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 13 hours ago
dessert
25.1k673106
asked 15 hours ago
grtgrt
16
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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 13 hours ago
dessert
25.1k673106
asked 15 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 13 hours ago
dessert
25.1k673106
asked 15 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 $14}' | sort | uniq -c
19404 circRNA
475 ciRNA
I want to produce a 'master' table of all identified circRNAs, with readnumber as column for each sample and flankintronas rownames:
command-line
command-line
edited 13 hours ago
dessert
25.1k673106
asked 15 hours ago
grtgrt
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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edited 13 hours ago
dessert
25.1k673106
asked 15 hours ago
grtgrt
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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edited 13 hours ago
dessert
25.1k673106
edited 13 hours ago
dessert
25.1k673106
edited 13 hours ago
dessert
25.1k673106
25.1k673106
asked 15 hours ago
grtgrt
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 15 hours ago
grtgrt
16
asked 15 hours ago
grtgrt
16
16
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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Check out our Code of Conduct.
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1 Answer
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If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 13 hours ago
dessert
25.1k673106
answered 14 hours ago
rm-vandarm-vanda
2,29821323
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 13 hours ago
dessert
25.1k673106
answered 14 hours ago
rm-vandarm-vanda
2,29821323
add a comment |
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 13 hours ago
dessert
25.1k673106
answered 14 hours ago
rm-vandarm-vanda
2,29821323
add a comment |
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 }' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
edited 13 hours ago
dessert
25.1k673106
answered 14 hours ago
rm-vandarm-vanda
2,29821323
If all of the columns in all of the files are in the same order, then just concat them together with >>:
for x in {1..60}; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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 13 hours ago
dessert
25.1k673106
answered 14 hours ago
rm-vandarm-vanda
2,29821323
edited 13 hours ago
dessert
25.1k673106
edited 13 hours ago
dessert
25.1k673106
edited 13 hours ago
dessert
25.1k673106
25.1k673106
answered 14 hours ago
rm-vandarm-vanda
2,29821323
answered 14 hours ago
rm-vandarm-vanda
2,29821323
answered 14 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.
grt is a new contributor. Be nice, and check out our Code of Conduct.
grt is a new contributor. Be nice, and check out our Code of Conduct.
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