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Error extracting faa sequences from multifasta using faidx

I have a multifasta file from which I want to extract some sequences using IDs.

Multifasta example:

>NITMOv2_RS22300
MAKTVAVVIREDPRRTHRPVEALRIALGLVAGNHATTVVLLNEAARLLSEDTDDVVDVEI
LEKYLPSIQQLEVPFVLPEFIDRSGVRTDFAVRYESDDTIRRLLQSMDRTLVF
>NITMOv2_RS22305
MSLSSSVYLIRKSAAALSPTLYVSGDSDWVVVEIGEDKRSSDYRELLELVLHAEKVITL

IDs example:

NITINOP_v2_3300
NITINOP_v2_3307

I usually do this using the following command

xargs faidx -d "" MULTIFASTA < IDs

It always worked fine, but with some new files it started to give me the following error I cannot understand:

Traceback (most recent call last):
  File "/usr/local/bin/faidx", line 9, in <module>
    load_entry_point('pyfaidx==0.3.4', 'console_scripts', 'faidx')()
  File "/usr/local/lib/python2.7/dist-packages/pyfaidx/cli.py", line 132, in main
    write_sequence(args)
  File "/usr/local/lib/python2.7/dist-packages/pyfaidx/cli.py", line 33, in write_sequence
    fasta = Fasta(args.fasta, default_seq=args.default_seq, strict_bounds=not args.lazy, split_char=args.delimiter)
  File "/usr/local/lib/python2.7/dist-packages/pyfaidx/__init__.py", line 527, in __init__
    read_ahead=read_ahead, mutable=mutable, split_char=split_char)
  File "/usr/local/lib/python2.7/dist-packages/pyfaidx/__init__.py", line 218, in __init__
    raise FastaIndexingError(e)

Any suggestion, what am I missing here?

genome software-error
• 3,269 views • link
updated by Ram Ram • written by dago dago

Thanks very much. This is another good option I guess.

However, whenever I try to run it I get the following error:

Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at faSomeRecords line 1.

I try to look into the code but I cannot even open it. Any suggestion?

EDIT

I did not make it executable...sorry! Thanks it worked!

• 1 views • link
updated by Ram Ram • written by dago dago

1 answer

Try with proper IDs.

NITINOP_v2_3300
NITINOP_v2_3307

Both are not present in your example and it works fine if I use NITMOv2_RS22300. So the problem might be with the match between Ids between fasta and Ids.txt

• 0 views • link
updated by Ram Ram • written by GouthamAtla GouthamAtla

Thanks. I just reported an example. I checked and my Ids are present in the multifasta I am using

• 0 views • link
updated by Ram Ram • written by dago dago

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