d/–d/—d	[reply] [d/l]