[BioPython] Does biopython have a parser for .qual files?
Martin MOKREJŠ
mmokrejs at ribosome.natur.cuni.cz
Fri Jan 9 14:24:02 UTC 2009
Hi,
is there a way in biopython to access the quality values from
NCBI trace archive? I had a look briefly into
http://biopython.org/DIST/docs/api/ but cannot find anything
related. NCBItrace provides some perl script (maybe I could the
same with Bio.Entrez.esearch (haven't tried yet) ... I will need
to revert the order of values to get them for minus strand
orientation. If nobody needed to do this before I will invent
the wheel. ;)
Thanks for your comments,
Martin
$ perl NCBItrace/query_tracedb "retrieve quality 5728631"
>gnl|ti|5728631 name:jea17d09.b1
7 7 7 7 7 7 10 9 8 6 6 9 9 9 7 10 9 13 13 10
19 8 6 6 13 8 4 4 4 6 13 13 6 6 9 9 10 16 19 19
19 4 0 4 13 19 19 32 32 25 19 15 6 6 9 19 19 22 25 25
25 25 22 22 22 29 29 27 22 16 10 19 16 15 6 6 6 6 6 6
8 19 23 33 39 34 34 34 34 39 39 39 39 39 39 39 39 40 28 19
11 9 15 11 28 37 40 45 35 35 35 35 39 39 51 51 39 39 39 39
39 39 35 35 32 33 33 33 32 32 40 40 56 56 40 32 32 32 32 34
35 51 51 51 51 35 34 34 34 35 35 39 40 40 51 51 51 51 51 51
51 45 40 40 40 40 40 40 51 45 45 45 45 51 51 56 56 51 51 51
51 51 40 45 45 45 45 45 56 56 56 56 56 56 56 56 40 28 28 23
23 23 25 29 35 38 38 38 38 38 38 38 38 40 51 51 51 51 56 56
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