[Bioperl-l] outfile question mark

Jordi Durban jordi.durban at gmail.com
Thu Jan 26 06:34:58 EST 2012


Thanks Frank! I knew the meaning of chomp but I didn't think that it was
the reason to include a question mark in the outfile.
The bioperl mail list has been useful for an non-wise perl user at least!!
Oh! I want to thank Liam too for its so helpul advice:
*I think you need to do your own homework...*

2012/1/26 Frank Schwach <fs5 at sanger.ac.uk>

> try
>
> chomp $line;
>
> after my $line =<STDIN>;
> at the moment you are creating a filename with a new-line in it
>
> Hope that helps
>
> Frank
>
>
>
>
> On 26/01/12 10:52, Jordi Durban wrote:
>
>> Hi all!
>> I'm trying to parse a a balstxml file using a homemade script. When I run
>> the script the output file has a question mark and I don't know how to
>> avoid it as it's really painful to deal whit a unix command line.
>> Has anyone idea what I'm doing wrong??
>> That's what I used to try:
>> *
>> print "Waiting for a query name...\n";
>> my $line =<STDIN>;
>> open OUTFILE , ">".$line."-UTR.txt" or die "can't open outfile\n";
>> my $gb = Bio::DB::GenBank->new();
>>     print "Waiting for reference id...\n";
>>     my $gi =<STDIN>;
>>     chomp($gi);*
>>
>>
>> And I get a $file?-UTR.txt file.
>> Thanks a lot!
>>
>
>
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-- 
Jordi


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