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Help with finding matching position on strings

 
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Top Forums UNIX for Dummies Questions & Answers Help with finding matching position on strings
# 8  
Old 03-23-2011
Hi Corona - nice code, but Pawan needs these lines concatenated, since this is DNA. Meaning, it is actually one long SINGLE string of information, he just broke it into 3 lines. So, if "GAT" is broken into two lines (at the end of one line going into the beginning of the next line), it has to be found too.
This User Gave Thanks to sgruenwald For This Post:
pawannoel
# 9  
Old 03-24-2011
Code:
# str="GAT"
# awk -F"$str" -v V="$str"  'NF>1{for(i=1;i<NF;i++){match($0,".*"$i);print "Line:"NR,"Pos:",RSTART+RLENGTH,"to",RSTART-1+RLENGTH+length(V)}}' infile

Code:
# cat tst
CAGCAGCAAGATTTGCAGCAACAGCAACAAGTAGTGACTACAGTTGCCTCGCAAAGTCCT
CATGCAACTGCAACGGAAAAGGAGCCAGTACCCGCCGTGGTTGACGACCCACTGGAGAAC
ATGTTCGGAGATTATTCCAATGAGCCGTTCAACACCAATTTCGACGATGAATTTGGAGAT
# str="GAT"
# awk -F"$str" -v V="$str" 'NF>1{for(i=1;i<NF;i++){match($0,".*"$i);print "Line:"NR,"Pos:",RSTART+RLENGTH,"to",RSTART-1+RLENGTH+length(V)}}' tst
Line:1 Pos: 10 to 12
Line:3 Pos: 10 to 12
Line:3 Pos: 46 to 48
Line:3 Pos: 58 to 60
#

---------- Post updated at 06:59 PM ---------- Previous update was at 06:53 PM ----------

@Corona688 :

What was the content of your input file ?

(thiis is because it looks as if you were missing the third "GAT" on the last line)

---------- Post updated 2011-03-24 at 10:06 AM ---------- Previous update was 2011-03-23 at 06:59 PM ----------

Could be adapted easy for 1 display per line :

Code:
# str="GAT"
# awk -F"$str" -v V="$str" 'NF>1{for(i=1;i<NF;i++){match($0,".*"$i);x=RSTART+RLENGTH;y=y" : "x"-"x-1+length(V)};print "Line "NR y;x=y=z}' tst
Line 1 : 10-12
Line 3 : 10-12 : 46-48 : 58-60
#

If on SunOS/Solaris, use nawk instead of awk
Last edited by ctsgnb; 03-24-2011 at 06:12 AM..
This User Gave Thanks to ctsgnb For This Post:
pawannoel
# 10  
Old 03-24-2011
@ctsgnb:

Thanks for the codes but as sgruenwald mentioned I'm working with a DNA sequence so all lines are part of the same string. I want positions not by where it matched in each line but over the entire length of the string composed of A,T, G and C letters, obviously excluding the header line.

Cheers and thanks for the input, but I think Bartus11 has already provided a solution.
I'll be back with more questions.

Hv a nice day all Smilie

---------- Post updated at 04:26 AM ---------- Previous update was at 04:23 AM ----------

By the way can someone explain in laymans terms what $_ $. and $& variables are? .... I have a hard time understanding this concept

Cheers Smilie
# 11  
Old 03-24-2011
Hi Pawan:

Maybe you should concatenate your DNA part. Use this code:
Code:
head -n +1 <dna >dna_concat; tail -n +2 <dna | tr -d '\n' >>dna_concat

It reads in the description/name of your code on the first line, produces a line feed and then concatenates the DNA code that follows.
Last edited by Franklin52; 03-25-2011 at 06:31 AM.. Reason: Please use code tags, thank you
# 12  
Old 03-24-2011
Quote:
Originally Posted by pawannoel
By the way can someone explain in laymans terms what $_ $. and $& variables are? .... I have a hard time understanding this concept

Cheers Smilie
Check: http://www.catonmat.net/download/per....variables.pdf
This User Gave Thanks to bartus11 For This Post:
pawannoel
# 13  
Old 03-24-2011
Did have a look at that already ... thanx though
 
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