This is what the file actually looks like. All fileds are
separated by tabs
Gene Start Stop strand Product
HMU00010 1 1290 chromosomal
replication initiator protein
HMU00020 1448 2512 DNA polymerase III,
beta chain
HMU00030 2522 4840 DNA gyrase subunit B
HMU00040 4841 5083 putative membrane
protein
HMU00050 5080 5739 c putative periplasmic
C39-family peptidase
HMU00060 5739 6549 c putative inner
membrane protein (pseudogene)
HMU00070 6592 7353 c putative secreted
protein
HMU00080 7375 7617 c putative membrane
protein
HMU00090 8072 9076 c UDP-glucose
4-epimerase
----- Original Message -----
From: "Shawn H. Corey" <shawnhco...@gmail.com>
To: 98447...@student.ucc.ie
Cc: beginners@perl.org
Subject: Re: if loop problem
Date: Fri, 31 Jul 2009 09:39:08 -0400
>98447...@student.ucc.ie wrote:
>> Hi All,
>>
>> I am having a small problem with my if looops. I have
>> written a small script to parse a file I have
>>
>> input:
>>
>> HMU00030 2522 4840 DNA gyrase subunit
>> B HMU00040 4841 5083 putative membrane
>> protein HMU00050 5080 5739 c putative
>> periplasmic C39-family peptidase
>> HMU00060 5739 6549 c putative inner
>> membrane protein
>> Wrote a perl script to convert c in fourth column to -
>> and if not equal to see then +
>>
>
>use strict;
>use warnings;
>
>> while(<>){
>> ($Gene, $Start, $Stop, $strand, $Product) =
>> split(/\t/, $_);
>
> my ($Gene, $Start, $Stop, $strand, $Product) =
>split(/\t/, $_);
>
>> if ($strand eq "c"){
>> print "$Gene\t-\t$Start\t$Stop\t$Product\n";
>> }else{
>> print "$Gene\t+\t$Start\t$Stop\t$Product\n";
>> }
>> }
>>
>> unfortunatly output is either all + or all - ?
>> any ideas?
>>
>
>Check your data. The data you posted had 'c ', that is, a
>'c' followed by a space between the tabs.
>
>
>--
>Just my 0.00000002 million dollars worth,
> Shawn
>
>Programming is as much about organization and communication
>as it is about coding.
>
>My favourite four-letter word is "Done!"
>
>--
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>
>
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