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Top Forums Shell Programming and Scripting Delete parts of a string of character in one given column of a tab delimited file Post 302293181 by matlavmac on Monday 2nd of March 2009 03:39:42 PM
Old 03-02-2009
Delete parts of a string of character in one given column of a tab delimited file

I would like to remove characters from column 7 so that from an input file looking like this:


>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD

I get something like that in an output file:

>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 chr8 6527777 F DD


where in column 7, "ref_chr8.fa" becomes "chr8" only.

Note: some lines of the file may present a letter instead of a number after chr, and two numbers before the dot and after chr: e.g. "ref_chrY.fa" should become "chrY", or "ref_chr10.fa" should become "chr10"

Thanks in advance for your help!!!!
 

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IPTCEMBED(3)								 1							      IPTCEMBED(3)

iptcembed - Embeds binary IPTC data into a JPEG image

SYNOPSIS
mixed iptcembed (string $iptcdata, string $jpeg_file_name, [int $spool]) DESCRIPTION
Embeds binary IPTC data into a JPEG image. PARAMETERS
o $iptcdata - The data to be written. o $jpeg_file_name - Path to the JPEG image. o $spool - Spool flag. If the spool flag is over 2 then the JPEG will be returned as a string. RETURN VALUES
If success and spool flag is lower than 2 then the JPEG will not be returned as a string, FALSE on errors. EXAMPLES
Example #1 Embedding IPTC data into a JPEG <?php // iptc_make_tag() function by Thies C. Arntzen function iptc_make_tag($rec, $data, $value) { $length = strlen($value); $retval = chr(0x1C) . chr($rec) . chr($data); if($length < 0x8000) { $retval .= chr($length >> 8) . chr($length & 0xFF); } else { $retval .= chr(0x80) . chr(0x04) . chr(($length >> 24) & 0xFF) . chr(($length >> 16) & 0xFF) . chr(($length >> 8) & 0xFF) . chr($length & 0xFF); } return $retval . $value; } // Path to jpeg file $path = './phplogo.jpg'; // We need to check if theres any IPTC data in the jpeg image. If there is then // bail out because we cannot embed any image that already has some IPTC data! $image = getimagesize($path, $info); if(isset($info['APP13'])) { die('Error: IPTC data found in source image, cannot continue'); } // Set the IPTC tags $iptc = array( '2#120' => 'Test image', '2#116' => 'Copyright 2008-2009, The PHP Group' ); // Convert the IPTC tags into binary code $data = ''; foreach($iptc as $tag => $string) { $tag = substr($tag, 2); $data .= iptc_make_tag(2, $tag, $string); } // Embed the IPTC data $content = iptcembed($data, $path); // Write the new image data out to the file. $fp = fopen($path, "wb"); fwrite($fp, $content); fclose($fp); ?> NOTES
Note This function does not require the GD image library. PHP Documentation Group IPTCEMBED(3)
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