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blast inputs for plasmarithm

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1 parent 043a9ba commit 5ed886b00b16978a4b3dedbca763af785a27931b Ben J Woodcroft committed Jan 27, 2012
Showing with 32 additions and 0 deletions.
  1. +26 −0 plasmarithm/blast_inputs_creation.rb
  2. +6 −0 plasmarithm/plasmarithm_generate_inputs.rb
@@ -0,0 +1,26 @@
+#!/usr/bin/env ruby
+
+pros = %w(
+PbergheiAnnotatedProteins_PlasmoDB-8.2.fasta
+PvivaxAnnotatedProteins_PlasmoDB-8.2.fasta
+
+TgondiiME49AnnotatedProteins_ToxoDB-7.2.fasta
+
+CmurisAnnotatedProteins_CryptoDB-4.6.fasta
+ChominisAnnotatedProteins_CryptoDB-4.6.fasta
+CparvumAnnotatedProteins_CryptoDB-4.6.fasta
+
+BbovisT2BoAnnotatedProteins_PiroplasmaDB-1.1.fasta
+TannulataAnkaraAnnotatedProteins_PiroplasmaDB-1.1.fasta
+TparvaMugugaAnnotatedProteins_PiroplasmaDB-1.1.fasta
+)
+
+pros.each do |pro|
+ Dir.chdir('/blastdb') do
+ puts `makeblastdb -in #{pro}`
+ end
+end
+
+pros.each do |pro|
+ puts `blastp -query '/home/ben/phd/data/Plasmodium falciparum/genome/PlasmoDB/8.2/PfalciparumAnnotatedProteins_PlasmoDB-8.2.fasta' -db /blastdb/#{pro} -evalue 1e-5 -out /home/ben/bin/plasmarithm/input_data/falciparum8.2versus#{pro}.blast.csv -outfmt 6`
+end
@@ -549,6 +549,12 @@ class Array; def sum; self.inject{|sum,x| sum + x }; end; end
output_line.push 500
end
+ # BLAST hits against the various species
+ all_blast_targets.each do |species|
+ headers.push "#{species}_blast_hit" if do_headers
+ output_line.push !(blast_hits[species][plasmodb].nil?)
+ end
+
# conserved between 20 and 100 amino acids after the start?
headers.push 'falciparum_toxo_blast_start_20_to_100' if do_headers
if falciparum_to_toxo_min_starts[plasmodb]

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