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Top Forums Shell Programming and Scripting awk conditional operators- lookup value in 2nd file Post 303024994 by vgersh99 on Monday 22nd of October 2018 11:13:48 AM
Old 10-22-2018
Quote:
Originally Posted by Geneanalyst
Sorry vgersh99, but your code doesn't produce the desired output. Only 2 rows were printed
please provide the output of cat -vet file1.txt using code tags.
With the properly formatted file1.txt (tab-delimited fields), I get:
Code:
awk -F '\t' 'FNR==NR {f3[$1];next} $1 in f3' OFS="\t" gene3.txt gene1.txt
BY1038  23497067        C->G
BY1039  14032743        A->T
BY2222  2720236 A->G
BY30211 7625503 C->A
CTS10416        16513268        T->C
CTS10700        16651541        G->T
CTS10879        14409483        A->C

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
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