How to reduce RNA_from_genomic file to just gene name and sequence

Question

[Chris]

I am working with an organism, and the RNA from genomic file is formatted as such

>lcl|NC_064920.1_mrna_XM_049993407.1_2 [gene=LOC126318536] [db_xref=GeneID:126318536] [product=protein flightless-1] [transcript_id=XM_049993407.1] [location=join(1505699..1505924,1512713..1512823,1522051..1522289,1525833..1525994,1526489..1526709,1527880..1528096,1535362..1535603,1536733..1536827,1578252..1578322,1590520..1590766,1602725..1602910,1614216..1614394,1617884..1618022,1625719..1625891,1625979..1626105,1626193..1626315,1644687..1644840,1651848..1652034,1652257..1652508,1654310..1654436,1660544..1660726,1660809..1660922,1661044..1661510)] [gbkey=mRNA]
GATAGTGTATCTTTGCCAAGGTGAAGTAGTGTCATGGGTTGTTTTGATTTTGGTGTATGTATGGGTGGACGTGTGTGAAT
TTTGAGAGTCTTGCGCGAAATAGTATTTGTTTGTGACATATAGATAGTTTATGAGCAGGGATTGAAAGTTGTCAATTAAC
ATCATGGCGAACACTGGCGTGTTACCGTTTGTTAGAGGTGTTGACTTCACAAGAAATGACTTCAGTAATGAAAGATTTCC

Is anyone aware of any posts that suggest how to reduce it down to:

>LOC126318536
GATAGTGTATCTTTGCCAAGGTGAAGTAGTGTCATGGGTTGTTTTGATTTTGGTGTATGTATGGGTGGACGTGTGTGAATTTTGAGAGTCTTGCGCGAAATAGTATTTGTTTGTGACATATAGATAGTTTATGAGCAGGGATTGAAAGTTGTCAATTAACATCATGGCGAACACTGGCGTGTTACCGTTTGTTAGAGGTGTTGACTTCACAAGAAATGACTTCAGTAATGAAAGATTTCC

I have tried looking, but can't find any

Many thanks,

Christian

Answer 1

[shenwei356]

Try seqkit seq:

seqkit seq --only-id --id-regexp 'gene=(\w+)' seqs.fasta -o result.fasta

Where --id-regexp is a global option to capture the sequence ID with regular expression.

[Chris]

That's amazing thank you so much! It worked so quickly! Installing seqkit was more complicated than using the tool! Thanks you again!