Printing character position of overlapping strings stored in looped variable using grep?
I have a really long string (stored in a file) filled with B's and E's and I'm trying to get position information within this file for all matches for a series of patterns that I'm looping through. I'm pretty close to getting it to work, but the problem is I'm missing instances of overlapping matches using grep.
For example, the list of strings and string I'm searching in look like this
$cat CNVE_list.txt
BEEBB
BBBBEE
EEEEE
BEEEBBBBB
$cat probe_profile.txt
BBBEBEEBEEEEEEBBEEBBBB
And the loop I try to run looks like this
filename='CNVE_list.txt'
while read p; do
echo $p | grep -aob -f - probe_profile.txt > probe_profile_$p.txt
done < $filename
The problem in this example is with line 3 in CNVE_list.txt (EEEEE). It should have two overlapping matches but only finds the first. I've read some other questions and found the issue solved with PERL with a lookbehind strategy, but not sure how to solve this with looped variables.
i.e.
Grep that works with overlapping patterns
I'm dealing with a very long list of patterns and a very long string, so the more efficient the better. Thanks in advance for the help!
grep
asked 7 mins ago
jfaberhajfaberha
31
add a comment |
I have a really long string (stored in a file) filled with B's and E's and I'm trying to get position information within this file for all matches for a series of patterns that I'm looping through. I'm pretty close to getting it to work, but the problem is I'm missing instances of overlapping matches using grep.
For example, the list of strings and string I'm searching in look like this
$cat CNVE_list.txt
BEEBB
BBBBEE
EEEEE
BEEEBBBBB
$cat probe_profile.txt
BBBEBEEBEEEEEEBBEEBBBB
And the loop I try to run looks like this
filename='CNVE_list.txt'
while read p; do
echo $p | grep -aob -f - probe_profile.txt > probe_profile_$p.txt
done < $filename
The problem in this example is with line 3 in CNVE_list.txt (EEEEE). It should have two overlapping matches but only finds the first. I've read some other questions and found the issue solved with PERL with a lookbehind strategy, but not sure how to solve this with looped variables.
i.e.
Grep that works with overlapping patterns
I'm dealing with a very long list of patterns and a very long string, so the more efficient the better. Thanks in advance for the help!
grep
asked 7 mins ago
jfaberhajfaberha
31
add a comment |
I have a really long string (stored in a file) filled with B's and E's and I'm trying to get position information within this file for all matches for a series of patterns that I'm looping through. I'm pretty close to getting it to work, but the problem is I'm missing instances of overlapping matches using grep.
For example, the list of strings and string I'm searching in look like this
$cat CNVE_list.txt
BEEBB
BBBBEE
EEEEE
BEEEBBBBB
$cat probe_profile.txt
BBBEBEEBEEEEEEBBEEBBBB
And the loop I try to run looks like this
filename='CNVE_list.txt'
while read p; do
echo $p | grep -aob -f - probe_profile.txt > probe_profile_$p.txt
done < $filename
The problem in this example is with line 3 in CNVE_list.txt (EEEEE). It should have two overlapping matches but only finds the first. I've read some other questions and found the issue solved with PERL with a lookbehind strategy, but not sure how to solve this with looped variables.
i.e.
Grep that works with overlapping patterns
I'm dealing with a very long list of patterns and a very long string, so the more efficient the better. Thanks in advance for the help!
grep
asked 7 mins ago
jfaberhajfaberha
31
I have a really long string (stored in a file) filled with B's and E's and I'm trying to get position information within this file for all matches for a series of patterns that I'm looping through. I'm pretty close to getting it to work, but the problem is I'm missing instances of overlapping matches using grep.
For example, the list of strings and string I'm searching in look like this
$cat CNVE_list.txt
BEEBB
BBBBEE
EEEEE
BEEEBBBBB
$cat probe_profile.txt
BBBEBEEBEEEEEEBBEEBBBB
And the loop I try to run looks like this
filename='CNVE_list.txt'
while read p; do
echo $p | grep -aob -f - probe_profile.txt > probe_profile_$p.txt
done < $filename
The problem in this example is with line 3 in CNVE_list.txt (EEEEE). It should have two overlapping matches but only finds the first. I've read some other questions and found the issue solved with PERL with a lookbehind strategy, but not sure how to solve this with looped variables.
i.e.
Grep that works with overlapping patterns
I'm dealing with a very long list of patterns and a very long string, so the more efficient the better. Thanks in advance for the help!
grep
grep
asked 7 mins ago
jfaberhajfaberha
31
asked 7 mins ago
jfaberhajfaberha
31
edited 1 min ago
jfaberha
asked 7 mins ago
jfaberhajfaberha
31
asked 7 mins ago
jfaberhajfaberha
31
asked 7 mins ago
jfaberhajfaberha
31
31
add a comment |
add a comment |
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