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Add specific string to last field of each line in perl based on value

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Top Forums Shell Programming and Scripting Add specific string to last field of each line in perl based on value
# 8  
Old 06-29-2016
Hi, cmccabe.

The following liner can be in three major parts
Code:
perl -ple '   # -p will print every line in a loop.
              # -l will remove the end of line and add it after each print.
              # -e will tell the binary perl to interpret the following as code.
BEGIN{%h=qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom)}  # Before any line is processed, create a lookup hash table
 /([0-2]\/[0-2])/ and $_ .=" $h{$1}"   # capture any combination of digit/digit from 0 to 2 inclusive
                                       # and use it as the index to the lookup hash table {$1} to append to the current line
' input > results.txt

However, I do believe you are a bit confused, there is no calculation of STB in this liner. You used another command previously to calculate that. Please, see here

In fact, the latest posted input, will not produced the previously shown achieved output. You run that command over the input shown in post number 1 of this thread.

If you were to run the following modified version with the input posted in #1, you might get what you want.
Code:
perl -plae 'BEGIN{%h=qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom)} /([0-2]\/[0-2])/ and $_ .=join ("\t", "", $h{$1}, int($F[5]/33+0.5), "score")' inputs > results.txt

I am going to leave it up to you to combine both commands, if you want to apply to the input shown in the following thread.
However, I am going to explain as well the additions highlighted in red.
Code:
-a  # creates an array @F for each line separating it by blank spaces.
 $_ .=join ("\t", "", $h{$1}, int($F[5]/33+0.5), "score") # insert a tab to the list of elements passed as argument to join, append to the current line.
int($F[5]/33+0.5) # use the value in the 5th column (starts at zero) to make the calculation you asked for.

Last edited by Aia; 06-29-2016 at 12:51 AM..
This User Gave Thanks to Aia For This Post:
cmccabe
# 9  
Old 06-29-2016
My attempt at combining the two threads into one perl code:

Code:
perl -plae 'BEGIN{%h=qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom)} /([0-2]\/[0-2])/ and $_ .=join ("\t", "", $h{$1}, int($F[5]/33+0.5)) and $_ .=join ("\t", "", /^[^#].*FDP=(\d+);.*STB=(\d+\.\d+);/ and $_.=($2 >= 0.8?" STRAND BIAS ":" GOOD ")).$1."' input > result
Can't find string terminator '"' anywhere before EOF at -e line 1.

I appreciate all your help and explanations Smilie
Last edited by cmccabe; 06-29-2016 at 06:53 PM.. Reason: added edit
# 10  
Old 06-29-2016
Code:
perl -plae '
    BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) }
    /^[^#].*FDP=(\d+);.*STB=(\d+\.\d+);.*([0-2]\/[0-2])/ and
    $_ .= join "\t", ("", ($2 >= 0.8 ? "STRAND BIAS" : "GOOD"), $1, "reads", $h{$3}, int($F[5]/33+0.5), "score")
' input > result

This User Gave Thanks to Aia For This Post:
cmccabe
# 11  
Old 06-30-2016
Why does the lines in bold repeat? I have tried different combinations with no luck in figuring it out. The lines in italics are correct, but the lines in bold are at the beginning and do not need to be there. Thank you very much Smilie.

Code:
perl -plae '
    BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) }
    /^[^#].*FDP=(\d+);.*STB=(\d+\.\d+);.*([0-2]\/[0-2])/ and
    $_ .= join "\t", ("", ($2 >= 0.8 ? "STRAND BIAS" : "GOOD"), $1, $h{$3}, int($F[5]/33+0.5))
' input > result

result
Code:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    9324670    .    A    G    672.016    PASS    AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73 GOOD 282 reads    GOOD    282    het    20
chr1    10318652    .    C    G    360.217    PASS    AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24 GOOD 127 reads    GOOD    127    hom    11
chr1    10355834    .    C    T    504.995    PASS

# 12  
Old 06-30-2016
Please, verify that your input does not terminate with the string GOOD number reads, already. The shown Perl run instance is not responsible for the highlighted bold string that you posted.
This User Gave Thanks to Aia For This Post:
cmccabe
# 13  
Old 07-01-2016
I didn't even notice that.... thank you very much Smilie.
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