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Top Forums UNIX for Beginners Questions & Answers How to extract the partial matching strings among two files? Post 303035964 by RudiC on Tuesday 11th of June 2019 03:29:16 AM
Old 06-11-2019
No surprise "it is not working" as none of your attempts is addressing your problem if at all syntactically correct.



Code:
awk 'FNR == NR {SRCH[$3 "-" $2]; next} $2 in SRCH {print ">" $0}' FS="[]- []*" file1 RS=">" ORS="" FS="[:
]" file2 
>Contig_152:50833-51615
CGGAGTAGCTTCGATCAGCGTGACCGGTACCGAGCGACCGTCTTCAGTGAAGACGCGGCT
CATACCAGCCTTGCGGCCCACGAAGCCCAACGAATATTTCTTCGTCATGGTCGTAGTCCT
CAGGTCAGCTTGATCTGGACGTCGACGCCAGCCGCGAGTTCGAGCTTCATCAGCGCGTCC
ACGGTCTTGTCGTTCGGGTCGACGATATCGAGCACACGCTTGTGCGTGCGGGTTTCGTAT
TGG
>Contig_152:50215-50829
TGCCAGCCACTCCTCGACCTTCTTGACCGCGTCGGCGGTGATCACGACCGTATCGGCCCC
GACCAGAGCGACCGGATCCAGACCCTGCACGTCACGCACCTGCACATACGGCAGGTTGCG
AGCGGACAGATACAGGTGCTCGGAAGCCTCTTCGGTGACGATCAGCGGGCGCTTGCCCAC
>Contig_152:45550-46116
GTTACGGAACGGGAACTTGAACGCTGCCAGCAGCGCCTTCGCTTCCGCATCCGTCTTGGC
GGTGGTGGTGATGGCGATATCCATACCGCGGATCGCGTCGACGGCGTCGAAGTCGATTTC
>Contig_152:44079-44618
AGCCTTCTTGGCTTCCTTGCGAATGATGACTTCACCGGCGTACTTCACACCCTTGCCCTT
GTAGGGCTCCGGCGGACGGAAACCGCGAATCTTGGCGGCAACTTCGCCGACGCGCTGCTT

Your desired output for "45550-46116" is missing a trailing "C".

Last edited by RudiC; 06-13-2019 at 05:02 AM..
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PHARDATA.EXTRACTTO(3)							 1						     PHARDATA.EXTRACTTO(3)

PharData::extractTo - Extract the contents of a tar/zip archive to a directory

SYNOPSIS
bool PharData::extractTo (string $pathto, [string|array $files], [bool $overwrite = false]) DESCRIPTION
Extract all files within a tar/zip archive to disk. Extracted files and directories preserve permissions as stored in the archive. The optional parameters allow optional control over which files are extracted, and whether existing files on disk can be overwritten. The sec- ond parameter files can be either the name of a file or directory to extract, or an array of names of files and directories to extract. By default, this method will not overwrite existing files, the third parameter can be set to true to enable overwriting of files. This method is similar to ZipArchive.extractTo(3). PARAMETERS
o $pathto - Path to extract the given files to o $files - The name of a file or directory to extract, or an array of files/directories to extract o $overwrite - Set to TRUE to enable overwriting existing files RETURN VALUES
returns TRUE on success, but it is better to check for thrown exception, and assume success if none is thrown. ERRORS
/EXCEPTIONS Throws PharException if errors occur while flushing changes to disk. EXAMPLES
Example #1 A PharData.extractTo(3) example <?php try { $phar = new PharData('myphar.tar'); $phar->extractTo('/full/path'); // extract all files $phar->extractTo('/another/path', 'file.txt'); // extract only file.txt $phar->extractTo('/this/path', array('file1.txt', 'file2.txt')); // extract 2 files only $phar->extractTo('/third/path', null, true); // extract all files, and overwrite } catch (Exception $e) { // handle errors } ?> SEE ALSO
Phar.extractTo(3). PHP Documentation Group PHARDATA.EXTRACTTO(3)
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