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Running rpsblast on all files in directory, using perl

by MoniqueLT (Initiate)
on Dec 20, 2012 at 17:26 UTC ( #1009765=perlquestion: print w/replies, xml ) Need Help??
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: 'd')
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Re: Running rpsblast on all files in directory, using perl
by erix (Parson) 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.

      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
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

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