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How to combine multiple text files of different lengths and multiple columns by a column

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.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty margin-bottom:0;

3

I have 60 text files of different lengths and same column names.

For example:

cat Sample_145_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19258 circRNA
 612 ciRNA

cat Sample_146_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 17791 circRNA
 729 ciRNA

cat Sample_147_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 22838 circRNA
 686 ciRNA

cat Sample_148_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19404 circRNA
 475 ciRNA

I want to produce a 'master' table of all identified circRNAs, with readnumber as column for each sample and flankintronas rownames:

command-line

share|improve this question

edited Mar 26 at 22:30

dessert

25.7k674108

asked Mar 26 at 20:14

grtgrt

161

add a comment | 

3

I have 60 text files of different lengths and same column names.

For example:

cat Sample_145_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19258 circRNA
 612 ciRNA

cat Sample_146_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 17791 circRNA
 729 ciRNA

cat Sample_147_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 22838 circRNA
 686 ciRNA

cat Sample_148_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19404 circRNA
 475 ciRNA

I want to produce a 'master' table of all identified circRNAs, with readnumber as column for each sample and flankintronas rownames:

command-line

share|improve this question

edited Mar 26 at 22:30

dessert

25.7k674108

asked Mar 26 at 20:14

grtgrt

161

add a comment | 

I have 60 text files of different lengths and same column names.

For example:

cat Sample_145_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19258 circRNA
 612 ciRNA

cat Sample_146_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 17791 circRNA
 729 ciRNA

cat Sample_147_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 22838 circRNA
 686 ciRNA

cat Sample_148_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19404 circRNA
 475 ciRNA

I want to produce a 'master' table of all identified circRNAs, with readnumber as column for each sample and flankintronas rownames:

command-line

share|improve this question

edited Mar 26 at 22:30

dessert

25.7k674108

asked Mar 26 at 20:14

grtgrt

161

cat Sample_145_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19258 circRNA
 612 ciRNA

cat Sample_146_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 17791 circRNA
 729 ciRNA

cat Sample_147_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 22838 circRNA
 686 ciRNA

cat Sample_148_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk 'print $14' | sort | uniq -c
 19404 circRNA
 475 ciRNA

share|improve this question

edited Mar 26 at 22:30

dessert

25.7k674108

asked Mar 26 at 20:14

grtgrt

161

share|improve this question

edited Mar 26 at 22:30

dessert

25.7k674108

asked Mar 26 at 20:14

grtgrt

161

edited Mar 26 at 22:30

dessert

25.7k674108

edited Mar 26 at 22:30

dessert

25.7k674108

asked Mar 26 at 20:14

grtgrt

161

asked Mar 26 at 20:14

grtgrt

161

1 Answer
1

active

oldest

votes

3

If all of the columns in all of the files are in the same order, then just concat them together with >>:

for x in 1..60; do 
 # These flags for tail just cut of the top line, which is your headers
 tail -n 2 Sample_$x_blah.txt >> Sample_master.txt
 # and the double carat makes the output append^ 
done 

If not, then you can write the translations in awk sort of like you had above, i.e.

$ cat Sample_1.txt 
col1,col2,col3,col4 #etc 
$ cat Sample_2.txt 
col4,col3,col2,col1 
$ cat Sample_1.txt > Sample_Master.txt # no translation needed
$ awk 'print $4","$3","$2","$1 ' Sample_2.txt >> Sample_Master.txt 

But with 60 files, that would be more work than- something like writing a python script using python's csv lib...

share|improve this answer

edited Mar 26 at 22:34

dessert

25.7k674108

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523

add a comment | 

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3

If all of the columns in all of the files are in the same order, then just concat them together with >>:

for x in 1..60; do 
 # These flags for tail just cut of the top line, which is your headers
 tail -n 2 Sample_$x_blah.txt >> Sample_master.txt
 # and the double carat makes the output append^ 
done 

If not, then you can write the translations in awk sort of like you had above, i.e.

$ cat Sample_1.txt 
col1,col2,col3,col4 #etc 
$ cat Sample_2.txt 
col4,col3,col2,col1 
$ cat Sample_1.txt > Sample_Master.txt # no translation needed
$ awk 'print $4","$3","$2","$1 ' Sample_2.txt >> Sample_Master.txt 

But with 60 files, that would be more work than- something like writing a python script using python's csv lib...

share|improve this answer

edited Mar 26 at 22:34

dessert

25.7k674108

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523

add a comment | 

3

If all of the columns in all of the files are in the same order, then just concat them together with >>:

for x in 1..60; do 
 # These flags for tail just cut of the top line, which is your headers
 tail -n 2 Sample_$x_blah.txt >> Sample_master.txt
 # and the double carat makes the output append^ 
done 

If not, then you can write the translations in awk sort of like you had above, i.e.

$ cat Sample_1.txt 
col1,col2,col3,col4 #etc 
$ cat Sample_2.txt 
col4,col3,col2,col1 
$ cat Sample_1.txt > Sample_Master.txt # no translation needed
$ awk 'print $4","$3","$2","$1 ' Sample_2.txt >> Sample_Master.txt 

But with 60 files, that would be more work than- something like writing a python script using python's csv lib...

share|improve this answer

edited Mar 26 at 22:34

dessert

25.7k674108

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523

add a comment | 

If all of the columns in all of the files are in the same order, then just concat them together with >>:

for x in 1..60; do 
 # These flags for tail just cut of the top line, which is your headers
 tail -n 2 Sample_$x_blah.txt >> Sample_master.txt
 # and the double carat makes the output append^ 
done 

If not, then you can write the translations in awk sort of like you had above, i.e.

$ cat Sample_1.txt 
col1,col2,col3,col4 #etc 
$ cat Sample_2.txt 
col4,col3,col2,col1 
$ cat Sample_1.txt > Sample_Master.txt # no translation needed
$ awk 'print $4","$3","$2","$1 ' Sample_2.txt >> Sample_Master.txt 

But with 60 files, that would be more work than- something like writing a python script using python's csv lib...

share|improve this answer

edited Mar 26 at 22:34

dessert

25.7k674108

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523

for x in 1..60; do 
 # These flags for tail just cut of the top line, which is your headers
 tail -n 2 Sample_$x_blah.txt >> Sample_master.txt
 # and the double carat makes the output append^ 
done 

$ cat Sample_1.txt 
col1,col2,col3,col4 #etc 
$ cat Sample_2.txt 
col4,col3,col2,col1 
$ cat Sample_1.txt > Sample_Master.txt # no translation needed
$ awk 'print $4","$3","$2","$1 ' Sample_2.txt >> Sample_Master.txt 

share|improve this answer

edited Mar 26 at 22:34

dessert

25.7k674108

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523

edited Mar 26 at 22:34

dessert

25.7k674108

edited Mar 26 at 22:34

dessert

25.7k674108

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523

answered Mar 26 at 20:43

rm-vandarm-vanda

2,37321523