converter format asn to gff
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1
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4.9 years ago
mimi ▴ 20

Hi,

I used prosplign ( https://www.ncbi.nlm.nih.gov/sutils/static/prosplign/prosplign.html). It generated a file ASN, but I need a gff3 format

Do you know an affective converter?

I used asn2flat -i file.asn -format gff3 -o out (but it does not support the gff3 format, it advises to use annotwriter to ncbi)

annotwriter -i file.asn -format gff3 -o out (It shows me errors)

Error: (311.26) SOCK#3000[3]@130.14.29.112:4445: [SOCK::Connect]  Failed pending connect(): Timeout[5.000000]
Error: (310.6) [ID2]  Stateful relay connection failure (Closed) usually indicates possible firewall configuration problems; please consult <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/dispatcher.html#Firewalling>
Error: (301.5) [CONN_Open(ID2)]  Failed to open connection: Closed
Error: (311.26) SOCK#6000[3]@130.14.29.112:4445: [SOCK::Connect]  Failed pending connect(): Timeout[5.000000]
Error: (310.6) [ID2]  Stateful relay connection failure (Closed) usually indicates possible firewall configuration problems; please consult <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/dispatcher.html#Firewalling>
Error: (301.5) [CONN_Open(ID2)]  Failed to open connection: Closed
Error: (311.26) SOCK#9000[3]@130.14.29.112:4454: [SOCK::Connect]  Failed pending connect(): Timeout[5.000000]
Error: (310.6) [ID2]  Stateful relay connection failure (Closed) usually indicates possible firewall configuration problems; please consult <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/dispatcher.html#Firewalling>
Error: (301.5) [CONN_Open(ID2)]  Failed to open connection: Closed
Error: (311.26) SOCK#12000[3]@130.14.29.112:4454: [SOCK::Connect]  Failed pending connect(): Timeout[5.000000]
Error: (310.6) [ID2]  Stateful relay connection failure (Closed) usually indicates possible firewall configuration problems; please consult <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/dispatcher.html#Firewalling>
Error: (301.5) [CONN_Open(ID2)]  Failed to open connection: Closed
Error: (311.26) SOCK#15000[3]@130.14.29.112:4445: [SOCK::Connect]  Failed pending connect(): Timeout[5.000000]
Error: (310.6) [ID2]  Stateful relay connection failure (Closed) usually indicates possible firewall configuration problems; please consult <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/dispatcher.html#Firewalling>
Error: (301.5) [CONN_Open(ID2)]  Failed to open connection: Closed
Error: (CLoaderException::eConnectionFailed) cannot open connection: ID2
Error: (CLoaderException::eNoConnection) cannot open initial connection
Error: (106.16) Application's execution failed(CLoaderException::eNoConnection) cannot open initial connection
ASN GFF3 • 1.7k views
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is there a XML output ? can you post a sample ?

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The asn format to prosplign :

Seq-align ::= {
  type disc,
  dim 2,
  score {
    {
      id str "num_ident",
      value int 0
    },
    {
      id str "num_positives",
      value int 0
    },
    {
      id str "num_negatives",
      value int 0
    },
    {
      id str "product_gap_length",
      value int 0
    },
    {
      id str "genomic_gap_length",
      value int 0
    },
    {
      id str "align_length",
      value int 0
    },
    {
      id str "product_internal_gap_length",
      value int 0
    }
  },
  segs spliced {
    product-id swissprot {
      accession "A0A023H3J7"
    },
    genomic-id local str "Lsta_scaffold1",
    genomic-strand plus,
    product-type protein,
    exons {
    },
    product-length 219
  },
  bounds {
    whole swissprot {
      accession "A0A023H3J7"
    },
    int {
      from 4280885,
      to 4282070,
      strand plus,
      id local str "Lsta_scaffold1"
    }
  },
  ext {
    {
      type str "info",
      data {
        {
          label str "CompartmentId",
          data int 1
        }
      }
    }
  }
 }
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That is not XML format output so not what @Pierre was asking. Do you know if prosplign is able to output XML?

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Duplicate question: Question: converting ASN to Gff3

prosplign -f x can output xml.

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Sorry !

Can I convert this xml format to gff3 ? Thanks

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Oups! Sorry @genomax

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if the XML is simple , one can use XSLT to transform it to something. while ASN1 requires a specific parser.

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