concatenating different columns of different files bash script
I have a bunch of files, I want to concatenate 5th column of these files, but I don't know the number of files that find will find so I don't know what numbers I should put after cut -f
file names 456Ecoli.bed, 568Ecoli.bed, ..... Each file has 6 columns
The command doesn't work at all, I just wrote it to give you some idea of what I need.
find -name '*Ecoli.bed' -exec paste {} > All_Ecoli.bed; | cut -f 5,11,17, ....
Each bed file is something like
chr1 102 203 gene1 0.05 +
chr1 300 403 gene2 0.6 +
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Alex Reynolds
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Fatima
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Fatima
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Yes, I ran all the commands. I mean something like
score1fromfile1 score1fromfile2 score1formfile3
score2fromfile1 score2fromfile2 score2formfile3
score3fromfile1 score3fromfile2 score3formfile3
But your command gives me:
score1fromfile1
score2fromfile1
score3fromfile1
score1fromfile2
score2fromfile2
score3fromfile2
score1fromfile3
score2fromfile3
score3fromfile3
Using BEDOPS bedmap and bedops:
$ bedops --everything *Ecoli.bed | awk '($6=="+")' - > Ecoli.union.for.bed
$ bedops --everything *Ecoli.bed | awk '($6=="-")' - > Ecoli.union.rev.bed
$ bedmap --echo --echo-map-score --exact --multidelim '\t' Ecoli.union.for.bed > answer.for.bed
$ bedmap --echo --echo-map-score --exact --multidelim '\t' Ecoli.union.rev.bed > answer.rev.bed
$ bedops --everything answer.*.bed > answer.bed
$ cut -f7- answer.bed > answer.txt
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Thank you, but I want the output to have one column for every file. Something like when we use
cut -f 5,11,17Have you tried running either script? Create a few lines of model output and show us how it's different from what these scripts produce.
copy/pasted from here:https://www.linuxquestions.org/questions/linux-newbie-8/merge-columns-from-multiple-files-851336/. Please upvote the OP in that forum:
This would give you output in columns instead of rows.
Works like a charm, could you help me to add the title of each file above each column?