Trim to a specified length about seqtk HOT 8 CLOSED

I found that FASTX-toolkit implements this feature.
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_trimmer_usage

   [-f N]       = First base to keep. Default is 1 (=first base).
   [-l N]       = Last base to keep. Default is entire read.

from seqtk.

This would be useful — I'd be happy to implement this and issue a pull request if it'll be incorporated. Note that bioawk can also do this pretty easily:

$ echo ">test-1\\nAGTATCTAGCATATCGT\\n>test-B\\nGCTAGCACGATC" | \
  bioawk -cfastx '{print fastx($name, substr($seq, 0, 10))}' # note this depends on fastx(), a function I implemented
>test-1
AGTATCTAGC
>test-B
GCTAGCACGA

from seqtk.

Release 1.0 does not support trimming to fixed length as adding the functionality may affect the stability of trimfq. You may use Vince's script to achieve the goal for now. I will leave the issue open.

from seqtk.

Actually release 1.0 supports trimming to fixed length!
Just try "seqtk -q 0 -l N input.fq" (it keeps the first N bp)!

from seqtk.

I have just commited some changes which does all these (i.e. shortcircuiting the q == 0, keep first last N bp).

from seqtk.

Implemented via 46cd37e ... after 3 years. Sorry.

from seqtk.

Thanks, Heng!

from seqtk.

Would you please tag a new stable release tagged either 1.1 or 87? The last stable release 1.0 was tagged in 2013. An out-of-date tagged stable release is more confusing than having no tagged stable release at all.

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