How to filter out special sequences from a fasta file based on sequence IDs txt

Question

[Ginsea Chen]

Dear all

I want to remove some sequences from a fasta file based on a sequence IDs txt file. I have known that a available python script (filter_fasta.py) can be used to do this, while the installation of this package (filter_fasta.py is one of scripts of QIIME suite, this package need real 64-bit machine, while all of my computers are 32-bit) is so complex. So I want to know if other script can be used.

Example

fasta file

>A
ATGCGGCGCGAGAGA
>B
AGCTCGATCGATACGTAG
>C
AGCTAAGCTAGATAGCTAG

sequence IDs file

A
B

I want to remove A and B sequences from fasta file. Thanks for your help!

Best Regards

[Pierre Lindenbaum]

duplicate of How To Remove Certain Sequences From A Fasta File ( but exclude with join -a ) , Extract Sequence From Fasta File Using Ids From A Separate File , ....

[venu]

some more

• A: Extracting Sequence From A 3Gb Fasta File
• A: Extract A Group Of Fasta Sequences From A File