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edited May 26, 2020 at 12:16

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Assuming the quoted string at the end of each line can't contain a tab or a ;, this is probably all you need:

$ awk -F'\t' -v OFS=',' '$3=="mRNA"{ gsub(/;/,FS); gsub(/[^\t=]+=|"/,""); print $9, $15 }' file
Nitab4.5_0006317g0010.1,Peptidase S59%2C nucleoporin
Nitab4.5_0006317g0020.1,Putative S-adenosyl-L-methionine-dependent methyltransferase
Nitab4.5_0006317g0030.1,Unknown
Nitab4.5_0006317g0040.1,Heavy metal-associated domain%2C HMA
Nitab4.5_0006317g0050.1,Unknown
Nitab4.5_0002367g0010.1,Auxin response factor%2C B3 DNA binding domain%2C DNA-binding pseudobarrel domain%2C AUX/IAA protein%2C Aux/IAA-ARF-dimeriion
Nitab4.5_0002367g0020.1,Cellulose synthase
Nitab4.5_0002367g0030.1,Cellulose synthase
Nitab4.5_0002367g0040.1,Zinc finger%2C RING-type%2C Zinc finger%2C RING/FYVE/PHD-type
Nitab4.5_0002367g0050.1,SAC3/GANP/Nin1/mts3/eIF-3 p25%2C 26S proteasome non-ATPase regulatory subunit Rpn12

or (original idea):

$ cat tst.awk
BEGIN { FS="\t"; OFS="," }
$3 == "mRNA" {
    split($NF,f,/;/)
    for (i in f) {
        gsub(/^[^=]+="?|"$/,"",f[i])
    }
    print f[1], f[7]
}

$ awk -f tst.awk file
Nitab4.5_0006317g0010.1,Peptidase S59%2C nucleoporin
Nitab4.5_0006317g0020.1,Putative S-adenosyl-L-methionine-dependent methyltransferase
Nitab4.5_0006317g0030.1,Unknown
Nitab4.5_0006317g0040.1,Heavy metal-associated domain%2C HMA
Nitab4.5_0006317g0050.1,Unknown
Nitab4.5_0002367g0010.1,Auxin response factor%2C B3 DNA binding domain%2C DNA-binding pseudobarrel domain%2C AUX/IAA protein%2C Aux/IAA-ARF-dimerisation
Nitab4.5_0002367g0020.1,Cellulose synthase
Nitab4.5_0002367g0030.1,Cellulose synthase
Nitab4.5_0002367g0040.1,Zinc finger%2C RING-type%2C Zinc finger%2C RING/FYVE/PHD-type
Nitab4.5_0002367g0050.1,SAC3/GANP/Nin1/mts3/eIF-3 p25%2C 26S proteasome non-ATPase regulatory subunit Rpn12

If it can contain a , then you should reconsider using , as the OFS and use tab or ; instead.

Assuming the quoted string at the end of each line can't contain a tab or a ;:

$ cat tst.awk
BEGIN { FS="\t"; OFS="," }
$3 == "mRNA" {
    split($NF,f,/;/)
    for (i in f) {
        gsub(/^[^=]+="?|"$/,"",f[i])
    }
    print f[1], f[7]
}

$ awk -f tst.awk file
Nitab4.5_0006317g0010.1,Peptidase S59%2C nucleoporin
Nitab4.5_0006317g0020.1,Putative S-adenosyl-L-methionine-dependent methyltransferase
Nitab4.5_0006317g0030.1,Unknown
Nitab4.5_0006317g0040.1,Heavy metal-associated domain%2C HMA
Nitab4.5_0006317g0050.1,Unknown
Nitab4.5_0002367g0010.1,Auxin response factor%2C B3 DNA binding domain%2C DNA-binding pseudobarrel domain%2C AUX/IAA protein%2C Aux/IAA-ARF-dimerisation
Nitab4.5_0002367g0020.1,Cellulose synthase
Nitab4.5_0002367g0030.1,Cellulose synthase
Nitab4.5_0002367g0040.1,Zinc finger%2C RING-type%2C Zinc finger%2C RING/FYVE/PHD-type
Nitab4.5_0002367g0050.1,SAC3/GANP/Nin1/mts3/eIF-3 p25%2C 26S proteasome non-ATPase regulatory subunit Rpn12

If it can contain a , then you should reconsider using , as the OFS and use tab or ; instead.

Assuming the quoted string at the end of each line can't contain a tab or a ;, this is probably all you need:

$ awk -F'\t' -v OFS=',' '$3=="mRNA"{ gsub(/;/,FS); gsub(/[^\t=]+=|"/,""); print $9, $15 }' file
Nitab4.5_0006317g0010.1,Peptidase S59%2C nucleoporin
Nitab4.5_0006317g0020.1,Putative S-adenosyl-L-methionine-dependent methyltransferase
Nitab4.5_0006317g0030.1,Unknown
Nitab4.5_0006317g0040.1,Heavy metal-associated domain%2C HMA
Nitab4.5_0006317g0050.1,Unknown
Nitab4.5_0002367g0010.1,Auxin response factor%2C B3 DNA binding domain%2C DNA-binding pseudobarrel domain%2C AUX/IAA protein%2C Aux/IAA-ARF-dimeriion
Nitab4.5_0002367g0020.1,Cellulose synthase
Nitab4.5_0002367g0030.1,Cellulose synthase
Nitab4.5_0002367g0040.1,Zinc finger%2C RING-type%2C Zinc finger%2C RING/FYVE/PHD-type
Nitab4.5_0002367g0050.1,SAC3/GANP/Nin1/mts3/eIF-3 p25%2C 26S proteasome non-ATPase regulatory subunit Rpn12

or (original idea):

$ cat tst.awk
BEGIN { FS="\t"; OFS="," }
$3 == "mRNA" {
    split($NF,f,/;/)
    for (i in f) {
        gsub(/^[^=]+="?|"$/,"",f[i])
    }
    print f[1], f[7]
}

$ awk -f tst.awk file
Nitab4.5_0006317g0010.1,Peptidase S59%2C nucleoporin
Nitab4.5_0006317g0020.1,Putative S-adenosyl-L-methionine-dependent methyltransferase
Nitab4.5_0006317g0030.1,Unknown
Nitab4.5_0006317g0040.1,Heavy metal-associated domain%2C HMA
Nitab4.5_0006317g0050.1,Unknown
Nitab4.5_0002367g0010.1,Auxin response factor%2C B3 DNA binding domain%2C DNA-binding pseudobarrel domain%2C AUX/IAA protein%2C Aux/IAA-ARF-dimerisation
Nitab4.5_0002367g0020.1,Cellulose synthase
Nitab4.5_0002367g0030.1,Cellulose synthase
Nitab4.5_0002367g0040.1,Zinc finger%2C RING-type%2C Zinc finger%2C RING/FYVE/PHD-type
Nitab4.5_0002367g0050.1,SAC3/GANP/Nin1/mts3/eIF-3 p25%2C 26S proteasome non-ATPase regulatory subunit Rpn12

If it can contain a , then you should reconsider using , as the OFS and use tab or ; instead.

Source Link

answered May 26, 2020 at 12:08

Ed Morton

35.9k
6
25
60

Assuming the quoted string at the end of each line can't contain a tab or a ;:

$ cat tst.awk
BEGIN { FS="\t"; OFS="," }
$3 == "mRNA" {
    split($NF,f,/;/)
    for (i in f) {
        gsub(/^[^=]+="?|"$/,"",f[i])
    }
    print f[1], f[7]
}

$ awk -f tst.awk file
Nitab4.5_0006317g0010.1,Peptidase S59%2C nucleoporin
Nitab4.5_0006317g0020.1,Putative S-adenosyl-L-methionine-dependent methyltransferase
Nitab4.5_0006317g0030.1,Unknown
Nitab4.5_0006317g0040.1,Heavy metal-associated domain%2C HMA
Nitab4.5_0006317g0050.1,Unknown
Nitab4.5_0002367g0010.1,Auxin response factor%2C B3 DNA binding domain%2C DNA-binding pseudobarrel domain%2C AUX/IAA protein%2C Aux/IAA-ARF-dimerisation
Nitab4.5_0002367g0020.1,Cellulose synthase
Nitab4.5_0002367g0030.1,Cellulose synthase
Nitab4.5_0002367g0040.1,Zinc finger%2C RING-type%2C Zinc finger%2C RING/FYVE/PHD-type
Nitab4.5_0002367g0050.1,SAC3/GANP/Nin1/mts3/eIF-3 p25%2C 26S proteasome non-ATPase regulatory subunit Rpn12

If it can contain a , then you should reconsider using , as the OFS and use tab or ; instead.