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|
#! /usr/bin/ruby
# subroutines
def firstnum str
a = str.index('(')
b = str.index('-')
loc = str.slice(a + 1 .. b - 1)
loc.to_i
end
def lastnum str
c = str.index('-')
d = str.index(')')
loc = str.slice(c + 1 .. d - 1)
loc.to_i
end
def getaa str
x = str.index(' ')
y = str.index("\t")
loc = str.slice(x + 1 .. y - 1)
loc.to_s
end
def getid str
z = str.index('.trna')
loc = str.slice(0 .. z - 1)
loc.to_s
end
# main program
idnotsent = true
st = 0;
sp = 0;
inst = 0
insp = 0
acst = 0
acsp = 0
id = ''
aa = ''
pseudo = false
name = gets
while name
name = name.chomp
if name.index('Seq:') != nil
if idnotsent
puts '>Features ' + id + ' tRNAscan-SE'
idnotsent = false
end
if inst == 0 and insp == 0
puts st.to_s + "\t" + sp.to_s + "\t" + "tRNA"
else
inst = inst - 1
insp = insp + 1
puts st.to_s + "\t" + inst.to_s + "\t" + "tRNA"
puts insp.to_s + "\t" + sp.to_s
end
puts "\t\t\tproduct\t" + aa
if pseudo
puts "\t\t\tpseudo"
else
if acst != 0 and acsp != 0
if acst < acsp
puts "\t\t\tanticodon\t(pos:" + acst.to_s + ".." + acsp.to_s + ",aa:" + aa + ")"
else
puts "\t\t\tanticodon\t(pos:complement(" + acsp.to_s + ".." + acst.to_s + "),aa:" + aa + ")"
end
end
end
puts "\t\t\tgene\t-"
st = 0;
sp = 0;
inst = 0
insp = 0
acst = 0
acsp = 0
id = ''
aa = ''
pseudo = false
elsif name.index('Type:') != nil
aa = getaa name
if aa == 'Undet' or aa == 'Sup'
aa = 'OTHER'
end
loc = name.slice(/[(].*[)]/)
acst = firstnum loc
acsp = lastnum loc
elsif name.index('Length') != nil
id = getid name
loc = name.slice(/[(].*[)]/)
st = firstnum loc
sp = lastnum loc
elsif name.index('Possible intron:') != nil
loc = name.slice(/[(].*[)]/)
inst = firstnum loc
insp = lastnum loc
elsif name.index('Possible pseudogene:') != nil
pseudo = true
end
name = gets
end
|
