Hi All,
I am using pyfaidx to extract fasta sequence from a multifasta file using a list of locus tags.
List.txt
JFCCLHHB_00692
CKEMPBAI_00693
FBNBCCDE_01742
OMPPMJLG_02124
GKEHKBJF_02074
file.fasta
>NOLHFCLD_00001 Magnesium-transporting ATPase, P-type 1
atgc
>NOLHFCLD_00003 Serine transporter
atgc
my command is
xargs faidx file.fasta < list.txt > out.fas
my problem is that faidix is being pretty non-specific in the output. Im getting hits back which I know I shouldnt and I was wondering would the underscore have anything to do with this?
I am using pyfaidx to extract fasta sequence from a multifasta file using a list of locus tags.
List.txt
JFCCLHHB_00692
CKEMPBAI_00693
FBNBCCDE_01742
OMPPMJLG_02124
GKEHKBJF_02074
file.fasta
>NOLHFCLD_00001 Magnesium-transporting ATPase, P-type 1
atgc
>NOLHFCLD_00003 Serine transporter
atgc
my command is
xargs faidx file.fasta < list.txt > out.fas
my problem is that faidix is being pretty non-specific in the output. Im getting hits back which I know I shouldnt and I was wondering would the underscore have anything to do with this?
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