Re: need help from a new hand for perl

[Fei Shi]

Hi, All:
Thank you for all your inputs. They really help me a lot~~[?]
I downloaded the package "UnxUtils" and put my perl program under its "bin"
folder. After I changed the windows system "path" variable, I can run the
perl in the DOS system.

Only when I run the code below I have a little problem:
*cat ids_overlap_* | sort -u > "a file name"*

I have 3 files named as *ids_overlap_*(21Us/coding/ram)*. The error message
is:
*The system cannot find the file specified.
cat.exe: write error : invalid argument*

I wonder there is more than one version of "cat.exe or sort.exe" or the
calling code (_*?) is not right?
Again, thanks for all your inputs.
Have a nice day!
Fei

On Wed, Aug 19, 2009 at 10:20 AM, Daniel Bara <
daniel.b...@predictionlabs.com> wrote:

> Hi Fei,
> I had the same problem some time ago.
> I solved it with tools from the following resource.
> http://www.math.utah.edu/~beebe/gnu-on-windows.html<http://www.math.utah.edu/%7Ebeebe/gnu-on-windows.html>
> Many DOS commands are different in UNIX. Like dir / ls or del rm.
> The other issue you will have to consider when modifying the script is how
> you move/direct to directories.
> I do not remember exactly but in some cases in windows // were necessary.
>
> I finally moved to Mac
>
> Hope it helps.
> *
> *
> Daniel
>
>
> On Aug 18, 2009, at 5:39 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<http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html>".
> 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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>
>
>
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need help from a new hand for perl

[Fei Shi]

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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