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Posted by ericbareke (ericbareke), 26 November 2007
Hi,

I am trying to write a perl script which will download data from ftp://ftp.ensembl.org/pub/current_genbank/homo_sapiens/ to a specified local directory and once done uncompress them and copied to another specified directory.

But I can't do it.

There are 5 files ( but I need the 4 ones uncompressed):

Homo_sapiens.0.dat.gz                      
Homo_sapiens.1000.dat.gz            
Homo_sapiens.2000.dat.gz            
Homo_sapiens.3000.dat.gz


Thanks in advance.

Posted by deep (deep), 26 November 2007
Can suggest two ways.
Use shell commands under backticks in your perlscript
something like
`gunzip -dvfr <Infilename >outfilename or path to it`
or `zcat -v <Infilename >outfilename`;

or use system () within perl.

Regarding downloading the files. I think there is a module in Bioperl for that.

Posted by admin (Graham Ellis), 26 November 2007
Thanks for adding those thoughts, Deep.    I was actually wondering whether Eric was looking for specific help with the FTP or untar/unzip elements, or if the question was more along the lines of "please write my application for me".

Eric - can you fill us in a little more - let us know if Deep's answer provides what you need or if there are other isssues .... and is so, post up sample code, etc, so that we can tune our reply

Posted by ericbareke (ericbareke), 26 November 2007
Thanks for your help,

I think I am far of what I hoped, I did not want to use bash commands in my perl codes.

After a closer look to my codes, I found out how to solve the problem in a proper manner without using bash or shell commands.


Interesting your forum.





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