manipulating string

paola82 has asked for the wisdom of the Perl Monks concerning the following question:

I have a problem with bioperl sequence alignment files..but It can be reduced to a problem of how to manipulate string. I have this type of file...I'll paste below a pice of it

                     1                                                
+   50
Sequence/23-178       NDPRVAAYGE VDELNSWVGY TKSLINSHTQ VLSNELEEIQ QLLF
+DCGHDL 
2zhz:A/1-148          DDARIAAIGD VDELNSQIGV L--LAEPLPD DVRAALSAIQ HDLF
+DLGGEL 


                      51                                              
+   100
Sequence/23-178       ATPADDERHS FKFKQEQPTV WLEEKIDNYT QVVPAVKKHI LPGG
+TQLASA 
2zhz:A/1-148          CIPGHAAITD AHLARLDG-- WLA----HYN GQLPPLEEFI LPGG
+ARGAAL
[download]

if I want to identify in that sequence which letter is at position 15 for example of "Sequence" and at the same position of the 2zhz" how can I count, walk...trough the sequence? Could anyone help me...I know I must use bioperl mailing list, but I've tried...actually noone replied and there aren't bioperl site as good as this web site. sorry also for my english...I'm trying to learn at the same time..bioinformatic, english and perl as well :-)

Comment on manipulating string Download Code

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Re: manipulating string by arun_kom (Monk) on Sep 01, 2009 at 13:23 UTC
The method slice() in Bio::SimpleAlign probably does what you need. Check out the bioperl tutorial.	[reply]
Re: manipulating string by Utilitarian (Vicar) on Sep 01, 2009 at 13:20 UTC
Knowing nothing about Bioperl, you could take the following approach Iterate through the file `while (<$FILE_HANDLE>){` split each line on space. `@record=split(/ /,$_);` if it consists of two integers ignore if not join the record elements from 1 to $#record `join ('',@record[1..$#record])` concatenate the resulting string onto `$hash{$record[0]}` use substr to find the character at a specific index in each sequence `for my $sequence (keys (%hash))` See how far that takes you along the path and let us know if you're stuck, no need to apologise we like to help.	[reply] [d/l] [select]
Re: manipulating string by biohisham (Priest) on Sep 01, 2009 at 14:33 UTC
In addition to Utilitarian's advice I would only add, take a look at the tutorials for the string manipulation functions substr, index, rindex, the index and rindex allow you to get the first and last position of a particular amino acid in your sequence, using these functions is direct forward. Here are the links Index, rindex, substr, and In Italiano. Have a happy programming experience :) Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.	[reply] [d/l]