修改注释文件mRNA行的第9列的顺序

awk -F '[\t;]' '{if($3~/mRNA/) {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9";"$14";"$10} else{print $0}}' Tcacao_523_v2.1.gene.gff3ne_check.gff3

JGI处理前

##gff-version 3
##annot-version v2.1
##species Theobroma cacao
Chromosome_1    phytozomev13    gene    5179    6646    .       +       .       ID=Thecc.01G000100.v2.1;Name=Thecc.01G000100;ancestorIdentifier=Thecc1EG000001.CGDv1.1
Chromosome_1    phytozomev13    mRNA    5179    6646    .       +       .       ID=Thecc.01G000100.1.v2.1;Name=Thecc.01G000100.1;pacid=42014905;longest=1;ancestorIdentifier=Thecc1EG000001t1.CGDv1.1;Parent=Thecc.01G000100.v2.1
Chromosome_1    phytozomev13    five_prime_UTR  5179    5317    .       +       .       ID=Thecc.01G000100.1.v2.1.five_prime_UTR.1;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     5318    5563    .       +       0       ID=Thecc.01G000100.1.v2.1.CDS.1;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     5705    5777    .       +       0       ID=Thecc.01G000100.1.v2.1.CDS.2;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     5865    6047    .       +       2       ID=Thecc.01G000100.1.v2.1.CDS.3;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     6307    6554    .       +       2       ID=Thecc.01G000100.1.v2.1.CDS.4;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    three_prime_UTR 6555    6646    .       +       .       ID=Thecc.01G000100.1.v2.1.three_prime_UTR.1;Parent=Thecc.01G000100.1.v2.1;pacid=42014905

处理后

##gff-version 3
##annot-version v2.1
##species Theobroma cacao
Chromosome_1    phytozomev13    gene    5179    6646    .       +       .       ID=Thecc.01G000100.v2.1;Name=Thecc.01G000100;ancestorIdentifier=Thecc1EG000001.CGDv1.1
Chromosome_1    phytozomev13    mRNA    5179    6646    .       +       .       ID=Thecc.01G000100.1.v2.1;Parent=Thecc.01G000100.v2.1;Name=Thecc.01G000100.1
Chromosome_1    phytozomev13    five_prime_UTR  5179    5317    .       +       .       ID=Thecc.01G000100.1.v2.1.five_prime_UTR.1;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     5318    5563    .       +       0       ID=Thecc.01G000100.1.v2.1.CDS.1;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     5705    5777    .       +       0       ID=Thecc.01G000100.1.v2.1.CDS.2;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     5865    6047    .       +       2       ID=Thecc.01G000100.1.v2.1.CDS.3;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    CDS     6307    6554    .       +       2       ID=Thecc.01G000100.1.v2.1.CDS.4;Parent=Thecc.01G000100.1.v2.1;pacid=42014905
Chromosome_1    phytozomev13    three_prime_UTR 6555    6646    .       +       .       ID=Thecc.01G000100.1.v2.1.three_prime_UTR.1;Parent=Thecc.01G000100.1.v2.1;pacid=42014905