split a file into different files based on an array

Question

I have a file that looks like this:

1   10000   10400   GI.STMC.GAST-EnhA
1   10000   10400   SKIN.PEN.FRSK.FIB.02-EnhA 
1   10000   10400   BRN.DL.PRFRNTL.CRTX-EnhA
1   10000   10400   BRN.ANT.CAUD-EnhA
1   10000   10400   HRT.ATR.R-EnhA 
1   10200   10400   ESDR.H1.MSC-EnhA
1   10200   10400   GI.ESO-EnhA
1   10200   10400   GI.DUO.SM.MUS-EnhA
1   10200   10400   LNG-EnhA
1   14800   15200   MUS.TRNK.FET-EnhA

I want to split the files based on the annotations in the 4th column, I can extract the unique annotations with the following code:

sort -u file.list > annotation.list # file.list file with the different annotations

And I can store the information in annotation in an array with:

 mapfile -t myARRAY < annotation.list,

However I don't know how to split the file in different files containing only annotation, an example would be including the annotation "ADRL.GLND.FET-TssA":

1   713800  714800  ADRL.GLND.FET-TssA
1   762000  763200  ADRL.GLND.FET-TssA 
1   948600  948800  ADRL.GLND.FET-TssA
1   1166800 1167400 ADRL.GLND.FET-TssA
1   1208600 1208800 ADRL.GLND.FET-TssA
1   1243400 1243800 ADRL.GLND.FET-TssA
1   1244000 1244200 ADRL.GLND.FET-TssA
1   1284000 1284400 ADRL.GLND.FET-TssA
1   1310200 1310400 ADRL.GLND.FET-TssA
1   1310800 1311200 ADRL.GLND.FET-TssA

I might grep the unique annotations and output it to a file, but I am sure that could be a most elegant way,

Thanks

EDIT: so far i have this

mapfile -t myARRAY < annotation.list;
for ann in ${myARRAY}; do
     grep ${ann} roadmap.core_active.bed > ${ann}.annotation
done

However, I only got an annotation made

Fix your loop as follows: for ann in "${myARRAY[@]}"; do ... — Leon
– Leon, Commented Sep 1, 2016 at 18:56

John1024 · Accepted Answer · 2016-09-01 20:05:06Z

1

This will create each of the annotation files that you ask for:

awk '{print >$4".annotation"}' file.list

Awk implicitly reads through a file line-by-line. Here, we use a print statement with its output re-directed to a file whose name is made up of the fourth field with the suffix .annotation added.

The above will work unless there are a very large number of different annotations. In that case, you may hit your system limit for open files. To avoid that, we need to close files explicitly:

awk '{fname=$4".annotation"; print>fname; close(fname)}' file.list

edited Sep 1, 2016 at 20:05

answered Sep 1, 2016 at 18:56

John1024

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