Perl to extract values and print at end of each line


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# 1  
Perl to extract values and print at end of each line

In the below perl I am trying to extract and print the values AF1=, the GT value, and F[5] or QUAL diveded by 33 (rounded to the nearest whole #). The GT value is at the end after the GT:PL so all the possibilities are read into a hash h, then depending on the value that is in the line the coresponding het ot hom results. The command does execute but the file is not changed. I know many of the regex in the command are not used but I need to keep the same format (this is a special case scenario). Thank you Smilie.



file
Code:
##bcftools_callVersion=1.8+htslib-1.8
##bcftools_callCommand=call -c -; Date=Thu May 16 12:25:46 2019
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	xxxx
chr1	235972435	.	T	C	195.009	.	DP=744;VDB=0.27972;SGB=-0.693147;RPB=0.506757;MQB=0.997295;MQSB=0.616175;BQB=0.810181;MQ0F=0;AF1=0.5;AC1=1;DP4=218,151,192,179;MQ=58;FQ=188.502;PV4=0.0462442,1,0.32459,1	GT:PL	0/1:225,0,216
chr2	220022998	.	G	.	283.236	.	DP=456;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.840495;BQB=1;MQ0F=0;AF1=0;AC1=0;DP4=245,209,1,0;MQ=59;FQ=-281.989;PV4=1,0.0010322,1,4.68871e-09	GT:PL	0/0:0
chr3	128205860	.	G	C	221.999	.	DP=353;VDB=0.00961268;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.685507;BQB=1;MQ0F=0;AF1=1;AC1=2;DP4=0,1,147,176;MQ=57;FQ=-281.989;PV4=1,1,1,0.30647	GT:PL	1/1:255,255,0
chr5	35871190	.	G	A	170.009	.	DP=173;VDB=0.000529499;SGB=-0.693147;RPB=0.605358;MQB=0.998833;MQSB=0.99703;BQB=0.113906;MQ0F=0;AF1=0.5;AC1=1;DP4=41,52,35,39;MQ=55;FQ=172.502;PV4=0.754883,1,1,1	GT:PL	0/1:200,0,209
chr5	77412011	.	A	G	161.009	.	DP=293;VDB=0.0010866;SGB=-0.693147;RPB=0.990047;MQB=0.923303;MQSB=0.967232;BQB=0.000232632;MQ0F=0;AF1=0.5;AC1=1;DP4=83,74,71,50;MQ=57;FQ=164.015;PV4=0.394406,2.23136e-05,1,1	GT:PL	0/1:191,0,225
chr7	66459269	.	C	.	136.006	.	DP=316;MQSB=0.314206;MQ0F=0.00316456;AF1=0;AC1=0;DP4=122,176,0,0;MQ=12;FQ=-281.989	GT:PL	0/0:0

perl
Code:
perl -plae ' 
 BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) } /^[^#].*AF1=(\d+\.?\d*);.*FDP=(\d+);.*FSAF=(\d+);.*FSAR=(\d+);.*HRUN=(\d+);.*STB=(\d+\.?\d*)[,;].*([0-2]\/[0-2])/ and $_ .= join "\t", ("",  sprintf("%1.3f",$9), $h{$7}, int($F[5]/33+0.5))' file

desired tab-delimited
Code:
##bcftools_callVersion=1.8+htslib-1.8
##bcftools_callCommand=call -c -; Date=Thu May 16 12:25:46 2019
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	xxxx
chr1	235972435	.	T	C	195.009	.	DP=744;VDB=0.27972;SGB=-0.693147;RPB=0.506757;MQB=0.997295;MQSB=0.616175;BQB=0.810181;MQ0F=0;AF1=0.5;AC1=1;DP4=218,151,192,179;MQ=58;FQ=188.502;PV4=0.0462442,1,0.32459,1	GT:PL	0/1:225,0,216	0.50	het	6
chr2	220022998	.	G	.	283.236	.	DP=456;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.840495;BQB=1;MQ0F=0;AF1=0;AC1=0;DP4=245,209,1,0;MQ=59;FQ=-281.989;PV4=1,0.0010322,1,4.68871e-09	GT:PL	0/0:0	0.00	hom	9
chr3	128205860	.	G	C	221.999	.	DP=353;VDB=0.00961268;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.685507;BQB=1;MQ0F=0;AF1=1;AC1=2;DP4=0,1,147,176;MQ=57;FQ=-281.989;PV4=1,1,1,0.30647	GT:PL	1/1:255,255,0	1.00	hom	7
chr5	35871190	.	G	A	170.009	.	DP=173;VDB=0.000529499;SGB=-0.693147;RPB=0.605358;MQB=0.998833;MQSB=0.99703;BQB=0.113906;MQ0F=0;AF1=0.5;AC1=1;DP4=41,52,35,39;MQ=55;FQ=172.502;PV4=0.754883,1,1,1	GT:PL	0/1:200,0,209	0.50	het	5
chr5	77412011	.	A	G	161.009	.	DP=293;VDB=0.0010866;SGB=-0.693147;RPB=0.990047;MQB=0.923303;MQSB=0.967232;BQB=0.000232632;MQ0F=0;AF1=0.5;AC1=1;DP4=83,74,71,50;MQ=57;FQ=164.015;PV4=0.394406,2.23136e-05,1,1	GT:PL	0/1:191,0,225
chr7	66459269	.	C	.	136.006	.	DP=316;MQSB=0.314206;MQ0F=0.00316456;AF1=0;AC1=0;DP4=122,176,0,0;MQ=12;FQ=-281.989	GT:PL	0/0:0	0.50	hom	4


Last edited by cmccabe; 05-16-2019 at 04:49 PM.. Reason: fixed format
# 2  
Your code regex part doesn't have reference for GT:PL value and need to modify the regex part.
Try the below code and you can add more regex based on your needs.

Code:
 perl -plane ' BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) } /^[^#].*AF1=(\d+\.?\d*);.*GT:PL\s*([^:]+):/ and $_ .= join "\t", ("",  sprintf("%1.2f",$1), $h{$2}, int($F[5]/33+0.5))' file

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