From: Alex Gutteridge <alexg@...>
Date: 2007-07-09T17:03:44+09:00
Subject: Re: Text parser / reformatting

On 9 Jul 2007, at 16:42, Marc Hoeppner wrote:

> Hi everyone,
>
> I expect this is a rather trivial problem, but I just started using  
> ruby
> and am a bit stuck right now.
> Here is what I want to do:
>
> I have a text file, that contains information in the following format:
>
> KOG0003
>     At2g36170
>     At3g52590
>     CE15495
>     7295730
> KOG0004
>     Hs20476120
>     YIL148w
>     YKR094c
>     SPAC11G7.04
>
> Now, this has to go into a relational database. But right now this is
> not really a table. The desired output would look something like this:
>
> KOG0003 At2g36170
> KOG0003 At3g52590
> KOG0003 CE15495
> KOG0003 7295730
> KOG0004 Hs20476120
> KOG0004 YIL148w
> KOG0004 YKR094c
>
> Well, you get the picture. What I tried to do is to read the text  
> file,
> than look for lines that start with a blank and replace that blank  
> with
> the first word of the previous line, given that this line does in fact
> starts with a word (could also be selected by using KOG[0-9]*). I
> thought of storing the KOG[0-9] in a variable, but overall I cant make
> it work and have no real idea how to solve this. Any help would be
> greatly appreciated. Guess for an experienced user this is a three- 
> liner
> ._.
>
> Cheers,
>
> Marc
>
> -- 
> Posted via http://www.ruby-forum.com/.
>

Not a very fancy solution, but it seems to work for the data you  
posted. Also uses the pattern you suggested, storing the KOG*  
identifier in a variable (field1):

[alexg@powerbook]/Users/alexg/Desktop(7): cat test.rb
field1 = nil
IO.foreach(ARGV[0]) do |l|
   if l.match(/^(\S+)/)
     field1 = $1
   else
     puts "#{field1} #{l.strip}"
   end
end
[alexg@powerbook]/Users/alexg/Desktop(8): cat data.dat
KOG0003
     At2g36170
     At3g52590
     CE15495
     7295730
KOG0004
     Hs20476120
     YIL148w
     YKR094c
     SPAC11G7.04
[alexg@powerbook]/Users/alexg/Desktop(9): ruby test.rb data.dat
KOG0003 At2g36170
KOG0003 At3g52590
KOG0003 CE15495
KOG0003 7295730
KOG0004 Hs20476120
KOG0004 YIL148w
KOG0004 YKR094c
KOG0004 SPAC11G7.04

Alex Gutteridge

Bioinformatics Center
Kyoto University