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Fix script for counting density

Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
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commit 9f16028bb3c41b0e8dd6555173b46a77b687c8c1 1 parent 32c46c2
@michaelbarton authored
Showing with 6 additions and 3 deletions.
  1. +3 −0  Makefile
  2. +1 −1  bin/count
  3. +2 −2 bin/plot_gene_density
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3  Makefile
@@ -13,3 +13,6 @@ genomes/.decompressed: genomes.tar.xz
genomes.tar.xz:
s3cmd get s3://com-cavescience-r124-manuscript/$@
+
+clean:
+ rm -rf genomes/ *.csv *.eps
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2  bin/count
@@ -7,7 +7,7 @@ file = ARGV.first
entry = Bio::FlatFile.auto(file).first
species, strain = file.gsub('.gb','').split('/')[-3,2]
-genome_length = entry.seq.length
+genome_length = entry.seq.gsub(/[Nn]+/,'').length
count = 0
entry.each_gene{ count += 1}
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4 bin/plot_gene_density
@@ -38,8 +38,8 @@ p <- p + geom_point(size=10)
# Highlight R124 genome
p <- p + geom_text(aes(
- x = 6250,
- y = 5600,
+ x = 6221,
+ y = 5200,
vjust = 1.5,
hjust = -0.5,
label = "R124"),
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