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When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or ) for no (known to me) reason.

In the majority of the strings mentioned above, the whitespace is removed:

  • input file:
    >tr|Q9UXV4|Q9UXV4_PYRAB Pyruvate formate-lyase activating enzyme ( act-1) OS=Pyrococcus abyssi (strain GE5 / Orsay) OX=272844 GN=act-1 PE=4 SV=1,
    output file:
    >tr|Q9UXV4|Q9UXV4_PYRAB Pyruvate formate-lyase activating enzyme (act-1) OS=Pyrococcus abyssi (strain GE5 / Orsay) OX=272844 GN=act-1 PE=4 SV=1,
  • input file:
    >tr|A0A5K1JWI6|A0A5K1JWI6_9APHY Cysteine protease ATG4 ) OS=Ganoderma boninense OX=34458 GN=Q523C3 PE=4 SV=1,
    output file:
    >tr|A0A5K1JWI6|A0A5K1JWI6_9APHY Cysteine protease ATG4) OS=Ganoderma boninense OX=34458 GN=Q523C3 PE=4 SV=1.

It isn't a significant change, but it complicates searching for headers in the output file.

However, the program is not consistent - if there is a comma (,) before the ) string, the whitespace is not removed:

  • input file:
    >tr|A0A3M9YA12|A0A3M9YA12_9PEZI Myeloid lymphoid or mixed-lineage leukemia 5 (Trithorax, ) OS=Verticillium nonalfalfae OX=1051616 GN=MLL5 PE=4 SV=1,
    output file:
    >tr|A0A3M9YA12|A0A3M9YA12_9PEZI Myeloid lymphoid or mixed-lineage leukemia 5 (Trithorax, ) OS=Verticillium nonalfalfae OX=1051616 GN=MLL5 PE=4 SV=1.

What's the reason for such a behaviour?
Is there any option to prevent it and keep headers unchanged?


edit.
The whitespace is also removed for:

  • ,
  • ,,.

Moreover, it removes a semicolon when it is at the end of a header:
>ABCD/1-4 ABCD;ABCD;>ABCD/1-4 ABCD;ABCD.

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    $\begingroup$ Weird... You could always run your input through something like sed 's/ *)/)/g; s/( */(/g' to remove the spaces yourself before using segmasker, but obviously that isn't ideal. $\endgroup$
    – terdon
    Nov 24, 2022 at 16:47

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