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Full Discussion: Check whether a given file is in ASCII format and data is tab-delimited
Top Forums Shell Programming and Scripting Check whether a given file is in ASCII format and data is tab-delimited Post 302116097 by cfajohnson on Tuesday 1st of May 2007 07:30:02 PM
Old 05-01-2007
Quote:
Originally Posted by Mandab
Hi,
I am trying to execute the following script but I am getting error:

What is the error?
Quote:
My requirement is to check whether the data in the file is tab delimited and pass error as say "105" to var1 and desc as "not tab delimited" to var2 and also check for the data which starts from 3rd line of the file. If the above condition satisfies it should check whether field 1 datatype and length(numeric(9)) are same or not and also whether it is null. If not var1 = "101" and var2 desc "Missing/wrong field1", field 2 datatype and length(char(9)) are same or not also for null. if not then var1 ="102" var2 "Missing/wrong field2" and so on. Any help would be appreciated.


Here is the code:

If it's code, please put it inside [CODE] tags so that it is properly formatted.
Quote:
#!/bin/ksh
eval $(awk 'BEGIN { IFS = "\t" }

What is the ouput of the awk script that you expect to eval?

In order to use eval, you need to output valid shell code.
Quote:
NR>=3 {print $1}
!/\t/ ## check whether lines contain tab else var1="105" and var2="No Tabs"
{
if ( length($1) == 0 || $1 !~ /[^0-9]/ ) ## check for null and numeric value and length(9)

You haven't checked that the length is 9. You have checked that it is not empty and that it doesn't contain any numbers.
Quote:
then

That is not awk syntax.
Quote:
var1="101"
var2="Missing or wrong First Field"
elif ( length($2) == 0 || $2 !~ /[a-zA-Z]/ ) ## check for null and char value and length(9)

There is no 'then', 'elif', or 'fi' keyword in awk.

You still haven't (even after the syntax is fixed) checked that the length is 9. You have checked that it is not empty and that it doesn't contain any letters.
Quote:
then
var1="102"
var2="Missing or Wrong Second Field"
fi
}
}' $1)

echo "$var1"
echo "$var2"

I suggest that you start with the code I posted, and tell us what it lacks. (Reply directly to that post, quoting relevant segments.)

 

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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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