How to remove some fasta sequences by header information from a large fasta file, any command and script please?

Question

[seta]

Dear all,

I would like to remove some fasta sequences within a large fasta file in term of header information (sequence name), could anybody please help me out to this end? Thanks so much in advance

The header information is like here:

> contig1
ATGCGTACGTCATG
>contig2
GCTACGTCCCA

Answer 1

[Brian Bushnell]

The BBMap package contains a tool called FilterByName which can do this:

filterbyname.sh in=file.fa out=filtered.fa names=contig1,contig2

It supports prefixes, case-sensitive or insensitive matching, inclusion or exclusion, and substring matching. Rather than a list of names, you can instead point "names=" to another fasta or fastq file.

[seta]

Thanks Brian. I'm trying to use your tool to this end, but I faced with the following error. Could you please let me know what is wrong and how to solve it?

Exception in thread "main" java.lang.AssertionError: Unknown parameter names.txt
        at driver.FilterReadsByName.<init>(FilterReadsByName.java:118)
        at driver.FilterReadsByName.main(FilterReadsByName.java:41)

Many thanks

[PoGibas]

What is wrong:

Unknown parameter names.txt

How to solve it:

Execute command as Brian suggested (using parameter names=).

Answer 2

[h.mon]

There are several threads with similar questions, just enjoy the multitude of answers and choose the one most suited for you, see here, or here, or here.