20220518_blastn结果转化为gff格式文件

(base) dell@dell-server:~/test$ ls -lhtr
总用量 904K
-rw-rw-r-- 1 dell dell 450K 5月  18 17:45 query.fastq
-rw-rw-r-- 1 dell dell 450K 5月  18 17:45 target_db.fastq

(base) dell@dell-server:~/test$  makeblastdb  -in  target_db.fasta  -dbtype nucl -parse_seqids  -out target_database


Building a new DB, current time: 05/18/2022 17:48:33
New DB name:   /home/dell/test/target_database
New DB title:  target_db.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 500 sequences in 0.0449848 seconds.




(base) dell@dell-server:~/test$ ls -lhtr
总用量 1.1M
-rw-rw-r-- 1 dell dell 450K 5月  18 17:45 query.fasta
-rw-rw-r-- 1 dell dell 450K 5月  18 17:45 target_db.fasta
-rw-rw-r-- 1 dell dell 109K 5月  18 17:48 target_database.nsq
-rw-rw-r-- 1 dell dell  849 5月  18 17:48 target_database.nsi
-rw-rw-r-- 1 dell dell  42K 5月  18 17:48 target_database.nsd
-rw-rw-r-- 1 dell dell 2.0K 5月  18 17:48 target_database.nog
-rw-rw-r-- 1 dell dell 6.0K 5月  18 17:48 target_database.nin
-rw-rw-r-- 1 dell dell  37K 5月  18 17:48 target_database.nhr

这是未转化为gff格式之前的比对结果
(base) dell@dell-server:~/test$ blastn -db target_database   -query  query.fasta   -outfmt 6  | head
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_031808.1;ATP6;LEN=684    100.00  684     0       0       1       684     1    684      0.0     1264
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_036746.1;ATP6;LEN=684    89.62   684     71      0       1       684     1    684      0.0     870
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_002079.1;ATP6;LEN=684    86.99   684     89      0       1       684     1    684      0.0     771
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_036383.1;ATP6;LEN=684    85.67   684     98      0       1       684     1    684      0.0     721
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_045918.1;ATP6;LEN=684    85.38   684     100     0       1       684     1    684      0.0     710
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_031813.1;ATP6;LEN=684    81.95   687     118     5       1       684     1    684      5e-166  577
animal_mito;NC_031808.1;ATP6;LEN=684    animal_mito;NC_027953.1;ATP6;LEN=684    76.56   687     155     6       1       684     1    684      2e-104  372
animal_mito;NC_004299.1;ATP6;LEN=684    animal_mito;NC_004299.1;ATP6;LEN=684    100.00  684     0       0       1       684     1    684      0.0     1264
animal_mito;NC_004299.1;ATP6;LEN=684    animal_mito;NC_011632.1;ATP6;LEN=683    94.57   681     35      2       1       680     1    680      0.0     1051
animal_mito;NC_045918.1;ATP6;LEN=684    animal_mito;NC_045918.1;ATP6;LEN=684    100.00  684     0       0       1       684     1    684      0.0     1264


这是转化为gff格式之后的比对结果
(base) dell@dell-server:~/test$ blastn -db target_database   -query  query.fasta   -outfmt 6  | awk -v OFS="\t" '{ if ($10 > $9) print $2, "tblastn", "match", $9, $10, $12, "+", ".", "ID="$1; else print $2, "tblastn", "match", $10, $9, $12, "-", ".", "ID="$1 }' | head
animal_mito;NC_031808.1;ATP6;LEN=684    tblastn match   1       684     1264    +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_036746.1;ATP6;LEN=684    tblastn match   1       684     870     +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_002079.1;ATP6;LEN=684    tblastn match   1       684     771     +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_036383.1;ATP6;LEN=684    tblastn match   1       684     721     +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_045918.1;ATP6;LEN=684    tblastn match   1       684     710     +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_031813.1;ATP6;LEN=684    tblastn match   1       684     577     +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_027953.1;ATP6;LEN=684    tblastn match   1       684     372     +       .       ID=animal_mito;NC_031808.1;ATP6;LEN=684
animal_mito;NC_004299.1;ATP6;LEN=684    tblastn match   1       684     1264    +       .       ID=animal_mito;NC_004299.1;ATP6;LEN=684
animal_mito;NC_011632.1;ATP6;LEN=683    tblastn match   1       680     1051    +       .       ID=animal_mito;NC_004299.1;ATP6;LEN=684
animal_mito;NC_045918.1;ATP6;LEN=684    tblastn match   1       684     1264    +       .       ID=animal_mito;NC_045918.1;ATP6;LEN=684


最后输出gff格式输出结果
(base) dell@dell-server:~/test$ blastn -db target_database   -query  query.fasta   -outfmt 6  | awk -v OFS="\t" '{ if ($10 > $9) print $2, "tblastn", "match", $9, $10, $12, "+", ".", "ID="$1; else print $2, "tblastn", "match", $10, $9, $12, "-", ".", "ID="$1 }' > blastn_result.gff
(base) dell@dell-server:~/test$ ls -lhtr
总用量 1.4M
-rw-rw-r-- 1 dell dell 450K 5月  18 17:45 query.fasta
-rw-rw-r-- 1 dell dell 450K 5月  18 17:45 target_db.fasta
-rw-rw-r-- 1 dell dell 109K 5月  18 17:48 target_database.nsq
-rw-rw-r-- 1 dell dell  849 5月  18 17:48 target_database.nsi
-rw-rw-r-- 1 dell dell  42K 5月  18 17:48 target_database.nsd
-rw-rw-r-- 1 dell dell 2.0K 5月  18 17:48 target_database.nog
-rw-rw-r-- 1 dell dell 6.0K 5月  18 17:48 target_database.nin
-rw-rw-r-- 1 dell dell  37K 5月  18 17:48 target_database.nhr
-rw-rw-r-- 1 dell dell 226K 5月  18 17:54 blastn_result.gff