Diary of an Autodidact: awk: How to remove the rest of a fasta header name after a specific character

Yedomon Ange Bovys Zoclanclounon

Brainstorming

I have a fasta file with the following sequence header name. See in my previous post.


>NC_030986.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 1, whole genome shotgun sequence
>NC_030987.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 2, whole genome shotgun sequence
>NC_030988.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 3, whole genome shotgun sequence
>NC_030989.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 4, whole genome shotgun sequence
>NC_030990.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 5, whole genome shotgun sequence
>NC_030991.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 6, whole genome shotgun sequence
>NC_030992.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 7, whole genome shotgun sequence
>NC_030993.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 8, whole genome shotgun sequence
>NC_030994.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 9, whole genome shotgun sequence
>NC_030995.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 10, whole genome shotgun sequence
>NC_030996.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 11, whole genome shotgun sequence
>NC_030997.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 12, whole genome shotgun sequence
>NC_030998.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 13, whole genome shotgun sequence
>NC_030999.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 14, whole genome shotgun sequence
>NC_031000.1 Fusarium oxysporum f. sp. lycopersici 4287 chromosome 15, whole genome shotgun sequence

I want to clean the sequence header by removing the remainings characters after NCxxxx.1

Solution


cat Fusarium_oxysporum_fsp_lycopersici_15_chromosomes.fasta | awk -F' ' '{print $1}' > Fusarium_oxysporum_fsp_lycopersici_15_chromosomes_header_cleaned.fasta

Let’s check


$ grep "^>" Fusarium_oxysporum_fsp_lycopersici_15_chromosomes_header_cleaned.fasta

The result is:


>NC_030986.1
>NC_030987.1
>NC_030988.1
>NC_030989.1
>NC_030990.1
>NC_030991.1
>NC_030992.1
>NC_030993.1
>NC_030994.1
>NC_030995.1
>NC_030996.1
>NC_030997.1
>NC_030998.1
>NC_030999.1
>NC_031000.1

Great!

In summary the syntax is


$ cat your.file | awk -F'the_character_of_your_interest' '{print $1}' > your_output

This syntax will return the text by excluding all others characters after the specified one.

Comment on this article Share:

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".

Citation

For attribution, please cite this work as

Zoclanclounon (2021, Jan. 12). Diary of an Autodidact: awk: How to remove the rest of a fasta header name after a specific character. Retrieved from https://yedomon.netlify.app/posts/2021-01-12-awk-how-to-remove-the-rest-of-a-fasta-header-name-after-a-specific-character/

BibTeX citation

@misc{zoclanclounon2021awk:,
  author = {Zoclanclounon, Yedomon Ange Bovys},
  title = {Diary of an Autodidact: awk: How to remove the rest of a fasta header name after a specific character},
  url = {https://yedomon.netlify.app/posts/2021-01-12-awk-how-to-remove-the-rest-of-a-fasta-header-name-after-a-specific-character/},
  year = {2021}
}