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Full Discussion: Need to convert a pipe delimited text file to tab delimited
Top Forums UNIX for Dummies Questions & Answers Need to convert a pipe delimited text file to tab delimited Post 302940448 by Don Cragun on Monday 6th of April 2015 12:52:22 AM
Old 04-06-2015
Hi wisecracker,
I readily agree that the thread title, the text in post #1, and the examples given in post #1 all conflict with each other. And, in post #7, raja kakitapall tells us that the text or cvs or xls file is to be created by an unnamed database, and magically get excel to format that data for display in a mail message without invoking excel and without telling us what mail reader will be used to display the created xls file. But, I would never suggest writing a file one byte at a time using non-standard extensions to POSIX shell parameter expansions without knowing what operating system and shell the user is using. (And, even if I did know what shell they are using, I'd still use tr (or, if they also wanted to convert <newline> to <carriage-return><newline> for a Windows formatted file; sed).

It still isn't at all clear to me whether the OP wants to include a formatted table in the mail message (which has nothing to do with excel), or if the OP wants to attach an xls formatted file to be opened by the person receiving the mail using excel (which, as we have both already said could be done with the current text file format or with a text file using a comma or a tab as the field separator if the file's named ended with .csv).

Without a much clearer description of the actual environment, constraints, and desired output; I think we're stuck wasting time trying to guess at what might satisfy the OP.
 

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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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