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Top Forums Shell Programming and Scripting awk to search field2 in file2 using range of fields file1 and using match to another field in file1 Post 302988185 by cmccabe on Wednesday 21st of December 2016 02:15:45 PM
Old 12-21-2016
Code:
awk -F'\t' -v OFS='\t' 'FNR==NR{A[$1]=$0;B[$1,++D[$1]]=$2;next} {++C[$1]}($2<B[$1,C[$1]] && $3>B[$1,C[$1]]){print A[$1]}' NA12878_GIAB_highconf.txt IDP.bed > NA12878_GIAB_highconf_IDP.txt

The above command works great except when I use my actual datasets, the output is blank. They are the exact same file formats


NA12878_GIAB_highconf is file2 in the example
~80MB
Code:
1    13116    .    T    G
1    13118    .    A    G
1    13656    .    CAG    C

IDP.txt is file1 in the example
~3MB
Code:
1    948953    948956    chr1:948953-948956    .    ISG15
1    949363    949858    chr1:949363-949858    .    ISG15

I was able to decrease the size but they are still too large to attach. Thank you Smilie.

Last edited by cmccabe; 12-21-2016 at 03:16 PM.. Reason: fixed format
 

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COMBINE(1)																COMBINE(1)

NAME
combine - combine sets of lines from two files using boolean operations SYNOPSIS
combine file1 and file2 combine file1 not file2 combine file1 or file2 combine file1 xor file2 _ file1 and file2 _ _ file1 not file2 _ _ file1 or file2 _ _ file1 xor file2 _ DESCRIPTION
combine combines the lines in two files. Depending on the boolean operation specified, the contents will be combined in different ways: and Outputs lines that are in file1 if they are also present in file2. not Outputs lines that are in file1 but not in file2. or Outputs lines that are in file1 or file2. xor Outputs lines that are in either file1 or file2, but not in both files. "-" can be specified for either file to read stdin for that file. The input files need not be sorted, and the lines are output in the order they occur in file1 (followed by the order they occur in file2 for the two "or" operations). Bear in mind that this means that the operations are not commutative; "a and b" will not necessarily be the same as "b and a". To obtain commutative behavior sort and uniq the result. Note that this program can be installed as "_" to allow for the syntactic sugar shown in the latter half of the synopsis (similar to the test/[ command). It is not currently installed as "_" by default, but you can alias it to that if you like. SEE ALSO
join(1) AUTHOR
Copyright 2006 by Joey Hess <joey@kitenet.net> Licensed under the GNU GPL. moreutils 2012-04-09 COMBINE(1)
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