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Full Discussion: Improve the performance of my C++ code
Top Forums Programming Improve the performance of my C++ code Post 302931808 by yifangt on Thursday 15th of January 2015 03:22:34 PM
Old 01-15-2015
achenle, I do not know what happened, but it is fine with my vim/gedit, and good viewed with cat/more/less/head etc on my Linux console: ubuntu/Mint 17.0.

corona688, can I make sure the difference between list<> and vector <> can be hours? I am aware the data is kind of big (~6MB, for 300 entries with 166,000bp in total), but it's nothing compared with ~10GB file with ~100 millions of entries. I did not try ~10BG file yet, which would be forever!! I must have missed something big for my code.
Last edited by yifangt; 01-15-2015 at 04:33 PM..
 

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LEARN ABOUT DEBIAN

glam2-purge

GLAM2-PURGE(1)							   glam2 Manual 						    GLAM2-PURGE(1)

NAME

       glam2-purge - Removes redundant sequences from a FASTA file

SYNOPSIS

       glam2-purge file score [options]

DESCRIPTION

       glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended
       in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates
       an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output
       file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA.
       Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose.

OPTIONS

       -n
	   Sequences are DNA (default: protein).

       -b
	   Use blast heuristic method (default for protein).

       -e
	   Use an exhaustive method (default for DNA).

       -q
	   Keep first sequence in the set.

       -x
	   Use xnu to mask protein tandem repeats.

SEE ALSO

       glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(1)

       The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in
       /usr/share/doc/glam2/.

REFERENCES

       Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer
       membrane protein repeats", Protein Science, 4:1618-1632, 1995. Please cite it if you use Purge.

       If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and
       deletions, PLoS Computational Biology (in press).

AUTHORS

       Andrew Neuwald
	   Author of purge, renamed glam2-purge in Debian.

       Martin Frith
	   Modified purge to be ANSI standard C and improved the user interface.

       Timothy Bailey
	   Modified purge to be ANSI standard C and improved the user interface.

       Charles Plessy <plessy@debian.org>
	   Formatted this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       The source code and the documentation of Purge and GLAM2 are released in the public domain.

GLAM2 1056							    05/19/2008							    GLAM2-PURGE(1)
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