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

Using text list to batch-rename filesNeeded simple script/loop/command for input command, execute and output within textfilesHow to combine multiple text files into one text file ordered by date created?Remove duplicated from two files and merge the unique onesDownloading email messages as text files (multiple accounts) from command lineMorge text files from CLI with sort order and rootReplacing text in multiple files with text from a list in orderCollate all data from each .txt file into one results fileRemove all non-numeric characters from text filesawk: pipe output of (conditional) print to gzip

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 2 hours ago

dessert

25.1k673106

asked 4 hours ago

grtgrt

16

New contributor

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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 2 hours ago

dessert

25.1k673106

asked 4 hours ago

grtgrt

16

New contributor

grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

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 2 hours ago

dessert

25.1k673106

asked 4 hours ago

grtgrt

16

New contributor

grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

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 2 hours ago

dessert

25.1k673106

asked 4 hours ago

grtgrt

16

New contributor

grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

edited 2 hours ago

dessert

25.1k673106

asked 4 hours ago

grtgrt

16

New contributor

grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

edited 2 hours ago

dessert

25.1k673106

edited 2 hours ago

dessert

25.1k673106

asked 4 hours ago

grtgrt

16

New contributor

grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

asked 4 hours ago

grtgrt

16

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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 2 hours ago

dessert

25.1k673106

answered 4 hours ago

rm-vandarm-vanda

2,29821323

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 2 hours ago

dessert

25.1k673106

answered 4 hours ago

rm-vandarm-vanda

2,29821323

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 2 hours ago

dessert

25.1k673106

answered 4 hours ago

rm-vandarm-vanda

2,29821323

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 2 hours ago

dessert

25.1k673106

answered 4 hours ago

rm-vandarm-vanda

2,29821323

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 2 hours ago

dessert

25.1k673106

answered 4 hours ago

rm-vandarm-vanda

2,29821323

edited 2 hours ago

dessert

25.1k673106

edited 2 hours ago

dessert

25.1k673106

answered 4 hours ago

rm-vandarm-vanda

2,29821323

answered 4 hours ago

rm-vandarm-vanda

2,29821323