Hi All,
I am working PROKKA v1.12 files. I have a list of gene names such as
sacX
arcB
metB
sprT
adrB_2
fadD
and my fasta file is like so
>BOKHJPML_00001 hypothetical protein
ATGC
>BOKHJPML_00002 hypothetical protein
ATGC
>BOKHJPML_00003 Protease HtpX
ATGC
>BOKHJPML_00006 ATP-dependent Clp protease ATP-binding subunit ClpC
ATGC
BOKHJPML_00016 Inner membrane protein YfdC
ATGC
I want to extract the fasta sequences from the list. I have tried following previous suggestions using faidhttps://www.biostars.org/p/126204/x and biopyhttps://www.biostars.org/p/2822/thon
With no success. This faidx example is the closest I have come to success but I get a string of errors
warning: sacX not found in file
warning: arcB not found in file
warning: metB not found in file
warning: sprT not found in file
warning: adrB_2 not found in file
warning: fadD not found in file
Thanks in advance
I am working PROKKA v1.12 files. I have a list of gene names such as
sacX
arcB
metB
sprT
adrB_2
fadD
and my fasta file is like so
>BOKHJPML_00001 hypothetical protein
ATGC
>BOKHJPML_00002 hypothetical protein
ATGC
>BOKHJPML_00003 Protease HtpX
ATGC
>BOKHJPML_00006 ATP-dependent Clp protease ATP-binding subunit ClpC
ATGC
BOKHJPML_00016 Inner membrane protein YfdC
ATGC
I want to extract the fasta sequences from the list. I have tried following previous suggestions using faidhttps://www.biostars.org/p/126204/x and biopyhttps://www.biostars.org/p/2822/thon
With no success. This faidx example is the closest I have come to success but I get a string of errors
warning: sacX not found in file
warning: arcB not found in file
warning: metB not found in file
warning: sprT not found in file
warning: adrB_2 not found in file
warning: fadD not found in file
Thanks in advance
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