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Help with editing string elements

 
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Top Forums UNIX for Dummies Questions & Answers Help with editing string elements
# 1  
Old 04-14-2011
Lightbulb Help with editing string elements
Hi All
I have a question.
I would like to edit some string characters by replacing with characters of choice located in another file. For example in sample file
Code:
>S5_SK1.chr01
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTT
CTCAACTTACCCTCCATTACCCTACCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCAC

excluding the first line beginning with ">" I would like to change string elements at position 10 which is N to T, at position 100 which is T to C and at position 157 which is an A to G in the above example based on information present in the following file:
Code:
chr01    10    T   
chr01    100   C    
chr01    157   G

So my expected output would be
Code:
>S5_SK1.chr01
NNNNNNNNNTNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTC
CTCAACTTACCCTCCATTACCCTACCTCCACTCGTTACCCTGTCCCATTCAACCATGCCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCAC

Can anyone suggest how I can do this, preferably using Perl as I'm learning that. I would like to perform this over multiple files and thus I'll really appreciate your input.
Hv a nice daySmilie
Cheers
# 2  
Old 04-14-2011
Try:
Code:
#!/usr/bin/perl
open I,"position_file";
@b=<I>;
%h=map {((split /\s+/)[1],(split /\s+/)[2]);} @b;
local $/;
open J,"main_file";
$_=<J>;
s/(>.*)//;
$n=$1;
s/\n//g;
@F=split //,$_;
for $i (keys %h){
  $F[$i-1]=$h{$i}
}
$_=join "", @F;
s/.{100}/$&\n/g;
print "$n\n";
print "$_\n";

Let me know if something needs explanation.
This User Gave Thanks to bartus11 For This Post:
pawannoel
# 3  
Old 04-14-2011
Code:
while read a a b
do
     sed "s/./$b/$a" infile >infile.tmp
     cat infile.tmp >infile
done <file2
rm infile.tmp

Where file2 is the file containing the
Code:
chr01 10 T  
chr01 100 C
...

stuff.
# 4  
Old 04-14-2011
@Bartus:
Hi Bartus I'm not getting any output with this apart from two blank lines !! Smilie
Any reason why that might be happening. My example main file is
Code:
>S5_SK1.chr01
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTT
CTCAACTTACCCTCCATTACCCTACCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCAC
CCACCGTTACCCTCCAATTACCCATATCCAACTCCACTGCCACTTACCCTGCCATTCCTCTACCATCCACCATCTGCTACTCACTGTACTGTTGTTCTAC

and position file is
Code:
chr01   62      C
chr01   63      A
chr01   70      G
chr01   80      C
chr01   100     A
chr01   200     T
chr01   300     G
chr01   400     C
chr01   550     A
chr01   599     A

Cheers and thanks for looking into my question
Hv a nice day Smilie
# 5  
Old 04-14-2011
Weird... It is working for me:
Code:
oracle@solaris:~/unix/dna$ cat file
>S5_SK1.chr01
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTT
CTCAACTTACCCTCCATTACCCTACCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCAC
CCACCGTTACCCTCCAATTACCCATATCCAACTCCACTGCCACTTACCCTGCCATTCCTCTACCATCCACCATCTGCTACTCACTGTACTGTTGTTCTAC

Code:
oracle@solaris:~/unix/dna$ cat pos
chr01   62      C
chr01   63      A
chr01   70      G
chr01   80      C
chr01   100     A
chr01   200     T
chr01   300     G
chr01   400     C
chr01   550     A
chr01   599     A

Code:
oracle@solaris:~/unix/dna$ ./a.pl
>S5_SK1.chr01
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCANNNNNNGNNNNNNNNNCNNNNNNNNNNNNNNNNNNNA
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAN
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTT
CTCAACTTACCCTCCATTACCCTACCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCAC
CCACCGTTACCCTCCAATTACCCATATCCAACTCCACTGCCACTTACCCTGCCATTCCTCTACCATCCACCATCTGCTACTCACTGTACTGTTGTTCTAC

Code:
oracle@solaris:~/unix/dna$ cat a.pl
#!/usr/bin/perl
open I,"pos";
@b=<I>;
%h=map {((split /\s+/)[1],(split /\s+/)[2]);} @b;
local $/;
open J,"file";
$_=<J>;
s/(>.*)//;
$n=$1;
s/\n//g;
@F=split //,$_;
for $i (keys %h){
  $F[$i-1]=$h{$i}
}
$_=join "", @F;
s/.{100}/$&\n/g;
print "$n\n";
print "$_\n";

This User Gave Thanks to bartus11 For This Post:
pawannoel
# 6  
Old 04-14-2011
Hi Bartus,
I understood why it was not workinig ... my file names were different from that in the script and so I changed it to
Code:
$ARGV[0] for position_file and $ARGV[1]

for main_file in the script and ran
Code:
./script.pl position_file main_file

and this worked Smilie
Cheers n hv a nice day ahead !!
Thanks

---------- Post updated at 11:46 AM ---------- Previous update was at 11:26 AM ----------

@Bartus:
Could you also explain the map part of the code the the use of Perl in built variables throughout the code? I'll appreciate that.
Cheers Smilie
# 7  
Old 04-14-2011
map function is used to create hash from the contents of @b array (which contains lines from postion_file). When map is executed, its code is run for each element of the @b array. When processing those elements, they are assigned into "$_" variable inside "map" block, so (split /\s+/)[1] and (split /\s+/)[2] operate on them, extracting second and third field (position and letter) from each line. Those two elements are then returned by map into %h hash, populating it with position as the key and the letter begin its value.

About second part of your question, which built-in variables do you have in mind?
This User Gave Thanks to bartus11 For This Post:
pawannoel
 
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