awk RS/ORS error Post: 302968361

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Top Forums Shell Programming and Scripting awk RS/ORS error Post 302968361 by yifangt on Tuesday 8th of March 2016 05:17:18 PM

03-08-2016

Registered User

awk RS/ORS problem

Hello,
I am trying to filter fastq file (in short, every 4 lines to be a record) based on the GC counts (GC-contents) in sequence (i.e. field 2), which is the count % of the G/C chars in the string. The example script is to pick up records with GC contents > 0.6 in the sequence (second field).
One thing special is the "@" symbol is always the first char of the first row in each record, but it may appear in the third field of anywhere except the first position.
A sample input.file is:

Code:

@HWI-ST1410:193:C7847ANXX:3:1101:3144:2591
CCGCTTGGAGCGGATCAGGTAGTCGACCTGCTTAAGGAGGGC
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@HWI-ST1410:193:C7847ANXX:3:1101:3050:2607
CAAAAAAAATTTTCTATTTTACATATACAATGAAGAACGTCACTG
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFHHH
@HWI-ST1410:193:C7847ANXX:3:1101:3075:2609
CACTGTACTAAGCTTTGGCGCTGATTCCATAATTTCTTTCTC
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@HWI-ST1410:193:C7847ANXX:3:1101:3098:2622
GGTACGTACACATAATCCGTTGACTAGCTCGATACGATTACG
+
BBBBBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFF
@HWI-ST1410:193:C7847ANXX:3:1101:3097:2667
CCCGGCGGGAGAGGGACGGCAGGCTCGTCGGCGCCACAATCG
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

So far, my script is:

Code:

awk 'BEGIN{RS="\n@", FS="\n"; OFS="\n"} {s=$2; if (gsub(/[GC]/, "x", $2)/length($2)>0.6) print "@"$1, s, $3, $4}' input.file

My script seems not doing what I want, as the first record always has double "@@" for its record/sequence name.
How to deal with the first record without the "\n@" as the RS? Sometimes the "@" symbol was NOT put back in front of $1 to have the original string.
I am using GNU Awk 4.0.1 under Linux 3.19.0-32-generic ~14.04.1 Ubuntu.
Thanks a lot for any clue!

Last edited by yifangt; 03-08-2016 at 06:59 PM.. Reason: typos

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LEARN ABOUT LINUX

igawk

IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME

       igawk - gawk with include files

SYNOPSIS

       igawk [ all gawk options ] -f program-file [ -- ] file ...
       igawk [ all gawk options ] [ -- ] program-text file ...

DESCRIPTION

       Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).

       AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like

	      @include getopt.awk

       in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.

OPTIONS

       See gawk(1) for a full description of the AWK language and the options that gawk supports.

EXAMPLES

       cat << EOF > test.awk
       @include getopt.awk

       BEGIN {
	    while (getopt(ARGC, ARGV, "am:q") != -1)
		 ...
       }
       EOF

       igawk -f test.awk

SEE ALSO

       gawk(1)

       Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.

AUTHOR

       Arnold Robbins (arnold@skeeve.com).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)

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