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Data Standards Hackathon for NGS based typing.
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HML Spec: Add IMGT position attribute to targeted-region. #12

Closed dvaliga closed 9 years ago

ghost commented 9 years ago

What does IMGT position mean?

dvaliga commented 9 years ago

For IMGT, refer to this (which was modeled in the 0.9.3 spec before the CDATA text was removed from targeted-region):

    <consensus-sequence>
      <targeted-region format="feature-table"><![CDATA[     exon            <1..61
                 /number="1"
                 /imgt="13..73"
 intron          62..191
                 /number="1"
                 /imgt="74..203"
 exon            192..510
                 /number="2"
                 /imgt="204..473"
 intron          511..752
                 /number="2"
                 /imgt="474..714"
 exon            753..1087
                 /number="3"
                 /imgt="715..990"
 intron          1088..>1353
                 /number="3"
                 /imgt="991..1255"

]]>

GCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCTCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACGGCCTCTGTGGGGAGAAGCAACGGGCCCGCCTGGCGGGGGCGCAGGACCCGGGAAGCCGCGCCGGGAGGAGGGTCGGGCGGGTCTCAGCCACTCCTCGTCCCCAGGCTCTCACTCCATGAGGTATTTCTACACCTCCGT-----GTCCCGGCCCGGCCGCGGGG-----------------------AGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGAC--------------------GCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGTCCGGAGTATTGGGACGGGGAGACACGGAAAGTGAAGG-CCCACTCACAGACTCACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCTCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCGCCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTA-CCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCAGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACCGGGCTGACCGCGGGGTCCGGGCCAGGGTCTCACACCGTCCAGAGGATGTATGGCTGCGACGTGGGGTCGGACTGGCGCTTCCTCCGCGGGTA?CACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAAAGAGGACCTGCGCTCTTGGACCGCG--------------------------------------GCGGACATGGCAGCTCAGACCACCAAGCACAAGTGGGAGGCG--GCCCATGTGGC-GGAGCAGTTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGG-----------------GAAGGAGACGCTGCAG-CGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTGTAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCGCCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAA-TCTCTGAAGGAATGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGA 
      <sequence>GCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGAGGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTACACCTCCGT-----GTCCCGGCCCGGCCGCGGGG-----------------------AGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGAC--------------------GCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGG-CCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCATCCCCCACGGACGGGCCAGGTGGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTA-CCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCCGGGCAGGGCTTGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTA?CGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCG--------------------------------------GCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCG--GCCCATGCGGC-GGAGCAGCAGAGAGCCTACCTGGAGGGCCGGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGG-----------------GAAGGAGACGCTGCAG-CGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTATAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAA-TCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGA</sequence>
    </consensus-sequence>
ghost commented 9 years ago

Fixed in HML version 1.0, see https://github.com/nmdp-bioinformatics/hml/issues/26