對(duì)于蛋白的fa文件饰豺，由于是每個(gè)轉(zhuǎn)錄本對(duì)應(yīng)一個(gè)蛋白序列晦闰。由于后期注釋需要以基因?yàn)閱挝唬虼诵枰獙?duì)fa文件進(jìn)行處理吻贿，計(jì)算每一個(gè)轉(zhuǎn)錄本的蛋白序列長(zhǎng)度串结，然后提取最長(zhǎng)的蛋白序列，該序列即為該基因的蛋白序列舅列。具體代碼(關(guān)鍵實(shí)現(xiàn)代碼是if 判斷語句)如下：
open FA, "$ARGV[0]";
$/=">";
<FA>;
while(<FA>){
chomp;
my($id,$seq)=(split /\n/,$_,2)[0,1];
$seq=~s/\n//g;
($ID1,$ID2)=split /\./,$id;
#print"$ID1\n$seq\n";
$length=length($seq);
if(exists $hash{$ID1}){
if($length > length($hash{$ID1})) {
$hash{$ID1}=$seq;
}
else{
next;
}
}
else{
$hash{$ID1}=$seq;
}
}
foreach (keys %hash){
#$len=length($hash{$_});
print">$_\n$hash{$_}\n";
}
運(yùn)行代碼：
perl longgest_protein_ID.pl SWO.v3.0.protein.fa > longgest_protein.fa
其中SWO.v3.0.protein.fa如下：
head -20 SWO.v3.0.protein.fa
>Cs_ont_5g000040.3
MTEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKI
WICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLP
DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPA
FDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSH
KDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSG
DYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQ
STNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLDKALI
HMCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYSFHSG
PEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIMKERFPVPRLVICDQH
GSQVGSYHNVQQMGGSLWMIVVCYLLSPGKDILGHSPMDVCT*
>Cs_ont_5g044840.1
MESLALPCLNSFTSSRASFHKEQSNKLLAKARYLNSSKPASLRLTPYYIAPSFNLGGIRMQAGGEEYELKQMRDMAAAKK
RWDALIRDGKVKVLTPREAGYAVQLSSKTLLDVRPSTERKKAWIKGSIWIPIFDIDDTFDAGSLPQKVTNFVMGGWWSGV
PTLSYNKQFLSKVEEKLPKDTDLIVACQKGLRSLAACELLYNAGYRNLFWVQGGLEAAEEEDLVREGPQPLKFAGIGGLS
EFLGWTGQQRAQAAREGWGYRLLYSARLVGVFLAADALIIGAQQVGRYIQDIRSH*
>Cs_ont_4g025730.1
MSVSMRDLDSAFQGAGQKAGIEIWRIENFKPVLVPKSSHGKFFTGDSYVILKTTASKSGALRHDIHYWLGKDTSQDEAGT
AAIKTVELDAALGGRAVQYREVQGHETEKFLSYFKPCIIPQEGGIASGFKRAEAEEHKIRLFVCRGKHVIHVKEVPFSRS
SLNHDDIFILDTQSKIFQFNGSNSSIQERAKALEVVQYIKDTYHDGKCEVAVVEDGKLMADAEAGEFWGFFGGFAPLPRK
