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finding unique headers in a fasta file using linux command line
Clash Royale CLAN TAG#URR8PPP
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I tried to use the following command
uniq -u reference.fasta >> reference_uniq.fasta
Id like a count of the unique headers
fasta linux
asked 1 hour ago
crispr
62
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up vote
1
down vote
favorite
I tried to use the following command
uniq -u reference.fasta >> reference_uniq.fasta
Id like a count of the unique headers
fasta linux
asked 1 hour ago
crispr
62
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Did you use python? It will be easier.
– tianhua liao
1 hour ago
add a comment |Â
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I tried to use the following command
uniq -u reference.fasta >> reference_uniq.fasta
Id like a count of the unique headers
fasta linux
asked 1 hour ago
crispr
62
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I tried to use the following command
uniq -u reference.fasta >> reference_uniq.fasta
Id like a count of the unique headers
fasta linux
fasta linux
asked 1 hour ago
crispr
62
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 1 hour ago
crispr
62
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 1 hour ago
crispr
62
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 1 hour ago
crispr
62
asked 1 hour ago
crispr
62
62
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
crispr is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Did you use python? It will be easier.
– tianhua liao
1 hour ago
add a comment |Â
Did you use python? It will be easier.
– tianhua liao
1 hour ago
Did you use python? It will be easier.
– tianhua liao
1 hour ago
Did you use python? It will be easier.
– tianhua liao
1 hour ago
add a comment |Â
3 Answers
3
active
oldest
votes
up vote
2
down vote
If you just want the number of unique headers, you can do this:
grep '>' reference.fasta | sort | uniq -c | wc -l
If you want a list of the unique headers, you can do this:
grep '>' reference.fasta | sort | uniq
If you want a histogram of how many times each header occurs, you can do this:
grep '>' reference.fasta | sort | uniq -c | awk 'printf("%st%sn", $1, $2)'
answered 1 hour ago
conchoecia
71215
add a comment |Â
up vote
1
down vote
You can achieve your goal with a one-liner:
grep '>' reference.fasta | cut -d '>' -f 2 | sort | uniq -c | sort
answered 1 hour ago
user3479780
712
add a comment |Â
up vote
0
down vote
The uniq command expects sorted input. Interestingly, the sort command actually has a "unique" option, -u, which means uniq is not strictly needed. For the fastest processing, you can look for the '>' character at the start of lines with grep:
grep '^>' reference.fasta | sort -u > reference_headers_unique.fasta
For returning the number of unique lines, pipe through wc -l:
grep '^>' reference.fasta | sort -u | wc -l
For more information about regular expressions, see here.
answered 4 mins ago
gringer
6,6132844
add a comment |Â
3 Answers
3
active
oldest
votes
3 Answers
3
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
2
down vote
If you just want the number of unique headers, you can do this:
grep '>' reference.fasta | sort | uniq -c | wc -l
If you want a list of the unique headers, you can do this:
grep '>' reference.fasta | sort | uniq
If you want a histogram of how many times each header occurs, you can do this:
grep '>' reference.fasta | sort | uniq -c | awk 'printf("%st%sn", $1, $2)'
answered 1 hour ago
conchoecia
71215
add a comment |Â
up vote
2
down vote
If you just want the number of unique headers, you can do this:
grep '>' reference.fasta | sort | uniq -c | wc -l
If you want a list of the unique headers, you can do this:
grep '>' reference.fasta | sort | uniq
If you want a histogram of how many times each header occurs, you can do this:
grep '>' reference.fasta | sort | uniq -c | awk 'printf("%st%sn", $1, $2)'
answered 1 hour ago
conchoecia
71215
add a comment |Â
up vote
2
down vote
up vote
2
down vote
If you just want the number of unique headers, you can do this:
grep '>' reference.fasta | sort | uniq -c | wc -l
If you want a list of the unique headers, you can do this:
grep '>' reference.fasta | sort | uniq
If you want a histogram of how many times each header occurs, you can do this:
grep '>' reference.fasta | sort | uniq -c | awk 'printf("%st%sn", $1, $2)'
answered 1 hour ago
conchoecia
71215
If you just want the number of unique headers, you can do this:
grep '>' reference.fasta | sort | uniq -c | wc -l
If you want a list of the unique headers, you can do this:
grep '>' reference.fasta | sort | uniq
If you want a histogram of how many times each header occurs, you can do this:
grep '>' reference.fasta | sort | uniq -c | awk 'printf("%st%sn", $1, $2)'
answered 1 hour ago
conchoecia
71215
answered 1 hour ago
conchoecia
71215
answered 1 hour ago
conchoecia
71215
answered 1 hour ago
conchoecia
71215
71215
add a comment |Â
add a comment |Â
up vote
1
down vote
You can achieve your goal with a one-liner:
grep '>' reference.fasta | cut -d '>' -f 2 | sort | uniq -c | sort
answered 1 hour ago
user3479780
712
add a comment |Â
up vote
1
down vote
You can achieve your goal with a one-liner:
grep '>' reference.fasta | cut -d '>' -f 2 | sort | uniq -c | sort
answered 1 hour ago
user3479780
712
add a comment |Â
up vote
1
down vote
up vote
1
down vote
You can achieve your goal with a one-liner:
grep '>' reference.fasta | cut -d '>' -f 2 | sort | uniq -c | sort
answered 1 hour ago
user3479780
712
You can achieve your goal with a one-liner:
grep '>' reference.fasta | cut -d '>' -f 2 | sort | uniq -c | sort
answered 1 hour ago
user3479780
712
answered 1 hour ago
user3479780
712
answered 1 hour ago
user3479780
712
answered 1 hour ago
user3479780
712
712
add a comment |Â
add a comment |Â
up vote
0
down vote
The uniq command expects sorted input. Interestingly, the sort command actually has a "unique" option, -u, which means uniq is not strictly needed. For the fastest processing, you can look for the '>' character at the start of lines with grep:
grep '^>' reference.fasta | sort -u > reference_headers_unique.fasta
For returning the number of unique lines, pipe through wc -l:
grep '^>' reference.fasta | sort -u | wc -l
For more information about regular expressions, see here.
answered 4 mins ago
gringer
6,6132844
add a comment |Â
up vote
0
down vote
The uniq command expects sorted input. Interestingly, the sort command actually has a "unique" option, -u, which means uniq is not strictly needed. For the fastest processing, you can look for the '>' character at the start of lines with grep:
grep '^>' reference.fasta | sort -u > reference_headers_unique.fasta
For returning the number of unique lines, pipe through wc -l:
grep '^>' reference.fasta | sort -u | wc -l
For more information about regular expressions, see here.
answered 4 mins ago
gringer
6,6132844
add a comment |Â
up vote
0
down vote
up vote
0
down vote
The uniq command expects sorted input. Interestingly, the sort command actually has a "unique" option, -u, which means uniq is not strictly needed. For the fastest processing, you can look for the '>' character at the start of lines with grep:
grep '^>' reference.fasta | sort -u > reference_headers_unique.fasta
For returning the number of unique lines, pipe through wc -l:
grep '^>' reference.fasta | sort -u | wc -l
For more information about regular expressions, see here.
answered 4 mins ago
gringer
6,6132844
The uniq command expects sorted input. Interestingly, the sort command actually has a "unique" option, -u, which means uniq is not strictly needed. For the fastest processing, you can look for the '>' character at the start of lines with grep:
grep '^>' reference.fasta | sort -u > reference_headers_unique.fasta
For returning the number of unique lines, pipe through wc -l:
grep '^>' reference.fasta | sort -u | wc -l
For more information about regular expressions, see here.
answered 4 mins ago
gringer
6,6132844
answered 4 mins ago
gringer
6,6132844
answered 4 mins ago
gringer
6,6132844
answered 4 mins ago
gringer
6,6132844
6,6132844
add a comment |Â
add a comment |Â
crispr is a new contributor. Be nice, and check out our Code of Conduct.
crispr is a new contributor. Be nice, and check out our Code of Conduct.
crispr is a new contributor. Be nice, and check out our Code of Conduct.
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Did you use python? It will be easier.
– tianhua liao
1 hour ago