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Full Discussion: Modifications to a file
Top Forums Shell Programming and Scripting Modifications to a file Post 302370568 by summer_cherry on Wednesday 11th of November 2009 09:47:28 PM
Old 11-11-2009
Code:
my $name;
my $header='track type=wiggle_0 name="Name" description="Name" visibility=full autoScale=off viewLimits=-5:1.25 color=0,100,0 altColor=0,100,0 priority=30 yLineOnOff=on variableStep chrom=<NAME> span=1';
while(<DATA>){
	chomp;
	my @tmp=split;
	if($name eq "" || $name ne $tmp[0]){
		$name=$tmp[0];
		(my $tmp_header=$header)=~s/<NAME>/$name/;
		print $tmp_header,"\n"; 
	}
	print "@tmp[1..$#tmp]\n";
}
__DATA__
chr1  2  4
chr1  2  5
chr1  3  6
chr2  1  4
chr2  2  5

 

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TE(1p)							User Contributed Perl Documentation						    TE(1p)

NAME
te (table editor) - front-end that simplifies editing tab-delimited text tables SYNOPSIS
te file1 [ file2 ... ] DESCRIPTION
This program makes it easier to edit tab-delimited ASCII tables, such as are used with Interchange (see icdevgroup.org), and can be exported from many popular spreadsheet and database applications. It converts tab-delimited ASCII files that have one record per line into temporary files with one field per line, each line beginning with the field name. It then sends each file to your favorite text editor. After you exit your editor, it checks to see if you changed anything in the file, and if so, it converts the data back to the tab-delimited format with one record per line, and replaces the original file. The first line of each input file must contain the field names, tab-delimited, that apply for that file. Editing is pretty straightforward when you see it in action. The rules are: o Empty lines are ignored. o Comment lines (beginning with "#") are ignored at the beginning of the file, and terminate a record in the middle. o The fields in the first record are used in all subsequent records, and the order in which they are specified are the order in which the columns will be written. o To delete a column, delete its line in the first record. o To change which order the columns are in, re-order the first record. o To add a column, add it to the first record (and as many subsequent records as you wish). Note that if you're using the "extended" option (-e), you can't add new columns, because they can't be distinguished from the extended fields that go into the serialized hash. You'd need to do that in a separate pass. o If you delete a column, you do not need to delete it from every record; any instances of that field in records after the first will be ignored. o Any space left after the field name and colon (like "fieldname:") will be included as part of the field. Any tabs you put in the field data itself will be converted to spaces (as they would corrupt the table otherwise). o A record can be deleted by removing all its fields. A new record can be added by inserting a new block of all fields at a record boundary. o If any errors are encountered, such as non-existent field names or lines that don't follow the prescribed format, processing aborts immediately and the original file is left untouched. You can edit several files in succession by naming each on the command line. The editor will be called for each one independently. If you start editing many files and decide you want to stop, add a line "#DONE" anywhere in the temporary file and save it. The current file will be processed and saved, but the rest will be skipped. As is customary with many Unix applications, you can set the environment variables VISUAL or EDITOR to point to your favorite text editor. If neither of those is set, my favorite editor, vi(1) is used. Options will also be read from environment variable TE_OPTIONS if it is set. AUTHOR
Jon Jensen <jon@endpoint.com> COPYRIGHT
Copyright (C) 2002-2008 Jon Jensen and others Copyright (C) 2001-2002 Red Hat, Inc. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License at http://www.fsf.org/copyleft/gpl.html for more details. VERSION
2008-04-12 02:33:40 CHANGELOG
2001-04-26. Initial release. 2001-05-04. Make temporary file in working directory instead of using POSIX::tmpnam. Keep ownership and permissions of original file. Fixed bug that caused fields with number "0" to be output as empty strings. 2001-05-06. Fix problem with how temporary file names were generated. 2001-07-31. Check for VISUAL environment variable, and handle editor options there or in EDITOR if given. Take advantage of Digest::MD5's native file reading instead of doing it ourselves. 2001-10-03. Added gvim support by forcing foreground option -f. 2002-07-23. Remove line endings whether CR, LF, or CRLF, instead of using running Perl's platform-specific chomp. If preserving a trailing solitary CR in the last field of a line is important, you'll want to change this behavior. 2002-08-30. Add option -s for starting value support (really only vi). te -s os28004 <file> Jumps to first occurrence of "os28004" in <file>. Option -i ignores case in the search. (By Mike Heins.) 2002-09-02. Add option -f to handle files without field names. 2002-09-03. Add option -n to number rows in comments. Allow setting of persistent options in environment variable TE_OPTIONS. 2004-06-07. Fixed bug that misinterpreted file as having no data rows when last line of file was empty. 2005-08-29. Added ability to delete, re-order, or add columns by placing them in the first record. 2005-11-15. Added support for extended columns containing Perl serialized hashes with the -e option. 2008-04-11. Added option -o to write output to a file and exit, never invoking an editor. By Greg Sabino Mullane. perl v5.14.2 2011-03-09 TE(1p)
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