Undefined method `map'

Ruby
1

Hi,

A biostar user helped me with a code to help me download fasta files
from KEGG. The code is named get_fasta4

-----CODE START HERE--------
#!/usr/bin/env ruby
require “rubygems”
require “bio”

serv = Bio::KEGG::API.new

search for xac + hypothetical

xac = serv.bfind(“T00084 hypothetical”)

get the IDS into an array

ids = xac.map { |gene| $1 if gene =~/^(.*?)\s+/ }

retrieve fasta and print

ids.each { |id| puts serv.bget("-f -n 1 #{id}") }
-----CODE END HERE--------

However, in my system, Debian Testing, I got an error:

marcelo@marcelo:~$ get_fasta4
/usr/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in require': iconv will be deprecated in the future, use String#encode instead. /home/marcelo/bin/scripts/get_fasta4:10:in‘: undefined method
`map’ for #String:0x87a9f38 (NoMethodError)
marcelo@marcelo:~$
marcelo@marcelo:~$ ruby -v
ruby 1.9.3p194 (2012-04-20 revision 35410) [i486-linux]
marcelo@marcelo:~$
marcelo@marcelo:~$ gem search soap

*** LOCAL GEMS ***

soap4r (1.5.8)
soap4r-ruby1.9 (2.0.5)
soap4r-ruby19 (1.5.9)
marcelo@marcelo:~$

Could you help me?

Thank you very much!

2

On 5/11/2012, at 10:35 AM, Marcelo L. [email protected] wrote:

It’s telling you what the problem is.

search for xac + hypothetical

xac = serv.bfind(“T00084 hypothetical”)

get the IDS into an array

ids = xac.map { |gene| $1 if gene =~/^(.*?)\s+/ }

retrieve fasta and print

ids.each { |id| puts serv.bget(“-f -n 1 #{id}”) }
-----CODE END HERE--------

/home/marcelo/bin/scripts/get_fasta4:10:in <main>': undefined method map’ for #String:0x87a9f38 (NoMethodError)

xac is a String which doesn’t have a method ‘map’. ‘map’ expects an
Array. You can either force xac to be an Array

ids = Array(xac).map { |gene| $1 if gene =~/^(.*?)\s+/ }

or fix the previous line to return an array.

Henry

3

On Nov 4, 2012, at 14:15 , Henry M. [email protected] wrote:

ids.each { |id| puts serv.bget(“-f -n 1 #{id}”) }
-----CODE END HERE--------

/home/marcelo/bin/scripts/get_fasta4:10:in <main>': undefined method map’ for #String:0x87a9f38 (NoMethodError)

xac is a String which doesn’t have a method ‘map’. ‘map’ expects an Array.

#map is a member of Enumerable, not just Array. String used to be
Enumerable in 1.8-, but it isn’t in 1.9+

10000 % irb

String.ancestors
=> [String, Enumerable, Comparable, Object, Kernel]
10001 % irb19
String.ancestors
=> [String, Comparable, Object, Kernel, BasicObject]

You can either force xac to be an Array

ids = Array(xac).map { |gene| $1 if gene =~/^(.*?)\s+/ }

xac.lines.map is clearer.

There should probably also be a #compact since the regexp could
potentially not match.