bioawk for identifiers that don't match pattern
Hi, I tried using bioawk as follows
bioawk -c fastx '$name !/P/ { print ">"$name; print $seq }' < mat.fasta
bioawk -c fastx '$name ! /P/ { print ">"$name; print $seq }' < mat.fasta
but it says
bioawk: syntax error at source line 1
context is
$name >>> !/ <<<
bioawk: bailing out at source line 1
Could someone tell me what silly error I'm doing? Thanks
1 answer
(not tested) try
!($name ~ /P/ )
• 0 views
•
link
updated
by
Ram
•
written
by
Pierre Lindenbaum
•
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
How to reference input variable in output section of rule of Snakemake rule
written by Dhatri Badri •
-
error while installing peertools
written by rheab1230 •
-
bioawk looping to retrieve fasta sequences by seq ID pattern
written by shaharbra •
-
Altering bioawk script to take list.txt file as a command line parameter
written by dk0319 •
-
Getting error with awk when using parallel processing in bedtools
written by nastaran.esfahani •
-
Bioawk - using bash variables
written by spiral01
-
Locating Multiple Alternate Alleles in gatk.vcf file
written by oars
-
FASTQ Phred33 average base quality score
written by oars
-
How to append strings (from one file) to Fasta headers (in another file)
written by al-ash
-
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
written by Istvan Albert
Thanks! Worked perfectly!