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Proper way to pipe into awk command

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# 1  
Old 10-20-2015
Proper way to pipe into awk command
What is the proper way to run two commands together?

For example, in the below I would like run a command in bold then pipe that output to awk to re-format it. Thank you Smilie.

Code:
bedtools nuc -fi /home/cmccabe/Desktop/bed/hg19.fa -bed /home/cmccabe/Desktop/bed/xgen_baits.bed > /home/cmccabe/Desktop/bed/xgen_GC_baits.bed | awk 'NR>1 {print $1, $2, $3, $4, $6, $8}' OFS="\t" xgen_GC_baits.bed > GC.bed

# 2  
Old 10-20-2015
Code:
command1 > tmp1
command2 < tmp1 > final.output

is functionally identical with
Code:
command1 | command2 > final.output

(and you don't need the tmp1 file)
awk can directly open a file if passed as an additional parameter. Do not pass one, and it reads from stdin (standard input).
Code:
bedtools nuc -fi /home/cmccabe/Desktop/bed/hg19.fa -bed /home/cmccabe/Desktop/bed/xgen_baits.bed |
 awk 'NR>1 {print $1, $2, $3, $4, $6, $8}' OFS="\t" > GC.bed

This User Gave Thanks to MadeInGermany For This Post:
cmccabe
# 3  
Old 10-20-2015
You can use stdout only once - either redirect to a file with > or pipe it to another command with | .
Should you REALLY need both, there's an equivalent to a plumber's T-fitting or T-piece: tee (surprise!). Use like cmd1 | tee outfile1 outfile2 ... | cmd2 > resfile1
This User Gave Thanks to RudiC For This Post:
cmccabe
# 4  
Old 10-20-2015
Thank you both Smilie.
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