Compare Columns of genes in file and output the gene and number of column it is present in linux
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I have 3 coumns of genes in a file like this
col1 col2 col3
CXCL9 CXCL9 CXCL9
MAP2K6 MAP2K6 MAP2K6
CXCL10 CXCL10 CXCL11
I want to match the 3 columns and see which gene is present in how many columns, The output desired is in the format as
CXCL9 3
MAP2K6 3
CXCL10 2
CXCL11 1
Can somebody help me, it would save me a lot of time
linux text-processing columns bioinformatics
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
asked Jan 13 at 16:11
saamar rajput
12
add a comment |Â
up vote
-2
down vote
favorite
I have 3 coumns of genes in a file like this
col1 col2 col3
CXCL9 CXCL9 CXCL9
MAP2K6 MAP2K6 MAP2K6
CXCL10 CXCL10 CXCL11
I want to match the 3 columns and see which gene is present in how many columns, The output desired is in the format as
CXCL9 3
MAP2K6 3
CXCL10 2
CXCL11 1
Can somebody help me, it would save me a lot of time
linux text-processing columns bioinformatics
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
asked Jan 13 at 16:11
saamar rajput
12
Is this homework? See unix.meta.stackexchange.com/questions/344/…
– mattdm
Jan 13 at 16:27
is the linecol1 col2 col3really appears as the header line in your file?
– RomanPerekhrest
Jan 13 at 16:29
add a comment |Â
up vote
-2
down vote
favorite
up vote
-2
down vote
favorite
I have 3 coumns of genes in a file like this
col1 col2 col3
CXCL9 CXCL9 CXCL9
MAP2K6 MAP2K6 MAP2K6
CXCL10 CXCL10 CXCL11
I want to match the 3 columns and see which gene is present in how many columns, The output desired is in the format as
CXCL9 3
MAP2K6 3
CXCL10 2
CXCL11 1
Can somebody help me, it would save me a lot of time
linux text-processing columns bioinformatics
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
asked Jan 13 at 16:11
saamar rajput
12
I have 3 coumns of genes in a file like this
col1 col2 col3
CXCL9 CXCL9 CXCL9
MAP2K6 MAP2K6 MAP2K6
CXCL10 CXCL10 CXCL11
I want to match the 3 columns and see which gene is present in how many columns, The output desired is in the format as
CXCL9 3
MAP2K6 3
CXCL10 2
CXCL11 1
Can somebody help me, it would save me a lot of time
linux text-processing columns bioinformatics
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
asked Jan 13 at 16:11
saamar rajput
12
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
edited Jan 13 at 17:40
Jeff Schaller
31.8k848109
31.8k848109
asked Jan 13 at 16:11
saamar rajput
12
asked Jan 13 at 16:11
saamar rajput
12
asked Jan 13 at 16:11
saamar rajput
12
12
Is this homework? See unix.meta.stackexchange.com/questions/344/…
– mattdm
Jan 13 at 16:27
is the linecol1 col2 col3really appears as the header line in your file?
– RomanPerekhrest
Jan 13 at 16:29
add a comment |Â
Is this homework? See unix.meta.stackexchange.com/questions/344/…
– mattdm
Jan 13 at 16:27
is the linecol1 col2 col3really appears as the header line in your file?
– RomanPerekhrest
Jan 13 at 16:29
Is this homework? See unix.meta.stackexchange.com/questions/344/…
– mattdm
Jan 13 at 16:27
Is this homework? See unix.meta.stackexchange.com/questions/344/…
– mattdm
Jan 13 at 16:27
is the line
col1 col2 col3 really appears as the header line in your file?– RomanPerekhrest
Jan 13 at 16:29
is the line
col1 col2 col3 really appears as the header line in your file?– RomanPerekhrest
Jan 13 at 16:29
add a comment |Â
3 Answers
3
active
oldest
votes
up vote
1
down vote
sed + sort + uniq solution:
sed 's/[[:space:]]+/n/g' file | sort | uniq -c
The output:
2 CXCL10
1 CXCL11
3 CXCL9
3 MAP2K6
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
. . . perhapssed -n '1!s/[[:space:]]+/n/gp'?
– steeldriver
Jan 13 at 16:26
add a comment |Â
up vote
0
down vote
If there are no spaces between the names of genes, and the names of the columns follow the pattern you gave, then you may use this following script as a hint:
#!/bin/bash
for i in `cat genes.txt`; do
[[ $i == "col"* ]] || echo $i;
done | sort | uniq -c
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
add a comment |Â
up vote
0
down vote
Awk solution:
awk ' for(i=1;i<=NF;i++) a[$i]++ END for(i in a) print i, a[i] ' file
The output:
CXCL11 1
MAP2K6 3
CXCL9 3
CXCL10 2
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
add a comment |Â
3 Answers
3
active
oldest
votes
3 Answers
3
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
1
down vote
sed + sort + uniq solution:
sed 's/[[:space:]]+/n/g' file | sort | uniq -c
The output:
2 CXCL10
1 CXCL11
3 CXCL9
3 MAP2K6
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
. . . perhapssed -n '1!s/[[:space:]]+/n/gp'?
– steeldriver
Jan 13 at 16:26
add a comment |Â
up vote
1
down vote
sed + sort + uniq solution:
sed 's/[[:space:]]+/n/g' file | sort | uniq -c
The output:
2 CXCL10
1 CXCL11
3 CXCL9
3 MAP2K6
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
. . . perhapssed -n '1!s/[[:space:]]+/n/gp'?
– steeldriver
Jan 13 at 16:26
add a comment |Â
up vote
1
down vote
up vote
1
down vote
sed + sort + uniq solution:
sed 's/[[:space:]]+/n/g' file | sort | uniq -c
The output:
2 CXCL10
1 CXCL11
3 CXCL9
3 MAP2K6
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
sed + sort + uniq solution:
sed 's/[[:space:]]+/n/g' file | sort | uniq -c
The output:
2 CXCL10
1 CXCL11
3 CXCL9
3 MAP2K6
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
answered Jan 13 at 16:22
RomanPerekhrest
22.4k12145
22.4k12145
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
. . . perhapssed -n '1!s/[[:space:]]+/n/gp'?
– steeldriver
Jan 13 at 16:26
add a comment |Â
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
. . . perhapssed -n '1!s/[[:space:]]+/n/gp'?
– steeldriver
Jan 13 at 16:26
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
What about the col1, col2, col3 headings?
– Mukesh Sai Kumar
Jan 13 at 16:24
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
@MukeshSaiKumar, I suppose that they were just for demonstration purpose
– RomanPerekhrest
Jan 13 at 16:25
. . . perhaps
sed -n '1!s/[[:space:]]+/n/gp' ?– steeldriver
Jan 13 at 16:26
. . . perhaps
sed -n '1!s/[[:space:]]+/n/gp' ?– steeldriver
Jan 13 at 16:26
add a comment |Â
up vote
0
down vote
If there are no spaces between the names of genes, and the names of the columns follow the pattern you gave, then you may use this following script as a hint:
#!/bin/bash
for i in `cat genes.txt`; do
[[ $i == "col"* ]] || echo $i;
done | sort | uniq -c
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
add a comment |Â
up vote
0
down vote
If there are no spaces between the names of genes, and the names of the columns follow the pattern you gave, then you may use this following script as a hint:
#!/bin/bash
for i in `cat genes.txt`; do
[[ $i == "col"* ]] || echo $i;
done | sort | uniq -c
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
add a comment |Â
up vote
0
down vote
up vote
0
down vote
If there are no spaces between the names of genes, and the names of the columns follow the pattern you gave, then you may use this following script as a hint:
#!/bin/bash
for i in `cat genes.txt`; do
[[ $i == "col"* ]] || echo $i;
done | sort | uniq -c
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
If there are no spaces between the names of genes, and the names of the columns follow the pattern you gave, then you may use this following script as a hint:
#!/bin/bash
for i in `cat genes.txt`; do
[[ $i == "col"* ]] || echo $i;
done | sort | uniq -c
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
answered Jan 13 at 16:23
Mukesh Sai Kumar
27819
27819
add a comment |Â
add a comment |Â
up vote
0
down vote
Awk solution:
awk ' for(i=1;i<=NF;i++) a[$i]++ END for(i in a) print i, a[i] ' file
The output:
CXCL11 1
MAP2K6 3
CXCL9 3
CXCL10 2
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
add a comment |Â
up vote
0
down vote
Awk solution:
awk ' for(i=1;i<=NF;i++) a[$i]++ END for(i in a) print i, a[i] ' file
The output:
CXCL11 1
MAP2K6 3
CXCL9 3
CXCL10 2
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
add a comment |Â
up vote
0
down vote
up vote
0
down vote
Awk solution:
awk ' for(i=1;i<=NF;i++) a[$i]++ END for(i in a) print i, a[i] ' file
The output:
CXCL11 1
MAP2K6 3
CXCL9 3
CXCL10 2
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
Awk solution:
awk ' for(i=1;i<=NF;i++) a[$i]++ END for(i in a) print i, a[i] ' file
The output:
CXCL11 1
MAP2K6 3
CXCL9 3
CXCL10 2
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
answered Jan 13 at 16:24
RomanPerekhrest
22.4k12145
22.4k12145
add a comment |Â
add a comment |Â
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Is this homework? See unix.meta.stackexchange.com/questions/344/…
– mattdm
Jan 13 at 16:27
is the line
col1 col2 col3really appears as the header line in your file?– RomanPerekhrest
Jan 13 at 16:29