faidx usage and non specific hits

[SeqTroubles]

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?

[GenoMax]

Are you referring to samtools faidx or something else?

[SeqTroubles]

Are you referring to samtools faidx or something else?

pyfaidx. Ill change my description now.

[GenoMax]

Tested and appears to work fine. Fasta ID's need to match exactly (unless you want to try reg exp/wild cards).

$ more list.fa
>JFCCLHHB_00692
AGCTCGAT
>CKEMPBAI_00693
ACGCTG
>FBNBCCDE_01742
ACGATCAC
>OMPPMJLG_02124
ACGCTCGCTGC
>GKEHKBJF_02074
AGCTCGC

$ more list.txt
JFCCLHHB_00692
CKEMPBAI_00693
GKEHKBJF_02074

$ xargs faidx list.fa < list.txt
>JFCCLHHB_00692
AGCTCGAT
>CKEMPBAI_00693
ACGCTG
>GKEHKBJF_02074
AGCTCGC

[SeqTroubles]

Tested and appears to work fine. Fasta ID's need to match exactly (unless you want to try reg exp/wild cards).

$ more list.fa
>JFCCLHHB_00692
AGCTCGAT
>CKEMPBAI_00693
ACGCTG
>FBNBCCDE_01742
ACGATCAC
>OMPPMJLG_02124
ACGCTCGCTGC
>GKEHKBJF_02074
AGCTCGC

$ more list.txt
JFCCLHHB_00692
CKEMPBAI_00693
GKEHKBJF_02074

$ xargs faidx list.fa < list.txt
>JFCCLHHB_00692
AGCTCGAT
>CKEMPBAI_00693
ACGCTG
>GKEHKBJF_02074
AGCTCGC

Thanks GenoMax.

I have two lists of tags and one list work perfect but when I execute the second it would appear its just copying all the information from the input fasta. Really weird. Ive already looked over all my data to ensure its valid so I cannot see where the issue is at present.

In actuality Im running a loop to execute this search looks like
for f in *.fna; do
f=$(basename $f .fna); xargs faidx $f.fna < tags.txt > $PWD/out/$f.fas; done

[GenoMax]

Examine your ID file (something like cat -vet yourFile) to see if there are any non-printable characters that could be causing potential issues.