[BioRuby] Indexing fasta file with Ruby 1.9.1

[Raoul Bonnal]

Hi all,
I'd like to index a fasta file and retrieve a bunch of sequences:
The dataset:
>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
UGAGGUAGUAGGUUGUAUAGUU
>cel-let-7* MIMAT0015091 Caenorhabditis elegans let-7*
UGAACUAUGCAAUUUUCUACCUUAC
>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
UCCCUGAGACCUCAAGUGUGA
>cel-lin-4* MIMAT0015092 Caenorhabditis elegans lin-4*
ACACCUGGGCUCUCCGGGUAC
>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
UGGAAUGUAAAGAAGUAUGUA
...
If you want to try
curl -O ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz

I tried 
br_bioflat.rb --makeindex mirna-mature-idx mature.fa

but I get this messages:
>bta-miR-3604 MIMAT0016939 Bos taurus miR-3604
UAACCAAUGUGCAGACUACUGU
===end===
This entry shall be incorrectly indexed.
Caught error: #<NoMethodError: undefined method `each' for "bta-miR-3596":String>
in "mature.fa" position 1178667
===begin===
>bta-miR-3596 MIMAT0016940 Bos taurus miR-3596
AACCACACAACCUACUACCUCA
===end===
This entry shall be incorrectly indexed.
Caught error: #<NoMethodError: undefined method `each' for "ath-miR854e":String>
in "mature.fa" position 1178737
===begin===
>ath-miR854e MIMAT0004283 Arabidopsis thaliana miR854e
GAUGAGGAUAGGGAGGAGGAG
===end===
This entry shall be incorrectly indexed.
Caught error: #<NoMethodError: undefined method `each' for "cre-miR1161b":String>
in "mature.fa" position 1178814
===begin===
>cre-miR1161b MIMAT0005413 Chlamydomonas reinhardtii miR1161b
UACUGGAGUUCUCAACAGC
===end===





NOTE: It works with 1.8.7

--
Raoul J.P. Bonnal
Life Science Informatics
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 006 623  26
fax: +39 02 006 623 46
http://www.ingm.it