parsingawkgff

parsing using multiple parameters - Awk

I having trouble parsing out a GFF file. I am using the code below as a one liner. I am obtaining an output filtered based on column 1 ($1) but when I add the additional filter of greater than 5000 but less than 150000, awk does not filter out my file appropriately. I am misunderstanding something and I am not quite sure what it is.

awk '{ $1 = "s10"; 
$4 >= 50000 && $4 <=150000; 
print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6""\t"$7"\t"$8"\t"$9}' infile > outfile

input

S03       GeneWise        mRNA    7000       84000     40.00   -       .       ID=NA;Source=NA;Function="NA";
S07       GeneWise        CDS     80450       96070     .       -       0       Parent=NA;
S10       GeneWise        mRNA    96000       105032     50.00   -       .       ID=NA;Source=NA;Function="NA";
S10       GeneWise        CDS     43800       76000     .       -       0       Parent=NA;
S10      GeneWise        mRNA    175032       190540     41.11   +       .       ID=NA;Source=NA;Function="NA";
S11       GeneWise        CDS     3700       15000     .       +       0       Parent=NA;
S15       GeneWise        mRNA    18055       25000     40.00   -       .       ID=S15;Source=NA;Function="NA";

output i am obtaining with the error

S10       GeneWise        mRNA    96000       105032     50.00   -       .       ID=NA;Source=NA;Function="NA";
S10       GeneWise        CDS     43800       76000     .       -       0       Parent=NA;
S10      GeneWise        mRNA    175032       190540     41.11   +       .       ID=NA;Source=NA;Function="NA";

expected output

S10       GeneWise        mRNA    96000       105032     50.00   -       .       ID=NA;Source=NA;Function="NA";
Solution

  • This is the correct form for the conditional. However, there is only one matching record for it:

    $ awk ' 
$1 == "S10" && $4 >= 50000 && $4 <=150000 { 
    print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9
}' file
S10     GeneWise        mRNA    96000   105032  50.00   -       .       ID=NA;Source=NA;Function="NA";

    unless you want records with $1 == "S10" || $4 $4 >= 50000 && $4 <=150000 ie. using logical OR) but that would bring one extra record:

    awk ' 
$1 == "S10" || $4 >= 50000 && $4 <=150000 { 
    print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9
}' file
S07     GeneWise        CDS     80450   96070   .       -       0       Parent=NA;
S10     GeneWise        mRNA    96000   105032  50.00   -       .       ID=NA;Source=NA;Function="NA";
S10     GeneWise        CDS     43800   76000   .       -       0       Parent=NA;
S10     GeneWise        mRNA    175032  190540  41.11   +       .       ID=NA;Source=NA;Function="NA";

    Better form of the first:

    $ awk ' 
BEGIN { OFS="\t" }                           # define OFS to \t
$1 == "S10" && $4 >= 50000 && $4 <=150000 { 
    $1=$1                                    # rebuild the record
    print                                    # output
}' file