Re: remove part of string (DNA)

[sundialsvc4]

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[BrowserUk]

Nothing you have said above is even vaguely relevant to the OPs question.

You get more fatuous by the day. Why? What are you hoping to achieve?

[clp]

I am not a Perl expert, and have learned from many authors on PerlMonks, including both BrowserUK and sundialsvc4.

If the comments by sundialsvc4 are inaccurate or not appropriate for the OP's problem, please tell us why. Pre-sorting the data seems like good advice to me, but I don't have your experience and knowledge of Perl. Please enlighten.

Thanks.

[BrowserUk]

Pre-sorting the data seems like good advice to me,

It is quite the opposite of good advice. Ie very bad advice.

1. Sorting is O(N logN). The OPs described processing is O(N).

   Sorting does not help the OPs processing at all.

2. FASTA file are multi-line record format files.

   If you sorted a FASTA file with the system sort utility, it would screw the file up in a completely irrecoverable way.

   Eg. This:

   c:\test>type 845226.fasta
   >uc002yje.1 chr21:13973492-13976330
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   acgcgccctacactctggcatgggggaacccggccccgcagagccctgga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   >uc002yje.1 chr21:13973492-13976330
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   acgcgccctacactctggcatgggggaaaaaacccggccccgcagagccctgga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   >uc002yje.1 chr21:13973492-13976330
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   acgcgccctacactctggcatgggggaacccggccccgcagagggccctgga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   

   becomes this:

   c:\test>sort 845226.fasta
   >uc002yje.1 chr21:13973492-13976330
   >uc002yje.1 chr21:13973492-13976330
   >uc002yje.1 chr21:13973492-13976330
   acgcgccctacactctggcatgggggaaaaaacccggccccgcagagccctgga
   acgcgccctacactctggcatgggggaacccggccccgcagagccctgga
   acgcgccctacactctggcatgggggaacccggccccgcagagggccctgga
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   cccctgccccaccgcaccctggattactgcacgccaagaccctcacctga
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   CTCTGACATTGGAGGACTCCTCGGCTACGTCCTGGACTCCTGCACAAGAG
   

   And so is rendered entirely useless.

[Furor]

BrowserUK is right (identifier and sequence should remain together), but they'll be sorted before exporting them to a fasta file. But I don't think it would really make a difference in speed anyway.