User:Lindenb/Notebook/UMR915/20110714: Difference between revisions
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(New page: {{PLNB|20110704|20110714}} #allonzenfan =playing with dbNSFP= <pre>curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | funzip -t | head -n1 |tr " " "\n" | ca...) |
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{{PLNB|20110704|20110714}} | {{PLNB|20110704|20110714}} | ||
(allonzenfan) | |||
=playing with dbNSFP= | =playing with dbNSFP= | ||
<pre>curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | funzip -t | head -n1 |tr " " "\n" | cat -n | <pre>curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | funzip -t | head -n1 |tr " " "\n" | cat -n | ||
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34 1000_genomes_low_coverage | 34 1000_genomes_low_coverage | ||
</pre> | </pre> | ||
==getting the columns== | |||
AA1, AA2 sift & pph2 predictions. | |||
<pre>curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | zcat | cut -d ' ' -f 5,6,19,20,21,22 | head | |||
aaref aaalt SIFT_score SIFT_pred Polyphen2_score Polyphen2_pred | |||
M L 1.0 D 0.997 D | |||
M V 0.945248 NA 0.999 D | |||
M L 1.0 D 0.997 D | |||
M K 1.0 D 0.999 D | |||
M T 1.0 D 0.999 D | |||
M R 0.942261 NA 0.999 D | |||
M I 1.0 D 0.999 D | |||
M I 1.0 D 0.999 D | |||
M I 1.0 D 0.999 D</pre> | |||
<html><script src="https://gist.github.com/1082406.js?file=predictions.cpp"></script></html> | |||
==Compile and run== | |||
<pre>g++ -I /usr/include/cairo predictions.cpp -lcairo | |||
curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | zcat |\ | |||
cut -d ' ' -f 5,6,19,20,21,22 | egrep '^[A-Z] [A-Z]'| ./a.out </pre> | |||
==Result== | |||
Revision as of 06:08, 14 July 2011
(allonzenfan)
playing with dbNSFP
curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | funzip -t | head -n1 |tr " " "\n" | cat -n
1 #chr
2 pos(1-based)
3 ref
4 alt
5 aaref
6 aaalt
7 hg19pos(1-based)
8 genename
9 geneid
10 CCDSid
11 refcodon
12 codonpos
13 fold-degenerate
14 aapos
15 cds_strand
16 LRT_Omega
17 PhyloP_score
18 PlyloP_pred
19 SIFT_score
20 SIFT_pred
21 Polyphen2_score
22 Polyphen2_pred
23 LRT_score
24 LRT_pred
25 MutationTaster_score
26 MutationTaster_pred
27 Ancestral_allele
28 UniSNP_ids
29 Allele_freq
30 Alt_gene_name
31 dbXrefs
32 Descriptive_gene_name
33 1000_genomes_high_coverage
34 1000_genomes_low_coverage
getting the columns
AA1, AA2 sift & pph2 predictions.
curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | zcat | cut -d ' ' -f 5,6,19,20,21,22 | head aaref aaalt SIFT_score SIFT_pred Polyphen2_score Polyphen2_pred M L 1.0 D 0.997 D M V 0.945248 NA 0.999 D M L 1.0 D 0.997 D M K 1.0 D 0.999 D M T 1.0 D 0.999 D M R 0.942261 NA 0.999 D M I 1.0 D 0.999 D M I 1.0 D 0.999 D M I 1.0 D 0.999 D
<html><script src="https://gist.github.com/1082406.js?file=predictions.cpp"></script></html>
Compile and run
g++ -I /usr/include/cairo predictions.cpp -lcairo curl -s "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP1.1.chr1-22XY.zip" | zcat |\ cut -d ' ' -f 5,6,19,20,21,22 | egrep '^[A-Z] [A-Z]'| ./a.out
