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# 1  
Old 08-10-2013
Question Search strings and highlight them using Perl or bash/awk/sed
Hi,

I have two files: a.doc and b.txt

Quote:
(1) a.doc with DNA sequences with lenghth at the end of sequence (no. of characters)

Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49
Quote:
(2) b.txt
GACAAGT
AAAAAG
TAATG
CAAGC
ACG
GCTTG
I wish to search the strings from file b.txt in a.doc and want to highlight them in a.doc with different colours using Perl or bash./awk/sed?

Please guide me. Smilie
Thanks!!!!!
# 2  
Old 08-10-2013
Try:
Code:
perl -lpe 'BEGIN{open b, "b.txt";chomp(@b=<b>)}{for $i (@b) {s/$i/\033[31m$i\033[0m/g}}' a.doc

This User Gave Thanks to bartus11 For This Post:
bioinfo
# 3  
Old 08-11-2013
Thanks Smilie
I would highly appreciate if you can explain this script.

I am getting following error while running the above script (1.pl):

Quote:
String found where operator expected at 1.pl line 1, near "lpe 'BEGIN{open b, "b.txt";chomp(@b=<b>)}{for $i (@b) {s/$i/\033[31m$i\033[0m/g}}'"
<Do you need to predeclare lpe?>
Bareword found where operator expected at 1.pl line 1, near "'BEGIN{open b, "b.txt";chomp(@b=<b>)}{for $i (@b) {s/$i/\033[31m$i\033[0m/g}}' a"
<Missing operator before a?>
syntax error at 1.pl line 1, near "lpe 'BEGIN{open b, "b.txt";chomp(@b=<b>)}{for $i (@b) {s/$i/\033[31m$i\033[0m/g}}' "
Execution of 1.pl aborted due to compilation errors.
Last edited by bioinfo; 08-11-2013 at 12:33 AM..
# 4  
Old 08-11-2013
I need some help here to help out Smilie
Whit this script I get only one single line, correct is 5, why?
Code:
awk 'NR==FNR {a[$0]=$0;next} {for (i in a) {if ($0~a[i]) print}}' b.txt a.txt
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48

correct answer is
Code:
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49

Running a test like this show correctly all possibility
Code:
awk 'NR==FNR {a[$0]=$0;next} {for (i in a) {print $0,a[i]}}' b.txt a.txt
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 ACG
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 TAATG
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 AAAAAG
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 GACAAGT
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 CAAGC
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21 GCTTG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 ACG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 TAATG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 AAAAAG
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 GACAAGT
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 CAAGC
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50 GCTTG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 ACG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 TAATG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 AAAAAG
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 GACAAGT
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 CAAGC
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48 GCTTG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 ACG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 TAATG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 AAAAAG
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 GACAAGT
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 CAAGC
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49 GCTTG

Last edited by Jotne; 08-11-2013 at 05:49 AM..
# 5  
Old 08-11-2013
bioinfo, don't put my code in a file. Simply run it in a terminal as I posted it, replacing a.doc and b.txt for the filenames you have (in case they differ from those two).
Last edited by bartus11; 08-11-2013 at 09:37 AM..
This User Gave Thanks to bartus11 For This Post:
bioinfo
# 6  
Old 08-11-2013
@bartus11
Here is what I got when run your code
Code:
perl -lpe 'BEGIN{open b, "b.txt";chomp(@b=<b>)}{for $i (@b) {s/$i/\033[31m$i\033[0m/g}}' a.txt
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49

As you see, it show the line with hits, but only highlight one hit, look at my post #4.
OP request is color on all data in bold.


For some strange reason this has same problem, it only highlight one hits.
Code:
awk 'NR==FNR {a[$0]=$0;next} {for (i in a) {gsub(a[i],"\033[1;31m&\033[0m",$0)}}1' b.txt a.txt
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49

Last edited by Jotne; 08-11-2013 at 09:36 AM..
This User Gave Thanks to Jotne For This Post:
bioinfo
# 7  
Old 08-11-2013
Jotne, post output of:
Code:
cat -ev a.txt
cat -ev b.txt

These 2 Users Gave Thanks to bartus11 For This Post:
bioinfo Jotne
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