unit_test/data/aligns4.asn

-- Denseg
Seq-align ::= {
  type partial,
  dim 2,
  segs denseg {
    dim 2,
    numseg 5,
    ids {
      gi 2,
      gi 3
    },
    starts {
      1000, 2000,
      1062, -1,
      1183, 2111,
      -1, 2159,
      1221, 2249
    },
    lens {
      25,
      56,
      15,
      62,
      70
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs denseg {
    dim 2,
    numseg 5,
    ids {
      gi 2,
      gi 3
    },
    starts {
      1000, 2294,
      1062, -1,
      1183, 2193,
      -1, 2098,
      1221, 2000
    },
    lens {
      25,
      56,
      15,
      62,
      70
    },
    strands {
      plus, minus,
      plus, minus,
      plus, minus,
      plus, minus,
      plus, minus
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs denseg {
    dim 2,
    numseg 7,
    ids {
      gi 2,
      gi 6
    },
    starts {
      1741, 2000,
      1627, 2021,
      1558, 2069,
      1477, -1,
      1435, 2125,
      -1, 2139,
      1000, 2212
    },
    lens {
      21,
      31,
      23,
      27,
      14,
      73,
      49
    },
    strands {
      minus, plus,
      minus, plus,
      minus, plus,
      minus, plus,
      minus, plus,
      minus, plus,
      minus, plus
    }
  }
}

-- Dendiag
Seq-align ::= {
  type partial,
  dim 2,
  segs dendiag {
    {
      dim 2,
      ids {
        gi 2,
        gi 3
      },
      starts {
        1000, 2000
      },
      len 25
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 3
      },
      starts {
        1183, 2111
      },
      len 15
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 3
      },
      starts {
        1221, 2249
      },
      len 70
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs dendiag {
    {
      dim 2,
      ids {
        gi 2,
        gi 3
      },
      starts {
        1000, 2294
      },
      len 25,
      strands {
        plus, minus
      }
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 3
      },
      starts {
        1183, 2193
      },
      len 15,
      strands {
        plus, minus
      }
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 3
      },
      starts {
        1221, 2000
      },
      len 70,
      strands {
        plus, minus
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs dendiag {
    {
      dim 2,
      ids {
        gi 2,
        gi 6
      },
      starts {
        1741, 2000
      },
      len 21,
      strands {
        minus, plus
      }
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 6
      },
      starts {
        1627, 2021
      },
      len 31,
      strands {
        minus, plus
      }
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 6
      },
      starts {
        1558, 2069
      },
      len 23,
      strands {
        minus, plus
      }
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 6
      },
      starts {
        1435, 2125
      },
      len 14,
      strands {
        minus, plus
      }
    },
    {
      dim 2,
      ids {
        gi 2,
        gi 6
      },
      starts {
        1000, 2212
      },
      len 49,
      strands {
        minus, plus
      }
    }
  }
}

-- Std-seg
Seq-align ::= {
  type partial,
  dim 2,
  segs std {
    {
      dim 2,
      loc {
        int {
          from 1000,
          to 1024,
          id gi 2
        },
        int {
          from 2000,
          to 2024,
          id gi 3
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1183,
          to 1197,
          id gi 2
        },
        int {
          from 2111,
          to 2125,
          id gi 3
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1221,
          to 1290,
          id gi 2
        },
        int {
          from 2249,
          to 2318,
          id gi 3
        }
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs std {
    {
      dim 2,
      loc {
        int {
          from 1000,
          to 1024,
          strand plus,
          id gi 2
        },
        int {
          from 2294,
          to 2318,
          strand minus,
          id gi 3
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1183,
          to 1197,
          strand plus,
          id gi 2
        },
        int {
          from 2193,
          to 2207,
          strand minus,
          id gi 3
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1221,
          to 1290,
          strand plus,
          id gi 2
        },
        int {
          from 2000,
          to 2069,
          strand minus,
          id gi 3
        }
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs std {
    {
      dim 2,
      loc {
        int {
          from 1741,
          to 1803,
          strand minus,
          id gi 2
        },
        int {
          from 2000,
          to 2020,
          id gi 6
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1627,
          to 1719,
          strand minus,
          id gi 2
        },
        int {
          from 2021,
          to 2051,
          id gi 6
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1435,
          to 1476,
          strand minus,
          id gi 2
        },
        int {
          from 2125,
          to 2138,
          id gi 6
        }
      }
    },
    {
      dim 2,
      loc {
        int {
          from 1000,
          to 1146,
          strand minus,
          id gi 2
        },
        int {
          from 2212,
          to 2260,
          id gi 6
        }
      }
    }
  }
}

-- Spliced-seg
Seq-align ::= {
  type partial,
  dim 2,
  segs spliced {
    product-id gi 3,
    genomic-id gi 2,
    product-type transcript,
    exons {
      {
        product-start nucpos 2000,
        product-end nucpos 2318,
        genomic-start 1000,
        genomic-end 1290,
        parts {
          match 25,
          genomic-ins 72,
          mismatch 86,
          diag 15,
          product-ins 100,
          mismatch 23,
          match 70
        }
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs spliced {
    product-id gi 3,
    genomic-id gi 2,
    product-type transcript,
    exons {
      {
        product-start nucpos 2000,
        product-end nucpos 2024,
        genomic-start 1000,
        genomic-end 1024,
        parts {
          match 25
        }
      },
      {
        product-start nucpos 2111,
        product-end nucpos 2125,
        genomic-start 1183,
        genomic-end 1197,
        parts {
          match 15
        }
      },
      {
        product-start nucpos 2249,
        product-end nucpos 2318,
        genomic-start 1221,
        genomic-end 1290,
        parts {
          match 70
        }
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs spliced {
    product-id gi 3,
    genomic-id gi 2,
    product-strand minus,
    genomic-strand plus,
    product-type transcript,
    exons {
      {
        product-start nucpos 2000,
        product-end nucpos 2318,
        genomic-start 1000,
        genomic-end 1290,
        parts {
          match 25,
          genomic-ins 72,
          mismatch 86,
          diag 15,
          product-ins 100,
          mismatch 23,
          match 70
        }
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs spliced {
    product-id gi 3,
    genomic-id gi 2,
    product-type transcript,
    exons {
      {
        product-start nucpos 2294,
        product-end nucpos 2318,
        genomic-start 1000,
        genomic-end 1024,
        product-strand minus,
        genomic-strand plus,
        parts {
          match 25
        }
      },
      {
        product-start nucpos 2193,
        product-end nucpos 2207,
        genomic-start 1183,
        genomic-end 1197,
        product-strand minus,
        genomic-strand plus,
        parts {
          match 15
        }
      },
      {
        product-start nucpos 2000,
        product-end nucpos 2069,
        genomic-start 1221,
        genomic-end 1290,
        product-strand minus,
        genomic-strand plus,
        parts {
          match 70
        }
      }
    }
  }
}
Seq-align ::= {
  type partial,
  dim 2,
  segs spliced {
    product-id gi 6,
    genomic-id gi 2,
    genomic-strand minus,
    product-type protein,
    exons {
      {
        product-start protpos { amin 2000, frame 1 },
        product-end protpos { amin 2260, frame 3 },
        genomic-start 1000,
        genomic-end 1803,
        parts {
          match 63,
          genomic-ins 21,
          match 93,
          product-ins 51,
          match 69,
          mismatch 81,
          product-ins 18,
          diag 42,
          mismatch 219,
          genomic-ins 69,
          match 147
        }
      }
    }
  }
}

-- Sparse-seg
Seq-align ::= {
  type global,
  dim 2,
  segs sparse {
    rows {
      {
        first-id gi 2,
        second-id gi 3,
        numseg 3,
        first-starts { 1000, 1183, 1221 },
        second-starts { 2000, 2111, 2249 },
        lens { 25, 15, 70 }
      }
    }
  }
}