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I would like to split a large file (10^6 rows) according to the value in the 6th column (about 10*10^3 unique values). However, I can't get it working because of the number of records. It should be easy but it's taking hours already and I'm not getting any further.
I've tried two options:
Option 1
awk '{print > $6".txt"}' input.file
awk: cannot open "Parent=mRNA:Solyc06g051570.2.1.txt" for output (Too many open files)
Option 2
awk '{print > $6; close($6)}' input.file
This doesn't cause an error but the files it creates contain only the last line corresponding to 'grouping' value $6
This is the beginning of my file, however, this file doesn't cause an error because it's so small:
exon 3688 4407 + ID=exon:Solyc06g005000.2.1.1 Parent=mRNA:Solyc06g005000.2.1
exon 4853 5604 + ID=exon:Solyc06g005000.2.1.2 Parent=mRNA:Solyc06g005000.2.1
exon 7663 7998 + ID=exon:Solyc06g005000.2.1.3 Parent=mRNA:Solyc06g005000.2.1
exon 9148 9408 + ID=exon:Solyc06g005010.1.1.1 Parent=mRNA:Solyc06g005010.1.1
exon 13310 13330 + ID=exon:Solyc06g005020.1.1.1 Parent=mRNA:Solyc06g005020.1.1
exon 13449 13532 + ID=exon:Solyc06g005020.1.1.2 Parent=mRNA:Solyc06g005020.1.1
exon 13711 13783 + ID=exon:Solyc06g005020.1.1.3 Parent=mRNA:Solyc06g005020.1.1
exon 14172 14236 + ID=exon:Solyc06g005020.1.1.4 Parent=mRNA:Solyc06g005020.1.1
exon 14717 14803 + ID=exon:Solyc06g005020.1.1.5 Parent=mRNA:Solyc06g005020.1.1
exon 14915 15016 + ID=exon:Solyc06g005020.1.1.6 Parent=mRNA:Solyc06g005020.1.1
exon 22106 22261 + ID=exon:Solyc06g005030.1.1.1 Parent=mRNA:Solyc06g005030.1.1
exon 23462 23749 - ID=exon:Solyc06g005040.1.1.1 Parent=mRNA:Solyc06g005040.1.1
exon 24702 24713 - ID=exon:Solyc06g005050.2.1.3 Parent=mRNA:Solyc06g005050.2.1
exon 24898 25402 - ID=exon:Solyc06g005050.2.1.2 Parent=mRNA:Solyc06g005050.2.1
exon 25728 25845 - ID=exon:Solyc06g005050.2.1.1 Parent=mRNA:Solyc06g005050.2.1
exon 36352 36835 + ID=exon:Solyc06g005060.2.1.1 Parent=mRNA:Solyc06g005060.2.1
exon 36916 38132 + ID=exon:Solyc06g005060.2.1.2 Parent=mRNA:Solyc06g005060.2.1
exon 57089 57096 + ID=exon:Solyc06g005070.1.1.1 Parent=mRNA:Solyc06g005070.1.1
exon 57329 58268 + ID=exon:Solyc06g005070.1.1.2 Parent=mRNA:Solyc06g005070.1.1
exon 59970 60505 - ID=exon:Solyc06g005080.2.1.24 Parent=mRNA:Solyc06g005080.2.1
exon 60667 60783 - ID=exon:Solyc06g005080.2.1.23 Parent=mRNA:Solyc06g005080.2.1
exon 63719 63880 - ID=exon:Solyc06g005080.2.1.22 Parent=mRNA:Solyc06g005080.2.1
exon 64143 64298 - ID=exon:Solyc06g005080.2.1.21 Parent=mRNA:Solyc06g005080.2.1
exon 66964 67191 - ID=exon:Solyc06g005080.2.1.20 Parent=mRNA:Solyc06g005080.2.1
exon 71371 71559 - ID=exon:Solyc06g005080.2.1.19 Parent=mRNA:Solyc06g005080.2.1
exon 73612 73717 - ID=exon:Solyc06g005080.2.1.18 Parent=mRNA:Solyc06g005080.2.1
exon 76764 76894 - ID=exon:Solyc06g005080.2.1.17 Parent=mRNA:Solyc06g005080.2.1
exon 77189 77251 - ID=exon:Solyc06g005080.2.1.16 Parent=mRNA:Solyc06g005080.2.1
exon 80044 80122 - ID=exon:Solyc06g005080.2.1.15 Parent=mRNA:Solyc06g005080.2.1
exon 80496 80638 - ID=exon:Solyc06g005080.2.1.14 Parent=mRNA:Solyc06g005080.2.1
317
AWK - 10 Examples to Split a File into Multiple Files 1. Split the file into 3 different files, one for each item. i.e, All records pertaining to Item1 into a file, records... 2. Split the files by having an extension of .txt to the new file names. $ awk -F, ' {print > $1".txt"}' file1 The only... ...
The files can be split into multiple files either based on a condition, or based on a pattern or because the file is big and hence needs to split into smaller files. Let us consider a sample file with the following contents: 1.
If you have more than one input file, which all have a header line, you can simply place them all as arguments to the awk call, as in awk -F'|' ' ... ' a.txt b.txt c.txt ... If, however, only the first file has a header line, you would need to change FNR to NR in the first rule.
As noted by Ed Morton, the simple approach only works if the number of different output files is small (max. around 10). GNU awk will still continue working, but become slower due to automatically closing and opening files in the background as needed; other awk implementations may simply fail due to "too many open files".
Option 2, use “>>” instead of “>”, to append.
awk '{print >> $6; close($6)}' input.file
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