python wrapper is slower than straight awk

[cc2qe]

time zcat Omni25_genotypes_2141_samples.b37.v2.vcf.gz | vawk --header '{ print $1,$2,$3,$4,$5,$6,$7,$8,$9,S$NA12878 }' | bgzip -c > NA12878.omni.vcf.gz
# real    19m43.893s
# user    21m27.138s
# sys     0m59.355s

# aside: outside python it's 25% faster
time zcat Omni25_genotypes_2141_samples.b37.v2.vcf.gz | awk 'BEGIN {FS=" "; OFS="\t"; } {if ($0~"^#") {if ($0!~"^##") { for (i=10;i<=NF;++i) SAMPLE[$i]=i; }; print} else {split($9,fmt,":"); SAMPLE_NA12878_ALL=$SAMPLE["NA12878"];  print $1,$2,$3,$4,$5,$6,$7,$8,$9,SAMPLE_NA12878_ALL }} END {}' - | bgzip -c > NA12878.omni2.vcf.gz
# real    15m28.737s
# user    17m1.151s
# sys     0m15.266s

[gpcr]

Thanks for creating and excellent tool; Is it possible to add a feature that affect all samples : ex: '{ if (I$AF>0.5) print $1,$2,$3,I$AN, $ALL_SAMPLES_section }'

PS: if VCF has hundreds of samples its difficult to input every sample tags (column format and all samples) in the command.
for example: S$*$GT represents all samples GT ?

[mdshw5]

Doesn't just plain "print" do that?

[cc2qe]

at the moment, " { print } | cut -f 10- " nearly accomplishes this, but I
will add that feature for cleaner queries.

On Monday, October 20, 2014, Matt Shirley notifications@github.com wrote:

Doesn't just plain "print" do that?

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Reply to this email directly or view it on GitHub
#4 (comment).

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[mdshw5]

Good point.

Matt Shirley http://mattshirley.com/

On Oct 20, 2014, at 2:27 PM, Colby Chiang notifications@github.com wrote:

at the moment, " { print } | cut -f 10- " nearly accomplishes this, but I
will add that feature for cleaner queries.

On Monday, October 20, 2014, Matt Shirley notifications@github.com wrote:

Doesn't just plain "print" do that?

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Reply to this email directly or view it on GitHub
#4 (comment).

Sent from mobile.
—
Reply to this email directly or view it on GitHub #4 (comment).

[gpcr]

It is very well acheived by regular awk and/or piping to post process...Combination of selection of info fileds and sub fileds of every sample information like GT etc directly though vawk...will be benefiial. As you are specialising the vawk for VCFs, I requested this feature....

@mdshw5 definelty plain "print" does not acheive that....needs post processing...

[cc2qe]

The feature described above has been added in commit a36785d

[gpcr]

@cc2qe : thanks working great