How to extract the partial matching strings among two files? Post: 303035964

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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

06-11-2019

Registered User

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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merge

merge(1)						      General Commands Manual							  merge(1)

NAME

       merge - three-way file merge

SYNOPSIS

       file1 file2 file3

DESCRIPTION

       combines  two  files  that are revisions of a single original file.  The original file is file2, and the revised files are file1 and file3.
       identifies all changes that lead from file2 to file3 and from file2 to file1, then deposits the merged text into file1.	If the	option	is
       used, the result goes to standard output instead of file1.

       An  overlap  occurs  if both file1 and file3 have changes in the same place.  prints how many overlaps occurred, and includes both alterna-
       tives in the result.  The alternatives are delimited as follows:

	      lines in file1
	      lines in file3

       If there are overlaps, edit the result in file1 and delete one of the alternatives.

       This command is particularly useful for revision control, especially if file1 and file3 are the ends of two branches that have file2  as  a
       common ancestor.

EXAMPLES

       A typical use for is as follows:

	      1.   To  merge  an  RCS branch into the trunk, first check out the three different versions from RCS (see co(1)) and rename them for
		   their revision numbers: 5.2, 5.11, and 5.2.3.3.  File 5.2.3.3 is the end of an RCS branch that split off the trunk at file 5.2.

	      2.   For this example, assume file 5.11 is the latest version on the trunk, and is also a revision  of  the  "original"  file,  5.2.
		   Merge the branch into the trunk with the command:

	      3.   File  5.11  now  contains  all  changes  made on the branch and the trunk, and has markings in the file to show all overlapping
		   changes.

	      4.   Edit file 5.11 to correct the overlaps, then use the command to check the file back in (see ci(1)).

WARNINGS

       uses the ed(1) system editor.  Therefore, the file size limits of ed(1) apply to

AUTHOR

       was developed by Walter F. Tichy.

SEE ALSO

       diff3(1), diff(1), rcsmerge(1), co(1).

																	  merge(1)

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