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From: Sébastien B. <seb...@ul...> - 2011-07-21 17:16:19
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> > ________________________________________ > De : David Eccles (gringer) [dav...@mp...] > Date d'envoi : 19 juillet 2011 10:34 > À : den...@li... > Objet : [Denovoassembler-devel] Colour-space loading / assembly now working (produces base-space output) > > So, things are finally looking like the colour-space stuff is going > somewhere. I've managed to get a good result from a Ray run with > colour-space input (no errors, first bases included), and it might be a > tad quicker than the sebhtml/ray colour-space assembler: > Nice ! So, the reads are in color-space and the contigs are in nucleotide-space ? If so, this is very cool ! > $ time ../../../sebgit/ray/code/Ray -p tests/phix/phix_5k_1.csfasta > tests/phix/phix_5k_2.csfasta | grep -A 7 'Number of contigs:' > Number of contigs: 1 > Total length of contigs: 5380 > Number of contigs >= 500 nt: 1 > Total length of contigs >= 500 nt: 5380 > Number of scaffolds: 1 > Total length of scaffolds: 5380 > Number of scaffolds >= 500 nt: 1 > Total length of scaffolds >= 500: 5380 > > real 0m3.107s > user 0m2.432s > sys 0m0.652s > > $ time ../code/Ray -p tests/phix/phix_5k_1.csfasta > tests/phix/phix_5k_2.csfasta | grep -A 7 'Number of contigs:' > Number of contigs: 1 > Total length of contigs: 5243 > Number of contigs >= 500 nt: 1 > Total length of contigs >= 500 nt: 5243 > Number of scaffolds: 1 > Total length of scaffolds: 5243 > Number of scaffolds >= 500 nt: 1 > Total length of scaffolds >= 500: 5243 > > real 0m2.894s > user 0m2.392s > sys 0m0.484s > > $ fasta_formatter -i tests/phix/phix.fasta | fastx_reverse_complement | > grep $(fasta_formatter -i RayOutput.Scaffolds.fasta | grep -v '^>') > > /dev/null && echo "success (match in reverse direction)" > success (match in reverse direction) > > There's nothing particularly impressive with this (apart from it > actually working...). For what it's worth, the sebhtml/ray also produces > a correct sequence, if you feed it the right starting base: > But mine does not produce the contigs in nucleotide space. And I believe yours does ! > $ fasta_formatter -i tests/phix/phix.fasta | fastx_reverse_complement | > grep $((echo -n 'G'; tail -n +2 RayOutput.Scaffolds.fasta) | > ~/scripts/cs2base.pl | fasta_formatter) > /dev/null && echo "success > (match in forward direction)" > success (match in forward direction) > > However, this is probably more interesting, using a colour-space > sequence for one end, and a base-space sequence for the other end: > What do you mean ? > $ time ../../../sebgit/ray/code/Ray -p tests/phix/phix_5k_1.fasta > tests/phix/phix_5k_2.csfasta | grep -A 7 'Number of contigs:' > Number of contigs: 3 > Total length of contigs: 15713 > Number of contigs >= 500 nt: 3 > Total length of contigs >= 500 nt: 15713 > Number of scaffolds: 3 > Total length of scaffolds: 15713 > Number of scaffolds >= 500 nt: 3 > Total length of scaffolds >= 500: 15713 > > real 0m4.246s > user 0m3.428s > sys 0m0.796s > bioinf@thaliana:~/install/ray/git/ray/system-tests$ time ../code/Ray -p > tests/phix/phix_5k_1.fasta tests/phix/phix_5k_2.csfasta | grep -A 7 > 'Number of contigs:' > Number of contigs: 1 > Total length of contigs: 5243 > Number of contigs >= 500 nt: 1 > Total length of contigs >= 500 nt: 5243 > Number of scaffolds: 1 > Total length of scaffolds: 5243 > Number of scaffolds >= 500 nt: 1 > Total length of scaffolds >= 500: 5243 > > real 0m2.892s > user 0m2.412s > sys 0m0.456s > > $ fasta_formatter -i tests/phix/phix.fasta | fastx_reverse_complement | > grep $(fasta_formatter -i RayOutput.Scaffolds.fasta | grep -v '^>') > > /dev/null && echo "success (match in reverse direction)" > success (match in reverse direction) > > [I haven't tried doing a match with the sebhtml/ray sequence.] > > The commit that actually got my code working properly with colour-space > is here: > > https://github.com/gringer/ray/commit/fbd1efd4c3dbe31df0de820167a068736de648f5 > OK > [I forgot to make the same changes for the KmerAcademyBuilder (lines > 109-113) that I made for the VerticesExtractor (lines 110-114)] > So the next steps is to test your work on the system tests I guess. I see that your are 0 commit away from my branch. (Cool) > -- David > > _______________________________________________ > Denovoassembler-devel mailing list > Den...@li... > https://lists.sourceforge.net/lists/listinfo/denovoassembler-devel > Sébastien Boisvert http://github.com/sebhtml/ray |
