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

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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 5 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 5 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 5 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 5 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 5 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 5 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 5 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