How to combine multiple text files of different lengths and multiple columns by a column
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
edited 3 hours ago
dessert
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asked 5 hours ago
grtgrt
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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
edited 3 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
edited 3 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.
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 $14}' | sort | uniq -c
19404 circRNA
475 ciRNA
I want to produce a 'master' table of all identified circRNAs, with readnumber as column for each sample and flankintronas rownames:
command-line
command-line
edited 3 hours ago
dessert
25.1k673106
asked 5 hours ago
grtgrt
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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edited 3 hours ago
dessert
25.1k673106
asked 5 hours ago
grtgrt
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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edited 3 hours ago
dessert
25.1k673106
edited 3 hours ago
dessert
25.1k673106
edited 3 hours ago
dessert
25.1k673106
25.1k673106
asked 5 hours ago
grtgrt
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 5 hours ago
grtgrt
16
asked 5 hours ago
grtgrt
16
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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1 Answer
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If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 3 hours ago
dessert
25.1k673106
answered 4 hours ago
rm-vandarm-vanda
2,29821323
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 3 hours ago
dessert
25.1k673106
answered 4 hours ago
rm-vandarm-vanda
2,29821323
add a comment |
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 3 hours ago
dessert
25.1k673106
answered 4 hours ago
rm-vandarm-vanda
2,29821323
add a comment |
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 3 hours ago
dessert
25.1k673106
answered 4 hours ago
rm-vandarm-vanda
2,29821323
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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...
edited 3 hours ago
dessert
25.1k673106
answered 4 hours ago
rm-vandarm-vanda
2,29821323
edited 3 hours ago
dessert
25.1k673106
edited 3 hours ago
dessert
25.1k673106
edited 3 hours ago
dessert
25.1k673106
25.1k673106
answered 4 hours ago
rm-vandarm-vanda
2,29821323
answered 4 hours ago
rm-vandarm-vanda
2,29821323
answered 4 hours ago
rm-vandarm-vanda
2,29821323
2,29821323
add a comment |
add a comment |
grt is a new contributor. Be nice, and check out our Code of Conduct.
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grt is a new contributor. Be nice, and check out our Code of Conduct.
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