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csw / bioruby-maf

MAF parser for BioRuby
MIT License
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Add extended UCSC bin support #106

Closed csw closed 12 years ago

csw commented 12 years ago 

ERROR bio-maf: Failed to index block at offset 33858098798677:
a score=-25272.000000
s hg19.chr21               45711888 49 +  48129895 CCCAGCCC-TGAGAGG-----CA---GGCA-AAGCC-ACCA-GGGCTCGCAGGTGTTGG-G-G
s panTro2.chr21            43929302 49 +  46489110 CCCAGCCC-TGAGAGG-----CA---GGCA-AAGCC-ACCG-GGGCTCACAGGTGTTGG-G-G
s ponAbe2.chr21            45798576 50 +  48394510 CCCAGCCC-TGAGAGG-----CA---GGCA-AAGCC-ACTGTGGGCTCGCAGGTGTTGG-G-G
s rheMac2.chr3            193989355 50 - 196418989 CCCAGCCC-TGAAAGG-----CA---GGCA-AAGCC-ACTGTGGGCTCGCAGGTGTTGG-G-G
s papHam1.scaffold2514       101078 50 +    173392 CCCAGCCC-TGAAAGG-----CA---GGCA-AAGCC-ACTGTGGGCTCACAGGTGTTGG-G-G
s calJac1.Contig29699          3423 38 -      5168 CCCAGCCC-TGAGAGG-----CA---GGCA-TGGCC-ACTG------------CACTGG-A-G
s tupBel1.scaffold_137154.1-133939        54180 52 +    133939 -CCAGCAT-TACTGGG-----CATGTGGGA-GGGTA-AGTGAGGTTAAGTGAGTGGAAG-G-A
s mm9.chr10                52493253 51 - 129993255 CCAGGCCTATGACAAG-----CA---AGCA-CAGGT-GCTGAAGGGTACTGGGCATAGA-G-T
s rn4.chr20                10986619 51 +  55268282 CGGGGCCTCTGACAAG-----CA---GTCA-TAGGT-GCTGAGGGGTACTGGGCATAGA-A-T
s cavPor3.scaffold_90        891768 52 +   6390908 CCAGGCCCATGATAAG-----TA---GGCA-CAGGTCACTGTGGGTTGCCAGGTGCGGG-G-A
s bosTau4.chr1             13859060 57 - 161106243 CAGGGTCCATGGGAGCCAACACA---GGCATGGGCC-ACTGCCGGTTCCCAGGCGTCAG-GA-
s equCab2.chr26            39517986 34 +  41866177 CAAGGCCCATGAGAGT-----CA---GGCACCGGCT-GCTGC------------------G--
s felCat3.scaffold_165895         2620 51 +     47387 CAAGGCCAGCGAGAGC-----CA---CGCACGGGGC-TCTGCAGGTCAACAGATGTCCG-G--
s canFam2.chr31            40480374 51 +  42263495 TGGGGCCCATGAGAGC-----CA---CGCACAGGCC-GCTCCAGGTTAGCTGGGGTCCG-G--
s pteVam1.scaffold_21546         5985 44 +     11734 TTGTGCC------AAC-----CG---GGCACAGGCC-ACTGCAGGT--GTGGCTGTCAGAC--
s loxAfr3.scaffold_67      11385509 50 +  12172725 CCAGGCCC-AGAGGAA-----CC---AGTG-TAGAC-CACTGGGGCAAGCAGGGGTTGG-G-G
s proCap1.scaffold_55822        10181 50 +     14856 CAAGGCTC-TGAGGAA-----CT---AGTG-TAGAC-CACTGGGGTGAGCAGGGGCTGG-G-G
s echTel1.scaffold_150201          192 49 +      1457 CAAGGCCG-AGGGTGG-----C----GGAG-GAGCT-CCCGGTGGTGAGCAGGGGTTGG-G-G
s monDom5.chr2            538457395 44 + 541556283 CCCAGTGC-AGAGAGG-----CT---GGCC-CAA-C-AATCCGGGAACATGGGTGA-------

NotImplementedError: Extended bins are not supported yet
  bin_from_range_extended at /Users/csw/src/bioruby-maf/lib/bio/ucsc/ucsc_bin.rb:91
           bin_from_range at /Users/csw/src/bioruby-maf/lib/bio/ucsc/ucsc_bin.rb:47
              entries_for at /Users/csw/src/bioruby-maf/lib/bio/maf/index.rb:811
                     each at org/jruby/RubyArray.java:1615
              entries_for at /Users/csw/src/bioruby-maf/lib/bio/maf/index.rb:806
             index_blocks at /Users/csw/src/bioruby-maf/lib/bio/maf/index.rb:724
                  collect at org/jruby/RubyArray.java:2341
                      map at org/jruby/RubyArray.java:2354
             index_blocks at /Users/csw/src/bioruby-maf/lib/bio/maf/index.rb:724
                   (root) at bin/maf_bgzip:56
    parse_blocks_parallel at /Users/csw/src/bioruby-maf/lib/bio/maf/parser.rb:975
                     call at org/jruby/RubyMethod.java:118
                    _wrap at /Users/csw/src/bioruby-maf/lib/bio/maf/parser.rb:889
           wrap_block_seq at /Users/csw/src/bioruby-maf/lib/bio/maf/parser.rb:881
               each_block at /Users/csw/src/bioruby-maf/lib/bio/maf/parser.rb:854
                   (root) at bin/maf_bgzip:52
               initialize at /Users/csw/src/bioruby-bgzf/lib/bio-bgzf/writer.rb:21
                   (root) at bin/maf_bgzip:49
                     open at org/jruby/RubyIO.java:1113
                   (root) at bin/maf_bgzip:48