[Bioperl-l] render_blast problem

Peter biopython at maubp.freeserve.co.uk
Tue Nov 3 10:45:37 EST 2009


On Tue, Nov 3, 2009 at 3:14 PM, Kie Kyon Huang <kiekyon.huang at gmail.com> wrote:
> Hi,
>
> I was trying to follow the HOWTO:Graphics at
> http://www.bioperl.org/wiki/HOWTO:Graphics
>
> When running the command line in cygwin
>
> $ perl render_blast1.pl data1.txt | display -
>
> I get the following error line,
>
> bash: display: command not found

That makes sense on Windows, since display is a Unix
command line tool.

> I also tried
>
> $ perl render_blast1.pl data1.txt > data1.png

Based on the wiki, I think that ought to have worked.

> however, I was unable to open the data1.png file using Microsoft
> Office Picture Manager or windows Photo Gallery

Did you do this step?:
>> Important!  If you are on a Windows platform, you need to put
>> STDOUT into binary mode so that the PNG file does not go
>> through Window's carriage return/linefeed transformations.
>> Before the final print statement, put the statement
>> binmode(STDOUT). This advice also applies to certain older
>> versions of RedHat, which ship with a patched (and possibly
>> broken) version of Perl.

(BioPerl devs - couldn't that be added to the default
render_blast1.pl script with an if statement checking for
Windows?)

Peter


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