Error extracting faa sequences from multifasta using faidx

Question: Error extracting faa sequences from multifasta using faidx

5.1 years ago by

dago • 2.6k

Germany

dago • 2.6k wrote:

I have a multifasta faa file from which I want to extract some seqeunces 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?

software error genome • 1.5k views

ADD COMMENT • link •

modified 5.1 years ago by geek_y ♦ 11k • written 5.1 years ago by dago • 2.6k

Alternatively you can use faSomeRecords,

./faSomeRecords input.faa ids.txt output.faa

Here is how A: perl code to extract sequences from multi-line fasta works on all test files but

ADD REPLY • link modified 16 months ago by _r_am ♦ 32k • written 5.1 years ago by venu ♦ 6.7k

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!

ADD REPLY • link modified 16 months ago by _r_am ♦ 32k • written 5.1 years ago by dago • 2.6k

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