不明白你要干啥，你是有一些基因ID，想把对应的基因序列提取出来到一个新文件，还是只是把fasta序列中的ID提取出来？问问题要明确，不要让人歧义：

perl遍历hash：

while(($key, $value) = each(%HASH)) {
    # do something with $key and $value
}

#-----------------------------

foreach $key (keys %HASH) {
    $value = $HASH{$key};
    # do something with $key and $value
}

#-----------------------------
# %food_color per the introduction

while(($food, $color) = each(%food_color)) {
    print "$food is $color.\n";
}

# Banana is yellow.
#
# Apple is red.
#
# Carrot is orange.
#
# Lemon is yellow.
 
foreach $food (keys %food_color) {
    my $color = $food_color{$food};
    print "$food is $color.\n";
}

处理fasta序列可以使用bioperl：

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