Netyjnd

Can somebody explain Brexit in a few child-proof sentences?

How can I replace every global instance of "x[2]" with "x_2"

The plural of 'stomach"

How could Frankenstein get the parts for his _second_ creature?

Is it okay / does it make sense for another player to join a running game of Munchkin?

Greatest common substring

There is only s̶i̶x̶t̶y one place he can be

Is there a problem with hiding "forgot password" until it's needed?

Implement the Thanos sorting algorithm

How does residential electricity work?

voltage of sounds of mp3files

What would happen if the UK refused to take part in EU Parliamentary elections?

What would be the benefits of having both a state and local currencies?

Star/Wye electrical connection math symbol

Do I need a multiple entry visa for a trip UK -> Sweden -> UK?

Best way to store options for panels

apt-get update is failing in debian

What is the term when two people sing in harmony, but they aren't singing the same notes?

Can a monster with multiattack use this ability if they are missing a limb?

Can I Retrieve Email Addresses from BCC?

Why does John Bercow say “unlock” after reading out the results of a vote?

Coordinate position not precise

Efficiently merge handle parallel feature branches in SFDX

At which point does a character regain all their Hit Dice?

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 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 | 

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

1 Answer
1

active

oldest

votes

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 | 

Your Answer

StackExchange.ready(function()
var channelOptions =
tags: "".split(" "),
id: "89"
;
initTagRenderer("".split(" "), "".split(" "), channelOptions);

StackExchange.using("externalEditor", function()
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled)
StackExchange.using("snippets", function()
createEditor();
);

else
createEditor();

);

function createEditor()
StackExchange.prepareEditor(
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader:
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
,
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
);



);

grt is a new contributor. Be nice, and check out our Code of Conduct.

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function ()
StackExchange.helpers.onClickDraftSave('#login-link');
);

Sign up using Google

Sign up using Facebook

Sign up using Email and Password

Post as a guest

Name

Email

Required, but never shown

StackExchange.ready(
function ()
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2faskubuntu.com%2fquestions%2f1128946%2fhow-to-combine-multiple-text-files-of-different-lengths-and-multiple-columns-by%23new-answer', 'question_page');

);

Post as a guest

Name

Email

Required, but never shown

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