need help from a new hand for perl

need help from a new hand for perl

am 18.08.2009 23:30:57 von Fei Shi

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Hi, Dear perl experts:

I am a new hand of perl. I use perl because I am trying to use a
package called "miRDeep".
I install the *activeperl 5.10 for windows*. Then I used the MS DOS to try
perl.

But there is an error coming out when I tried to run this command
their demo: "*perl auto_blast.pl 454_aligned.fa precursors. fa-b >
signatures*".

The error message is as follows:
*Copying subject file 'cp' is not recognized as an internal or external
command, operable program or batch file.
formatting subject file [NULL_Caption] ERROR: Could not open
blast_dir_temp/file_subject

* *Blasting query file against subject file
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make
database blast_dir_temp/file_subject.
[NULL_Caption] WARNING: bartel_100023_x1: readdb: wrong version of formatdb
was used to make database blast_dir_temp/file_subject.
Parsing blast output:
'cat' is not recognized as an internal or external command,
operable program or batch file.
'cat' is not recognized as an internal or external command,
operable program or batch file.
'cat' is not recognized as an internal or external command,
operable program or batch file.
'rm' is not recognized as an internal or external command,
operable program or batch file.
'rm' is not recognized as an internal or external command,
operable program or batch file.
*
But I think the perl code "*auto_blast.pl*" is tested maturely by the author
of the package so I am suspicious that there may be something wrong with my
system?
*The MS DOS is 5.1.2600 by windows XP. *I wonder if the above error message
due to this or other reasons? I really appreciate if someone can point me
out of this and give me a clue of the problem.

Thank you very much for your time.

Sincerely,
Fei

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Hi, Dear perl experts:

    =A0    I am a new hand of per=
l. I use perl because I am trying to use a package called " http://www.mdc-berlin.de/en/research/research_teams/systems_ biology_of_gene=
_regulatory_elements/projects/miRDeep/index.html">miRDeep
". I inst=
all the activeperl 5.10 for windows. Then I used the MS DOS to try p=
erl.


         But there is
an error coming out when I tried to run this command their demo: "p=
erl auto_blast.pl 454_aligned.fa precursors. fa-b > signatures
"=
..


The error message is as follows:
Copying subject file 'cp'=
; is not recognized as an internal or external command, operable program or=
batch file.
formatting subject file [NULL_Caption] ERROR: Could not op=
en blast_dir_temp/file_subject



Blasting query file against subject file
[NULL_Caption] WARNING: read=
db: wrong version of formatdb was used to make database blast_dir_temp/file=
_subject.
[NULL_Caption] WARNING: bartel_100023_x1: readdb: wrong versio=
n of formatdb was used to make database blast_dir_temp/file_subject.

Parsing blast output:
'cat' is not recognized as an internal or =
external command,
operable program or batch file.
'cat' is no=
t recognized as an internal or external command,

operable program or batch file.
'cat' is not recognized as an in=
ternal or external command,

operable program or batch file.
'rm' is not recognized as an int=
ernal or external command,

operable program or batch file.
'rm' is not recognized as an int=
ernal or external command,

operable program or batch file.

But I think the perl code "=
auto_blast.pl" is tested maturely by the author of the package =
so I am suspicious that there may be something wrong with my system?

The MS DOS is 5.1.2600 by windows XP. I wonder if the above error me=
ssage due to this or other reasons? I really appreciate if someone can poin=
t me out of this and give me a clue of the problem.

Thank you very m=
uch for your time.


Sincerely,
Fei


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Re: need help from a new hand for perl

am 19.08.2009 00:55:08 von jwkenne

On Aug 18, 2009, at 5:30 PM, Fei Shi wrote:

> Hi, Dear perl experts:
>
> I am a new hand of perl. I use perl because I am trying to
> use a package called "miRDeep". I install the activeperl 5.10 for
> windows. Then I used the MS DOS to try perl.
>
> But there is an error coming out when I tried to run this
> command their demo: "perl auto_blast.pl 454_aligned.fa precursors.
> fa-b > signatures".
>
> The error message is as follows:
> Copying subject file 'cp' is not recognized as an internal or
> external command, operable program or batch file.
> formatting subject file [NULL_Caption] ERROR: Could not open
> blast_dir_temp/file_subject
>
> Blasting query file against subject file
> [NULL_Caption] WARNING: readdb: wrong version of formatdb was used
> to make database blast_dir_temp/file_subject.
> [NULL_Caption] WARNING: bartel_100023_x1: readdb: wrong version of
> formatdb was used to make database blast_dir_temp/file_subject.
> Parsing blast output:
> 'cat' is not recognized as an internal or external command,
> operable program or batch file.
> 'cat' is not recognized as an internal or external command,
> operable program or batch file.
> 'cat' is not recognized as an internal or external command,
> operable program or batch file.
> 'rm' is not recognized as an internal or external command,
> operable program or batch file.
> 'rm' is not recognized as an internal or external command,
> operable program or batch file.
>
> But I think the perl code "auto_blast.pl" is tested maturely by the
> author of the package so I am suspicious that there may be something
> wrong with my system?
> The MS DOS is 5.1.2600 by windows XP. I wonder if the above error
> message due to this or other reasons? I really appreciate if someone
> can point me out of this and give me a clue of the problem.

This is not a pure Perl program, but a mixed Perl-and-Unix program.

--
John W Kennedy
Having switched to a Mac in disgust at Microsoft's combination of
incompetence and criminality.

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Re: need help from a new hand for perl

am 19.08.2009 02:58:15 von Bill Luebkert

John W Kennedy wrote:
>
> This is not a pure Perl program, but a mixed Perl-and-Unix program.

I think what he means to say is that there are embedded shell commands
intended for a UNIX platform (something that you would normally want to
avoid when writing a script for portability). Check for 'system' and
'open' pipe types of commands and either replace them with equivalent
code to do the same thing or install the appropriate Windoze versions
of the UNIX utilities that are being called. You should be able to
find native Windoze versions of cp/cat/rm etc or maybe try Cygwin
emulator.
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