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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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MU-EXTRACT(1)                                                 General Commands Manual                                                MU-EXTRACT(1)

NAME
mu_extract - display and save message parts (attachments), and open them with other tools. SYNOPSIS
mu extract [options] <file> mu extract [options] <file> <pattern> DESCRIPTION
mu extact is the mu sub-command for extracting MIME-parts (e.g., attachments) from mail messages. It works on message files, and does not require the message to be indexed in the database. For attachments, the file name used when saving it, is the name of the attachment in the message. If there is no such name, or when saving non-attachment MIME-parts, a name is derived from the message-id of the message. If you specify a pattern (a case-insensitive regular expression) as the second argument, all attachments with filenames matching that pat- tern will be extracted. The regular expressions are Perl-compatible (as per the PCRE-library). Without any options, mu extract simply outputs the list of leaf MIME-parts in the message. Only 'leaf' MIME-parts (including RFC822 attach- ments) are considered, multipart/* etc. are ignored. OPTIONS
-a, --save-attachments save all MIME-parts that look like attachments. --save-all save all non-multipart MIME-parts. --parts=<parts> only consider the following numbered parts (comma-separated list).The numbers for the parts can be seen from running mu extract without any options but only the message file. --target-dir=<dir> save the parts in the target directory rather than the current working directory. --overwrite overwrite existing files with the same name; by default overwriting is not allowed. --play Try to 'play' (open) the attachment with the default application for the particular file type. On MacOS, this uses the open program, on other platforms is uses xdg-open. You can choose a different program by setting the MU_PLAY_PROGRAM environment variable. EXAMPLES
To display information about all the MIME-parts in a message file: $ mu extract msgfile To extract MIME-part 3 and 4 from this message, overwriting existing files with the same name: $ mu extract --parts=3,4 --overwrite msgfile To extract all files ending in '.jpg' (case-insensitive): $ mu extract msgfile '.*.jpg' To extract an mp3-file, and play it in the the default mp3-playing application. $ mu extract --play msgfile 'whoopsididitagain.mp3' BUGS
Please report bugs if you find them: http://code.google.com/p/mu0/issues/list AUTHOR
Dirk-Jan C. Binnema <djcb@djcbsoftware.nl> SEE ALSO
mu(1) User Manuals February 2012 MU-EXTRACT(1)
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