How to reduce RNA_from_genomic file to just gene name and sequence
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
1 answer
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.
• 0 views
•
link
written
by
shenwei356
Log in to answer this question.