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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










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:



screen shot of the file










share|improve this question









New contributor




grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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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:



    screen shot of the file










    share|improve this question









    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.






















      3












      3








      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:



      screen shot of the file










      share|improve this question









      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:



      screen shot of the file







      command-line






      share|improve this question









      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









      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




      share|improve this question








      edited Mar 26 at 22:30









      dessert

      25.3k673107




      25.3k673107






      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 Mar 26 at 20:14









      grtgrt

      161




      161




      New contributor




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      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.






      grt is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.




















          1 Answer
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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

























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            1 Answer
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            active

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            1 Answer
            1






            active

            oldest

            votes









            active

            oldest

            votes






            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





























              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



























                3












                3








                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

















                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














                share|improve this answer



                share|improve this answer








                edited Mar 26 at 22:34









                dessert

                25.3k673107




                25.3k673107










                answered Mar 26 at 20:43









                rm-vandarm-vanda

                2,35321423




                2,35321423




















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