Question

I am not a programmer, but I am taking a bioinformatics class as I’m a molecular genetics major… our assignment is to take a file of multiple entries like this:

77: XP_001929585
PREDICTED: similar to BRCA1 associated protein [Sus scrofa]
gi|194042959|ref|XP_001929585.1| [194042959]

and extract the items I’ve bolded, then save the results into a pipe-delimited file like this:

194042959|Sus scrofa|PREDICTED: similar to BRCA1 associated protein.

We are using the Sublime editor to write our scripts in Ruby. I know how to open the file and then… well, here’s my script so far…

#!/usr/local/bin/ruby
File.open("mmg231_hw5_brca1.txt").each do |file_line|
  if file_line =~ /^(.+)\[([A-Z].+)\]/
    description = $1
    taxon_name = $2
    puts "#{taxon_name}|#{description}" 
  elsif file_line =~ /\[([0-9].+)\]/
    gi_number = $1
    puts "#{gi_number}"
  end
end

I know that it’s wrong… the regular expressions do capture what they need to. the first puts does put out the taxon name and the description properly, but I can’t figure out how to get the gi number in there too, as its on a different line… I can pull out the gi number on its own also, but have no way of linking it to the other two parts. Also, when I pull them out using the regular expressions I developed, they stay in the right order as they were in the file, so I was trying to think of a way to tell the computer to like number each taxon name/description pair 1, 2, 3, etc as in the file, and then do the same with the gi numbers, and then you could just say like taxon name/description 1 goes with gi number 1, etc… or have the computer get the taxon name and description pair, then just look in the next line for the gi number, but I don’t know how to do this…

help? And in plain english would be helpful, most help sites I feel like I would be able to use, but I just don’t understand the language…

first 4 entries:

1: ZP_00239925
BRCA1 [Bacillus cereus G9241]
gi|47569239|ref|ZP_00239925.1||gnl|WGS:NZ_AAEK|BCE_G9241_3679 [47569239]

2: NP_009225
breast cancer 1, early onset isoform 1 [Homo sapiens]
gi|6552299|ref|NP_009225.1| [6552299]

3: NP_033894
breast cancer 1 [Mus musculus]
gi|161016835|ref|NP_033894.3| [161016835]

4: NP_036646
breast cancer 1 [Rattus norvegicus]
gi|6978573|ref|NP_036646.1| [6978573]

Answer 1

Do the lines always come in pairs?

If so, why not doing:

description = taxon_name = gi_number = nil
first = false
File.open("mmg231_hw5_brca1.txt").each do |file_line|

  if file_line =~ /^(.+)\[([A-Z].+)\]/    
    description = $1
    taxon_name = $2
    first = true #Just to check they are consecutive 
  else
    if file_line =~ /\[([0-9].+)\]/
      gi_number = $1
      if first == true
        puts "#{gi_number}|#{taxon_name}|#{description}"
      end
    end
    first = false
  end
end