Find duplicate String inside a text with middle near each other
Clash Royale CLAN TAG#URR8PPP
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I need to find a string of 13 character length in a text file that has a duplicate close to it.
It referencing to the mutation 13 of the genomes.
For example:
ACGAATTGCAGCCACAGTACGAATCGCAGCC.
It starts with ACGAATTGCAGCC and ends with it, but in between are random chars of unknown length.
What I've come up so far is:
grep -Eo '((.)13).1,1001'
I have to find it in this
GTACCATAACTAACAACCTGAAAAGTCACAAAAACATATACAATAAAAGAACTAGATTTCGCATAGGATATATATTAATAAAGTGAACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAAAACTTACTCATACGAGGACTAATAAAAGATTCAAAACAATACAATTGACGAAAACTCAACGAGGAAAGCTAGAAAACCACCAGAGAAACTCAAAACACAAATAGAGATAAAAAAAAAAACCATAAAGAAAAATTCTTACATCGTCACAGCCAAGGAAAAAAAGAAATCGTTAAAATGGAACGCAGTCGAACACAAAAAGACAACACAGAACAAAAAAGGCAAACAGCGTAGAAACAAATACACTCGCGTAGCAAAGGGGCGGCGTCACGCTTGAAACATAAAAATAACCACTGTATATCACGACAATCAACAAAGTCTACATCAAGAAAATCAAAAAAATAC
grep scripting bioinformatics
edited Dec 1 at 21:18
fra-san
1,110214
asked Nov 30 at 23:21
Jan Villapaz
123
add a comment |
up vote
2
down vote
favorite
I need to find a string of 13 character length in a text file that has a duplicate close to it.
It referencing to the mutation 13 of the genomes.
For example:
ACGAATTGCAGCCACAGTACGAATCGCAGCC.
It starts with ACGAATTGCAGCC and ends with it, but in between are random chars of unknown length.
What I've come up so far is:
grep -Eo '((.)13).1,1001'
I have to find it in this
GTACCATAACTAACAACCTGAAAAGTCACAAAAACATATACAATAAAAGAACTAGATTTCGCATAGGATATATATTAATAAAGTGAACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAAAACTTACTCATACGAGGACTAATAAAAGATTCAAAACAATACAATTGACGAAAACTCAACGAGGAAAGCTAGAAAACCACCAGAGAAACTCAAAACACAAATAGAGATAAAAAAAAAAACCATAAAGAAAAATTCTTACATCGTCACAGCCAAGGAAAAAAAGAAATCGTTAAAATGGAACGCAGTCGAACACAAAAAGACAACACAGAACAAAAAAGGCAAACAGCGTAGAAACAAATACACTCGCGTAGCAAAGGGGCGGCGTCACGCTTGAAACATAAAAATAACCACTGTATATCACGACAATCAACAAAGTCTACATCAAGAAAATCAAAAAAATAC
grep scripting bioinformatics
edited Dec 1 at 21:18
fra-san
1,110214
asked Nov 30 at 23:21
Jan Villapaz
123
add a comment |
up vote
2
down vote
favorite
up vote
2
down vote
favorite
I need to find a string of 13 character length in a text file that has a duplicate close to it.
It referencing to the mutation 13 of the genomes.
For example:
ACGAATTGCAGCCACAGTACGAATCGCAGCC.
It starts with ACGAATTGCAGCC and ends with it, but in between are random chars of unknown length.
What I've come up so far is:
grep -Eo '((.)13).1,1001'
I have to find it in this
GTACCATAACTAACAACCTGAAAAGTCACAAAAACATATACAATAAAAGAACTAGATTTCGCATAGGATATATATTAATAAAGTGAACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAAAACTTACTCATACGAGGACTAATAAAAGATTCAAAACAATACAATTGACGAAAACTCAACGAGGAAAGCTAGAAAACCACCAGAGAAACTCAAAACACAAATAGAGATAAAAAAAAAAACCATAAAGAAAAATTCTTACATCGTCACAGCCAAGGAAAAAAAGAAATCGTTAAAATGGAACGCAGTCGAACACAAAAAGACAACACAGAACAAAAAAGGCAAACAGCGTAGAAACAAATACACTCGCGTAGCAAAGGGGCGGCGTCACGCTTGAAACATAAAAATAACCACTGTATATCACGACAATCAACAAAGTCTACATCAAGAAAATCAAAAAAATAC
grep scripting bioinformatics
edited Dec 1 at 21:18
fra-san
1,110214
asked Nov 30 at 23:21
Jan Villapaz
123
I need to find a string of 13 character length in a text file that has a duplicate close to it.
It referencing to the mutation 13 of the genomes.
For example:
ACGAATTGCAGCCACAGTACGAATCGCAGCC.
It starts with ACGAATTGCAGCC and ends with it, but in between are random chars of unknown length.
What I've come up so far is:
grep -Eo '((.)13).1,1001'
I have to find it in this
GTACCATAACTAACAACCTGAAAAGTCACAAAAACATATACAATAAAAGAACTAGATTTCGCATAGGATATATATTAATAAAGTGAACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAAAACTTACTCATACGAGGACTAATAAAAGATTCAAAACAATACAATTGACGAAAACTCAACGAGGAAAGCTAGAAAACCACCAGAGAAACTCAAAACACAAATAGAGATAAAAAAAAAAACCATAAAGAAAAATTCTTACATCGTCACAGCCAAGGAAAAAAAGAAATCGTTAAAATGGAACGCAGTCGAACACAAAAAGACAACACAGAACAAAAAAGGCAAACAGCGTAGAAACAAATACACTCGCGTAGCAAAGGGGCGGCGTCACGCTTGAAACATAAAAATAACCACTGTATATCACGACAATCAACAAAGTCTACATCAAGAAAATCAAAAAAATAC
grep scripting bioinformatics
grep scripting bioinformatics
edited Dec 1 at 21:18
fra-san
1,110214
asked Nov 30 at 23:21
Jan Villapaz
123
edited Dec 1 at 21:18
fra-san
1,110214
asked Nov 30 at 23:21
Jan Villapaz
123
edited Dec 1 at 21:18
fra-san
1,110214
edited Dec 1 at 21:18
fra-san
1,110214
edited Dec 1 at 21:18
fra-san
1,110214
1,110214
asked Nov 30 at 23:21
Jan Villapaz
123
asked Nov 30 at 23:21
Jan Villapaz
123
asked Nov 30 at 23:21
Jan Villapaz
123
123
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
up vote
3
down vote
You were quite close, the problem was the 100, too narrow! You may want to consider using Perl PCRE as opposed to Posix Extended. The performance difference is quite noticeable.
grep -Po '((.)13).1,1000?1' genom
AACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAA
Timing comparison on my machine:
Posix: (-E) 0m4.816s
Perl: (-P) 0m0.011s
answered Dec 1 at 0:03
tink
4,07511218
4
You may want to make the repetition non greedy.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with-Elooks like a bug (LC_ALL=Cwill cut it to 1/3, but still orders of magnitude slower than-P).
– mosvy
Dec 1 at 0:55
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to0m0.714s... almost sevenfold faster. Still a good tick slower than-P. :)
– tink
Dec 1 at 3:23
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
add a comment |
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
3
down vote
You were quite close, the problem was the 100, too narrow! You may want to consider using Perl PCRE as opposed to Posix Extended. The performance difference is quite noticeable.
grep -Po '((.)13).1,1000?1' genom
AACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAA
Timing comparison on my machine:
Posix: (-E) 0m4.816s
Perl: (-P) 0m0.011s
answered Dec 1 at 0:03
tink
4,07511218
4
You may want to make the repetition non greedy.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with-Elooks like a bug (LC_ALL=Cwill cut it to 1/3, but still orders of magnitude slower than-P).
– mosvy
Dec 1 at 0:55
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to0m0.714s... almost sevenfold faster. Still a good tick slower than-P. :)
– tink
Dec 1 at 3:23
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
add a comment |
up vote
3
down vote
You were quite close, the problem was the 100, too narrow! You may want to consider using Perl PCRE as opposed to Posix Extended. The performance difference is quite noticeable.
grep -Po '((.)13).1,1000?1' genom
AACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAA
Timing comparison on my machine:
Posix: (-E) 0m4.816s
Perl: (-P) 0m0.011s
answered Dec 1 at 0:03
tink
4,07511218
4
You may want to make the repetition non greedy.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with-Elooks like a bug (LC_ALL=Cwill cut it to 1/3, but still orders of magnitude slower than-P).
– mosvy
Dec 1 at 0:55
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to0m0.714s... almost sevenfold faster. Still a good tick slower than-P. :)
– tink
Dec 1 at 3:23
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
add a comment |
up vote
3
down vote
up vote
3
down vote
You were quite close, the problem was the 100, too narrow! You may want to consider using Perl PCRE as opposed to Posix Extended. The performance difference is quite noticeable.
grep -Po '((.)13).1,1000?1' genom
AACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAA
Timing comparison on my machine:
Posix: (-E) 0m4.816s
Perl: (-P) 0m0.011s
answered Dec 1 at 0:03
tink
4,07511218
You were quite close, the problem was the 100, too narrow! You may want to consider using Perl PCRE as opposed to Posix Extended. The performance difference is quite noticeable.
grep -Po '((.)13).1,1000?1' genom
AACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAA
Timing comparison on my machine:
Posix: (-E) 0m4.816s
Perl: (-P) 0m0.011s
answered Dec 1 at 0:03
tink
4,07511218
edited Dec 1 at 1:24
answered Dec 1 at 0:03
tink
4,07511218
answered Dec 1 at 0:03
tink
4,07511218
answered Dec 1 at 0:03
tink
4,07511218
4,07511218
4
You may want to make the repetition non greedy.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with-Elooks like a bug (LC_ALL=Cwill cut it to 1/3, but still orders of magnitude slower than-P).
– mosvy
Dec 1 at 0:55
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to0m0.714s... almost sevenfold faster. Still a good tick slower than-P. :)
– tink
Dec 1 at 3:23
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
add a comment |
4
You may want to make the repetition non greedy.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with-Elooks like a bug (LC_ALL=Cwill cut it to 1/3, but still orders of magnitude slower than-P).
– mosvy
Dec 1 at 0:55
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to0m0.714s... almost sevenfold faster. Still a good tick slower than-P. :)
– tink
Dec 1 at 3:23
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
4
4
You may want to make the repetition non greedy
.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with -E looks like a bug (LC_ALL=C will cut it to 1/3, but still orders of magnitude slower than -P).– mosvy
Dec 1 at 0:55
You may want to make the repetition non greedy
.1,1000?, even if this may not matter in this exact case, you only want to include up to the nearest repetition. That horrible slowness with -E looks like a bug (LC_ALL=C will cut it to 1/3, but still orders of magnitude slower than -P).– mosvy
Dec 1 at 0:55
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
Good suggestion! Thanks - will incorporate :)
– tink
Dec 1 at 1:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to
0m0.714s ... almost sevenfold faster. Still a good tick slower than -P. :)– tink
Dec 1 at 3:23
P.S.: @mosvy - nice catch w/ the LC_ALL ... that brings the runtime down to
0m0.714s ... almost sevenfold faster. Still a good tick slower than -P. :)– tink
Dec 1 at 3:23
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
Note that POSIX EREs don't have back references. (POSIX BREs do). The OP is probably using an implementation that offers it as an extension.
– Stéphane Chazelas
Dec 1 at 22:04
add a comment |
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