如何使用Perl从FASTA文件中提取序列？

Question

我有一个包含许多蛋白质序列的FASTA文件。我需要阅读FASTA文件，删除标题并将序列保存在不同的变量中。关于如何在Perl中做这些建议（请不是Bio Perl）？

FASTA文件的示例：

gi|542264878|ref|XP_003460692.2| PREDICTED: myosin heavy chain, fast skeletal muscle-like, partial [Oreochromis niloticus|
KCFEKPKPAKGKAEAHFSLVHYAGTVDYNITGWLDKNKDPLNDSVVQLYQKSSNKLLALLYVAHAGGEEAGGGKKGGKKKGGSFQTVSALFRENLGKLMTNLRSTHPHFVRCLIPNETKTPGLMENFLVIHQLRCNGVLEGIRICRKGFPSRILYGDFKQRYKVLNASVIPEGQFIDNKKAS

我只想要序列：

KCFEKPKPAKGKAEAHFSLVHYAGTVDYNITGWLDKNKDPLNDSVVQLYQKSSNKLLALLYVAHAGGEEAGGGKKGGKKKGGSFQTVSALFRENLGKLMTNLRSTHPHFVRCLIPNETKTPGLMENFLVIHQLRCNGVLEGIRICRKGFPSRILYGDFKQRYKVLNASVIPEGQFIDNKKAS

Answer 1

如果awk对你来说没问题，那么这个简单的单行就可以了

# cat test 
gi|542264878|ref|XP_003460692.2| PREDICTED: myosin heavy chain, fast skeletal muscle-like, partial [Oreochromis niloticus| KCFEKPKPAKGKAEAHFSLVHYAGTVDYNITGWLDKNKDPLNDSVVQLYQKSSNKLLALLYVAHAGGEEAGGGKKGGKKKGGSFQTVSALFRENLGKLMTNLRSTHPHFVRCLIPNETKTPGLMENFLVIHQLRCNGVLEGIRICRKGFPSRILYGDFKQRYKVLNASVIPEGQFIDNKKAS

# awk '{print $NF}' test
KCFEKPKPAKGKAEAHFSLVHYAGTVDYNITGWLDKNKDPLNDSVVQLYQKSSNKLLALLYVAHAGGEEAGGGKKGGKKKGGSFQTVSALFRENLGKLMTNLRSTHPHFVRCLIPNETKTPGLMENFLVIHQLRCNGVLEGIRICRKGFPSRILYGDFKQRYKVLNASVIPEGQFIDNKKAS

以下是perl方式：

# perl -lane 'print $F[-1]' test 
KCFEKPKPAKGKAEAHFSLVHYAGTVDYNITGWLDKNKDPLNDSVVQLYQKSSNKLLALLYVAHAGGEEAGGGKKGGKKKGGSFQTVSALFRENLGKLMTNLRSTHPHFVRCLIPNETKTPGLMENFLVIHQLRCNGVLEGIRICRKGFPSRILYGDFKQRYKVLNASVIPEGQFIDNKKAS

请参阅此链接以获取每个单行说明：https://blogs.oracle.com/ksplice/entry/the_top_10_tricks_of