090622_blast-clustalw

2009/06/22

kaneko.satoko(at)ocha.ac.jp

BLAST CLUSTALW

TogoWS REST SOAP (step )

(11):E‐value

(1)
blast_clustalw.rb
blast_clustalw.rb
$ ruby blast_clustalw.rb hsa:6469
( has:6469 blast + clustalw

blast_clustalw.rb

step10.rb
step20.rb Blastp
step30.rb Blastp ID E‐value
step40.rb ID E‐value E‐value
step50.rb
step60.rb ClustalW mulSple alignment

(2) step10.rb
k.step10.txt
‐ hsa:6469 ( ID kegg_id )
‐blast_clustalw.rb 8‐12 get_aaseq
‐ last_clustalw.rb
b get_aaseq 79

#!/usr/bin/env ruby

require ‘open‐uri’ # 8 open URL REST

# kegg_id
kegg_id = "hsa:6469";
#  kegg_id aaseq
aaseq = open("hap://togows.dbcls.jp/entry/gene/" + kegg_id + "/aaseq").read
#REST hap://togows.dbcls.jp/entry/gene/has:6469/aaseq
# aaseq

# aaseq k.step10.txt
out = open("k.step10.txt","w")
out.puts aaseq
out.close

(3) step20.rb
Sonic Hedgehog query BLAST
‐blast_clustalw.rb 15‐25
‐ blast_clustalw.rb 81
#!/usr/bin/env ruby
require 'soap/wsdlDriver'

# step10.rb aaseq
aaseq = File.read("k.step10.txt”)
# blast result_blast
wsdl_blast = "hap://togows.dbcls.jp/soap/wsdl/ddbj_blast.wsdl"
serv_blast = SOAP::WSDLDriverFactory.new(wsdl_blast).create_rpc_driver
program = "blastp"
database = "SWISS"
result_blast = serv_blast.DdbjBlastSearchSimple(program,database,aaseq)
# ↑SOAP blast
# result_blast k.step20.txt
out = open("k.step20.txt","w")
out.puts result_blast
out.close

(4) step30.rb
BLAST clustalw
‐ blast_clustalw.rb 27 47 84

#!/usr/bin/env ruby
require 'soap/wsdlDriver'

# step20.rb blast result_blast
result_blast = File.read("k.step20.txt")

# result_blast spid_hash
#

spid_hash = Hash.new #
# blast line
result_blast.each_line do |line|
  # blast sp
if line =~ /^sp|(.+)|(.+)s+.+s+[0‐9]+s+(.+)$/
    spid = $1      # spid
spname = $2    # spname
evalue = $3    # evalue
if evalue =~ /^e/ # evalue e
evalue = “1.0” + evalue # 1.0
    end
#

#
# evalue evalue_float
evalue_float = evalue.to_f
    # spid_hash[spid] spname evalue_float
spid_hash[spid] = {:name=>spname, :evalue=>evalue_float}
  end
end

# spid_hash k.step30.txt
#
out = open("k.step30.txt","w");
spid_hash.each {|spid,value|
  out.prinv("%s|%s|%sn",spid,value[:name],value[:evalue]);
}
out.close

step20 blast k.step20.txt ID e‐value
k.step30.txt

‐blast_clustalw.rb 28‐47 parse_blast
‐ last_clustalw.rb
b get_aaseq 84

: step30.rb

‐ if line =~ /^sp|(.+)|(.+)s+.+s+[0‐9]+s+(.+)$/
BLAST 1

‐ f
I if )
spid spname evalue

.: , +: 1 , s: , $:
(): , []: []

Score E
Sequences producing significant alignments: (bits) Value

sp|Q15465|SHH_HUMAN Sonic hedgehog... 720 0.0
sp|Q62226|SHH_MOUSE Sonic hedgehog... 682 0.0
sp|Q63673|SHH_RAT Sonic hedgehog... 679 0.0
sp|Q91035|SHH_CHICK Sonic hedgehog... 605 e-172
sp|Q90385|SHH_CYNPY Sonic hedgehog... 510 e-144

spid
spname
evalue

spid_hash[spid][:name]
spid_hash[spid][:evalue]

(11):E‐value

(ex. 0.0, e‐100 )

query E‐value query

‐

*E‐value

*

(5) step40.rb
Blast E‐value
Step30 k.step30.txt E‐value
k.step40.txt
‐blast_clustalw.rb 39‐43
‐blast_clustalw.rb e‐value 6
#!/usr/bin/env ruby

#
min_evalue = 1e‐170
# step30.rb
# spid_hash
lns_spid = File.read("k.step30.txt")
spid_hash = Hash.new
lns_spid.each_line do |line|
  raise unless line =~ /^(.+)|(.+)|(.+)$/
  spid = $1
  spname = $2
  evalue = $3
  spid_hash[spid] =
   {:name=>spname, :evalue=>evalue.to_f}
end #

#
#
#
  #
if value[:evalue] > min_evalue then
    spid_hash.delete(spid)   #
end
}
# k.step40.txt
  out.prinv("%s|%s|%sn",
  spid,value[:name],value[:evalue]);
}
out.close

(6) step50.rb
Sonic Hedgehog

#!/usr/bin/env ruby
require 'open‐uri’

#
# spid_hash
lns_spid = File.read("k.step40.txt")
spid_hash = Hash.new
lns_spid.each_line do |line|
  raise unless line =~ /^(.+)|(.+)|(.+)$/
  spid = $1
  spname = $2
  evalue = $3
  spid_hash[spid] = {:name=>spname, :evalue=>evalue.to_f}
end
#

#
# spid_hash
  #
uri = "hap://togows.dbcls.jp/entry/uniprot/" + spid + "/seq”
# REST
  value[:seq] = open(uri).read
}

# fasta
out = open("k.step50.fa","w");
  out.prinv(">%s|%s|%sn",spid,value[:name],value[:evalue]);
  out.prinv("%sn",value[:seq]);
}
out.close

(7) step60.rb
CLUSTALW alignment
Step50.rb clustalw SOAP
#!/usr/bin/env ruby
require 'soap/wsdlDriver’

# fasta query
query           = File.read("k.step50.fa")
# query mulSple alignment
wsdl_clustalw   = "hap://togows.dbcls.jp/soap/wsdl/ddbj_clustalw.wsdl"
serv_clustalw   = SOAP::WSDLDriverFactory.new(wsdl_clustalw).create_rpc_driver
param           = "‐align ‐matrix=blosum ‐gapdist=8 ‐maxdiv=40 ‐outorder=aligned ‐
pwmatrix=blosum”
# SOAP CLUSTALW
result_clustalw = serv_clustalw.DdbjClustalwAnalyzeParam(query,param)

# k.step60.txt
out.puts result_clustalw
out.close

(8) blast_clustalw.rb
blast_clustalw.rb 77‐97 Step10‐60

shiz
# ID hsa:6469
# step10.rb

# step20.rb

#step30.rb step40.rb

#step50.rb

#step60.rb

# auto.txt

blast_clustalw.rb

1) hsa:6469 MIN_EVALUE ( 1.0e‐140, 1.0e‐120,
1.0e‐100 ) mulSple alignment ( )

2) rat Olr1082 mulSple alignment human mouse
ortholog
‐
rat Olr1082 UniProt ID
REST Entry retrieval UniProt KEGG ID
blast_clustalw.rb (MIN_EVALUE 1.0e‐100)
mulSple alignment ortholog
Ensembl Synteny ortholog

090622_blast-clustalw

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