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Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951309 by Scrutinizer on Wednesday 5th of August 2015 03:39:48 AM
Old 08-05-2015
Maybe because FS is set to '\t' and there appear to be no TABs in your second sample file, so the fields will not match. And you are setting the index to the entire record, save the first character. which is probably not what you want (you probably meant to use $1 here, but that would not be a sure way to do it either, because in the FASTA format the identifier is allowed to contain spaces). And the FASTA file is word wrapped, so you need to take out the newlines and not use getline to get only the second line ....

The best way to do that is is to use ">" as a record separator and use "\n" as the field separator. By setting OFS as the empty string, and assigning a value to one of the fields, all newlines will be replaced by empty strings, so this will effectively remove the word wrap. And the sequence will become one continuous string, which will make it suitable for substring selection.

Using your file order, we would get something like this.
Code:
awk 'NR==FNR{i=$1; $1=x; A[i]=$0; next} $1 in A{print ">" $1 ORS substr(A[$1], $2, $3-$2+1)}' RS=\> FS='\n' OFS= file1 FS=" " RS="\n" file2


If we read the files the other way around, then it becomes more memory efficient:
Code:
awk 'NR==FNR{S[$1]=$2; E[$1]=$3; next} $1 in S{i=$1; $1=x; print RS i FS substr($0,S[i],E[i]-S[i]+1)}' file2 RS=\> FS='\n' OFS= file1


Last edited by Scrutinizer; 08-05-2015 at 04:52 AM..
 

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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 one of the file names 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. Input fields are normally separated spaces or tabs; output fields by space. In this case, multiple separators count as one, and leading separators are discarded. The following options are recognized, with POSIX syntax. -a n In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -v n Like -a, omitting output for paired lines. -e s Replace empty output fields by string s. -1 m -2 m Join on the mth field of file1 or file2. -jn m Archaic equivalent for -n m. -ofields Each output line comprises the designated fields. The comma-separated field designators are either 0, meaning the join field, or have the form n.m, where n is a file number and m is a field number. Archaic usage allows separate arguments for field designators. -tc Use character c as the only separator (tab character) on input and output. Every appearance of c in a line is significant. EXAMPLES
sort /adm/users | join -t: -a 1 -e "" - bdays Add birthdays to password information, leaving unknown birthdays empty. The layout of is given in users(6); bdays contains sorted lines like tr : ' ' </adm/users | sort -k 3 3 >temp join -1 3 -2 3 -o 1.1,2.1 temp temp | awk '$1 < $2' Print all pairs of users with identical userids. SOURCE
/sys/src/cmd/join.c SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b -ky,y; with -t, the sequence is that of sort -tx -ky,y. One of the files must be randomly accessible. JOIN(1)
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