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How to combine multiple text files of different lengths and multiple columns by a column
The Next CEO of Stack OverflowUsing 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
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 flankintron
as rownames:
command-line
New contributor
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 flankintron
as rownames:
command-line
New contributor
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 flankintron
as rownames:
command-line
New contributor
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 $14' | sort | uniq -c
19404 circRNA
475 ciRNA
I want to produce a 'master' table of all identified circRNAs
, with readnumber
as column for each sample and flankintron
as rownames:
command-line
command-line
New contributor
New contributor
edited 2 days ago
dessert
25.2k673106
25.2k673106
New contributor
asked 2 days ago
grtgrt
161
161
New contributor
New contributor
add a comment |
add a comment |
1 Answer
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If all of the columns in all of the files are in the same order, then just concat them together with >>
:
for x in 1..60; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 ' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
add a comment |
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1 Answer
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1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
If all of the columns in all of the files are in the same order, then just concat them together with >>
:
for x in 1..60; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 ' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
add a comment |
If all of the columns in all of the files are in the same order, then just concat them together with >>
:
for x in 1..60; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 ' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
add a comment |
If all of the columns in all of the files are in the same order, then just concat them together with >>
:
for x in 1..60; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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","$1 ' Sample_2.txt >> Sample_Master.txt
But with 60 files, that would be more work than- something like writing a python script using python's csv lib...
If all of the columns in all of the files are in the same order, then just concat them together with >>
:
for x in 1..60; do
# These flags for tail just cut of the top line, which is your headers
tail -n 2 Sample_$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 2 days ago
dessert
25.2k673106
25.2k673106
answered 2 days ago
rm-vandarm-vanda
2,31821323
2,31821323
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.
grt is a new contributor. Be nice, and check out our Code of Conduct.
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