從同一行中的特定字符開始提取字符串

如果在發佈之前沒有遇到類似的問題並回答問題，請首先道歉。我有一套（72）基因註釋文件。我想提取的GO術語（獎金將其他標註計算）的格式像下面從同一行中的特定字符開始提取字符串

HORVU1Hr1G002090   GO:0003824 
HORVU1Hr1G002090   GO:0006527 
HORVU1Hr1G002090   GO:0008295 
HORVU1Hr1G002090   GO:0008792 
HORVU1Hr1G005360   GO:0004497 
HORVU1Hr1G005360   GO:0005506 
HORVU1Hr1G005360   GO:0016705 
HORVU1Hr1G005360   GO:0020037 
HORVU1Hr1G005360   GO:0055114 
HORVU1Hr1G087600   GO:0009055 
HORVU1Hr1G087600   GO:0015035 
HORVU1Hr1G087600   GO:0016705 
. 
. 
.

我INPUT_FILE看起來是這樣的：

HORVU1Hr1G002090.11 HORVU1Hr1G002090 chr1H:4283580-4286133 HC_G arginine decarboxylase 1 GO:0003824, GO:0006527, GO:0008295, GO:0008792 PF00278, PF02784 IPR000183, IPR002985, IPR009006, IPR022643, IPR022644, IPR022657, IPR029066 HORVU1Hr1G002090 
HORVU1Hr1G005360.1 HORVU1Hr1G005360 chr1H:11579708-11582804 HC_G Cytochrome P450 superfamily protein GO:0004497, GO:0005506, GO:0016705, GO:0020037, GO:0055114 PF00067 IPR001128, IPR002403, IPR017972 HORVU1Hr1G005360 
HORVU1Hr1G087600.1 HORVU1Hr1G087600 chr1H:539679073-539680597 HC_G Glutaredoxin family protein GO:0009055, GO:0015035, GO:0045454 PF00462 IPR002109, IPR011905, IPRHORVU1Hr1G087600 
HORVU1Hr1G087620.1 HORVU1Hr1G087620 chr1H:539699799-539703594 HC_G S-adenosyl-L-methionine-dependent methyltransferases superfamily protein none PF10294 IPR019410, IPR029063 HORVU1Hr1G087620 
HORVU1Hr1G089380.1 HORVU1Hr1G089380 chr1H:543801190-543806492 HC_G Subtilisin-like protease GO:0004252, GO:0006508 PF00082, PF05922 IPR000209, IPR010259, IPR015500, IPR023828 HORVU1Hr1G089380 
HORVU1Hr1G093570.2 HORVU1Hr1G093570 chr1H:553490639-553492292 HC_G Ribonuclease T2 family protein GO:0003723, GO:0033897 PF00445 IPR001568 HORVU1Hr1G093570 
HORVU1Hr1G093660.11 HORVU1Hr1G093660 chr1H:553651123-553709366 HC_G ribonuclease 3 GO:0003723, GO:0033897 PF00445 IPR001568 HORVU1Hr1G093660 
HORVU1Hr1G094970.1 HORVU1Hr1G094970 chr1H:556830249-556834411 HC_G Mitochondrial outer membrane protein porin 5 none none IPR023614 HORVU1Hr1G094970 
HORVU1Hr1G016140.3 HORVU1Hr1G016140 chr1H:49798715-49799683 HC_u undescribed protein none none none HORVU1Hr1G016140

我敢肯定的grep -oP能做的伎倆，或更好的awk或sed。但我無法讓它工作...請幫助！

我試過，沒有運氣以下：

grep -oP 'GO.*\[,|\|]\K+' input_file 
grep -oP 'GO.*+' input_file #prints the whole line after the first match 
sed -n 's/.*\(GO:[[:alnum:]]*\).*,/\1/p' input_file 
grep -oP 'GO:.*' input_file | tr ',' '|'| tr ' ' '|' | tr '\t' '|'| awk 'BEGIN {FS=OFS="|"}; {for(i=10;i<NF;i++){if($i~/^GO/){a=$i}} print $(NF),a}'

非常感謝提前！

來源

2017-07-11 Shani A.

嘗試awk這樣的：

awk '{for(i=1;i<=NF;i++){if($i~"^GO:"){gsub(",","");print $2,$i}}}' input

它通過循環每場尋找一個場GO:開始時，如果它發現它，它打印領域$2其次是匹配GO:領域。 gsub是刪除尾隨逗號。

來源

2017-07-11 01:33:20 archemiro

哇！你是明星！有用！ –

從同一行中的特定字符開始提取字符串

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