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filter out fasta File by pattern

Hi,

I would like to filter out some sequences from a fasta file by using a specific pattern.

For example I have this file:

>input1
UGAGGUAGUAGG
>input2
CUAUGCUUACC
>out1
UCCCUGAGACCGUGA
>out2
CUCCGGGUACC
>desc1
ACUUCCUUACAUGCCC

I know already how I can extract all the fasta sequences with a specific pattern into a new file by using awk.

But what I would like to do is to remove all entries of a specific pattern from the original fasta file and save the newly made file into a new one. In my file above, I would like for example to remove all sequences with the header pattern out. and save only the other to a new file.

Is there a tool somewhere for doing that, or is it possible in awk/sed or even grep

Thanks

Assa

fasta awk regexp sed
• 11,373 views • link
updated by Ram Ram • written by Assa Yeroslaviz Assa Yeroslaviz

4 answers

I would like for example to remove all sequences with the header pattern out. and save only the other to a new file

awk '/^>/ {P=index($0,"out")==0} {if(P) print} ' in.fasta > out.fasta
• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre! Thanks for your command.

I have a question on this issue. Instead of one header pattern "out" (in your case), I am looking for many patterns that are stored in a file. So what should I do? Your help is appreciated in advance.

• 0 views • link
written by xiachongjing • xiachongjing

You could modify my answer below:

$ pip install pyfaidx
$ xargs faidx in.fasta -g > out.fasta < patterns.txt
• 0 views • link
updated by Ram Ram • written by Matt Shirley Matt Shirley

Thank you Pierre for your answer. I used your command and it seems it is removing the header with a particular pattern from fasta file . I was wondering if this line of command removes the whole sequence associated to that header as my fasta file is not linearized and sequences are stored in multiple lines.

Also do you have any Idea how can I store the target sequences for deletion in another file?

• 0 views • link
written by bioyas • bioyas

Please

  1. Do not revive years old post as the answers are years old and new tools have come in.
  2. Post your query as a new post with example input and output
• 0 views • link
written by cpad0112 cpad0112

I like Pierre's answer to this since it's simple. However, I had been thinking about adding regular expression filtering to my pyfaidx project, and this morning I finished up adding this functionality:

$ pip install pyfaidx
$ faidx in.fasta -g "out" > out.fasta

The (small) advantage here is that faidx will perform filtering on an indexed file, preventing you from reading the entire file through your filter.

• 0 views • link
updated by Ram Ram • written by Matt Shirley Matt Shirley

Using samtools

$ samtools faidx in.fasta
$ awk '/^>/ {print substr($1,2,400) }'  in.fasta | grep -v "out" list >selected_list
$ samtools faidx in.fasta -r selected_list > out.fasta

This will give you all the functionality of "grep" to select the desired sequences.

• 0 views • link
written by hans • hans

Why print substr($1,2,400)?

Why piping in grep -v "out" while the same grep reads a file list?

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum 
print substr($1,2,400)

Keeps only the first field of the pasta header while deleting the ">" from the header. The file name "list" in the grep command is a mistake, it should be deleted:

awk '/^>/ {print substr($1,2,400) }'  in.fasta | grep -v "out"  >selected_list
• 0 views • link
written by hans • hans

I wanted to do something similar but my fasta files have more than one line of DNA/RNA and I wanted to only use awk. This is the command that worked for me:

awk '/^>/ {keep = ($0 ~ /^>NM/)} keep {print}' input.fasta > NM_only.fasta
• 0 views • link
written by eidriangm • eidriangm

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