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Question: Error extracting faa sequences from multifasta using faidx
0
gravatar for dago
3.3 years ago by
dago • 2.5k
Germany
dago • 2.5k 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 • 1.0k views
ADD COMMENT • link •
modified 3.3 years ago by geek_y ♦ 9.3k • written 3.3 years ago by dago • 2.5k
1

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 3.3 years ago • written 3.3 years ago by venu ♦ 6.0k

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 3.3 years ago • written 3.3 years ago by dago • 2.5k
0
gravatar for geek_y
3.3 years ago by
geek_y ♦ 9.3k
Barcelona/CRG/London/Imperial
geek_y ♦ 9.3k wrote:

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

ADD COMMENT • link written 3.3 years ago by geek_y ♦ 9.3k

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

 

ADD REPLY • link written 3.3 years ago by dago • 2.5k
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