Question: How to filter out special sequences from a fasta file based on sequence IDs txt
0
gravatar for Ginsea Chen
3.5 years ago by
Ginsea Chen120
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Ginsea Chen120 wrote:

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!

Beast Regards

 

scripts fasta • 3.5k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Ginsea Chen120
1

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 , ....

ADD REPLYlink written 3.5 years ago by Pierre Lindenbaum119k
1

some more A: Extracting Sequence From A 3Gb Fasta File,

A: Extract A Group Of Fasta Sequences From A File

ADD REPLYlink written 3.5 years ago by venu6.1k
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