Extracting specific ORFs from a complete metagenomic ORF file?

Question

[microbez.uaf]

I have a list of ORF (1159) that i want to extract from a complete metagenomic ORF file that contain 597500 ORF. Is there any tool or script with which i can do that. Or should i do this with assembled contigs, if yes then how can i extract those contgs/ORFs. I want to do blast with only 1159 ORF not with whole metagenomic ORFs. Thank you

Answer 1

[colindaven]

What's a metagenomics ORF file ?

If it is a FASTA, you can use

# index the fasta 
samtools faidx test.fasta
#extract orf78
samtools faidx test.fasta orf78 

samtools faidx test.fasta orf78  > myORF.fasta

[microbez.uaf]

Hye Collin, Thanks for your response. I have contigs and translated ORFs from those contigs (Approximately 900,000 contigs and 597500 translated ORFs) . I want to extract specific contigs/ORFs (1159) from those files. Can you help me in this regard.