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Full Discussion: splitting tab-delimited file with awk
Top Forums Shell Programming and Scripting splitting tab-delimited file with awk Post 302296184 by perkele on Tuesday 10th of March 2009 02:51:24 PM
Old 03-10-2009
splitting tab-delimited file with awk
Hi all, I need help to split a tab-delimited list into separate files by the filename-field. The list is already sorted ascendingly by filename, an example list would look like this;

filename001 word1 word2
filename001 word3 word4
filename002 word1 word2
filename002 word3 word4
filename002 word5 word6

I have tried this using a slightly modified bash script which I found here on unix.com :

awk -F"\t" 'OFS="\t"{print >> ($1 ".tab")}' tabdelimitedfile.tab

This outputs the files filename001.tab and filename002.tab

Unfortuneatly this will not work on larger files than the example listed above if too many different file names are found. I get the error message "awk: *.tab makes too many open files" on exit.

I would be grateful if anyone could suggest an alternative way which outputs one file at a time every time a new filename is encountered.

Cheers

Per
 

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LEARN ABOUT DEBIAN

vcf-isec

VCF-ISEC(1)							   User Commands						       VCF-ISEC(1)

NAME

       vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files

SYNOPSIS

       vcf-isec [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.

	      Note that lines from all files can be intermixed together on the output, which can yield unexpected results.

OPTIONS

       -C, --chromosomes <list|file>
	      Process the given chromosomes (comma-separated list or one chromosome per line in a file).

       -c, --complement
	      Output positions present in the first file but missing from the other files.

       -d, --debug
	      Debugging information

       -f, --force
	      Continue even if the script complains about differing columns.

       -o, --one-file-only
	      Print only entries from the left-most file. Without -o, all unique positions will be printed.

       -n, --nfiles [+-=]<int>
	      Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.

       -p, --prefix <path>
	      If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)

       -t, --tab <chr:pos:file>
	      Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)

       -w, --win <int>
	      In  repetitive  sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
	      SNP or an indel).

       -h, -?, --help
	      This help message.

EXAMPLES

	      bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz

vcf-isec 0.1.5							     July 2011							       VCF-ISEC(1)
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