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Extracting specific ORFs from a complete metagenomic ORF file?

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

assembly sequencing gene
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updated by colindaven colindaven • written by microbez.uaf • microbez.uaf

1 answer

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
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written by colindaven colindaven

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.

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written by microbez.uaf • microbez.uaf

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