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comparison snpEff_2_1a/scripts/genesTxtColumnNames.sh @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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1 #!/bin/sh
2
3 #-------------------------------------------------------------------------------
4 # Convert the gene names in order to be used in an R script
5 #
6 # Usage: cat snpEff_genes.txt | ./scripts/genesTxtColumnNames.sh > genes.txt
7 #
8 # Once in R, you can:
9 # - Load this table:
10 # data <- read.csv("genes.txt", sep= "\t", header=TRUE);
11 #
12 # - Access the data:
13 # data$countINTRON
14 #
15 # - Add missing or empty columns:
16 # if( is.null(data$countINTRON ) { data$countINTRON <- 0 * (1:length(data$geneId) ); }
17 #
18 # Pablo Cingolani
19 #-------------------------------------------------------------------------------
20
21 cat \
22 | grep -v "^# The following"\
23 | sed "s/Bases affected (/bases/g" \
24 | sed "s/Length (/len/g" \
25 | sed "s/Count (/count/g" \
26 | sed "s/Total score (/score/g" \
27 | sed "s/)//g" \
28 | sed "s/#GeneId/geneId/" \
29 | sed "s/GeneName/geneName/" \
30 | sed "s/BioType/bioType/" \
31 | sed "s/_PRIME//g" \
32 | sed "s/SPLICE_SITE_//g" \
33 | sed "s/SYNONYMOUS_CODING/SYN/g" \