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Top Forums Shell Programming and Scripting Count and search by sequence in multiple fasta file Post 302892110 by Don Cragun on Tuesday 11th of March 2014 04:27:00 AM
Old 03-11-2014
Without seeing your code, it is impossible to guess at whether or not something else is faster. You could try something like:
Code:
awk '
FNR == NR {
	if($1 ~ /^>/)
		t[++tn] = substr($1, 2)
	else {	s[$1] = tn
		seq[tn] = $1
	}
	next
}
FNR == 1 {
	fn++
}
$1 in s {
	tc[s[$1], fn]++
}
END {	# Print header:
	printf("\t\tsequence")
	for(i = 1; i <= fn; i++)
		printf("\tfile%d", i)
	printf("\n")
	# Print tag data:
	for(i = 1; i <= tn; i++) {
		printf("%s\t%s", t[i], seq[i])
		for(j = 1; j <= fn; j++)
			printf("\t\t%d", tc[i, j])
		printf("\n")
	}
}' Query File1 File2 File3

which with your sample input files produces:
Code:
		sequence	file1	file2	file3
tag1	TCGGA		1		0		1
tag2	TCTCA		2		2		0
tag3	TCTCGC		0		2		2

 

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SEQ(1)									FSF								    SEQ(1)

NAME
seq - print a sequence of numbers SYNOPSIS
seq [OPTION]... LAST seq [OPTION]... FIRST LAST seq [OPTION]... FIRST INCREMENT LAST DESCRIPTION
Print numbers from FIRST to LAST, in steps of INCREMENT. -f, --format=FORMAT use printf style floating-point FORMAT (default: %g) -s, --separator=STRING use STRING to separate numbers (default: ) -w, --equal-width equalize width by padding with leading zeroes --help display this help and exit --version output version information and exit If FIRST or INCREMENT is omitted, it defaults to 1. FIRST, INCREMENT, and LAST are interpreted as floating point values. INCREMENT should be positive if FIRST is smaller than LAST, and negative otherwise. When given, the FORMAT argument must contain exactly one of the printf- style, floating point output formats %e, %f, %g AUTHOR
Written by Ulrich Drepper. REPORTING BUGS
Report bugs to <bug-coreutils@gnu.org>. COPYRIGHT
Copyright (C) 2002 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU- LAR PURPOSE. SEE ALSO
The full documentation for seq is maintained as a Texinfo manual. If the info and seq programs are properly installed at your site, the command info seq should give you access to the complete manual. seq (coreutils) 4.5.3 February 2003 SEQ(1)
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