删除重复的fasta序列（biopython方法的重击）

Question

您好，我有一个Fasta文件，例如：

>sequence1_CP [seq  virus]
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNL
DITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

>sequence2 [virus]
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNL
DITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

>sequence3
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNL
DITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

>sequence4_CP hypothetical protein [another virus]
MLRHSCVMPQQKLKKRFFFLRRLRKILRYFFTCNFLNLFFINREYNIENITLSYLKKERIPVWKTSDMSN
IVRKWWMFHRKTQLEDNIEIKKDIQLYHFFYNGLFIKTNYPYVYHIDKKKKYDFNDMKVIYLPAIHMHSK

>sequence5 hypothetical protein [another virus]
MLRHSCVMPQQKLKKRFFFLRRLRKILRYFFTCNFLNLFFINREYNIENITLSYLKKERIPVWKTSDMSN
IVRKWWMFHRKTQLEDNIEIKKDIQLYHFFYNGLFIKTNYPYVYHIDKKKKYDFNDMKVIYLPAIHMHSK

>sequence6 |hypothetical protein[virus]
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNLD
ITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

>sequence7 |hypothetical protein[virus]
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNLD
ITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

并且在此文件中，我想删除重复的序列并获取：

>sequence1_CP [seq  virus]
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNL
DITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

>sequence4_CP hypothetical protein [another virus]
MLRHSCVMPQQKLKKRFFFLRRLRKILRYFFTCNFLNLFFINREYNIENITLSYLKKERIPVWKTSDMSN
IVRKWWMFHRKTQLEDNIEIKKDIQLYHFFYNGLFIKTNYPYVYHIDKKKKYDFNDMKVIYLPAIHMHSK

>sequence6 |hypothetical protein[virus]
MQCKSGTNNVFTAIKYTTNNNIIYKSENNDNIIFTKNIFNVVTTKDAFIFSKNRGIMNLD
ITKKFDYHEHRPKLCVFKIINTQYVNSPEKMIDAWPTMDIVALITE

在这里您可以看到> name，sequence1_CP和sequence2的sequence3后面的内容相同，那么我只想保留其中的3个。但是，如果3个序列之一具有_CP的名称，那么我要特别保留此名称。如果它们中的任何一个都没有_CP，则不会保留我所保留的那个。

• 因此，对于Sequence1_CP，Sequence2和Sequence3之间的第一个重复项，我保留sequence1_CP
• 对于sequence4_CP和sequence5之间的第二个副本，我保留sequence4_CP
• 对于在sequence6和sequence7之间的第三个重复项，我保留第一个sequence6

有人使用biopython或bash方法有想法吗？非常感谢

Answer 1

$ awk 'BEGIN{FS="\n";RS=""}{if(!seen[$2,$3]++)print}' file

Answer 2

Answer 3