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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 4 | 6 | 6 | 0.969 | test_plus |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 4 | 18 | Bio/Blast/Applications.py |
| 2 | 4 | 215 | Bio/Emboss/Applications.py |
| 3 | 4 | 253 | Bio/Emboss/Applications.py |
| 4 | 4 | 416 | Bio/Emboss/Applications.py |
| 5 | 4 | 739 | Bio/Emboss/Applications.py |
| 6 | 4 | 757 | Bio/Emboss/Applications.py |
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_Option(["-d","database"],["input"],None,1,"The database to retrieve from."),_Option(["-s","search_string"],["input"],None,1,"The id to search for.") |
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_Option(["-msf","msf"],["input"],None,1,"File containing sequences"),_Option(["-method","method"],["input"],None,1,"Choose the method to use") |
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_Option(["-infile","infile"],["input"],None,1,"infile value"),_Option(["-trout","trout"],["input"],None,1,"Create a tree file") |
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_Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-method","method"],["input"],None,1,"sub. model [f,k,j,l,s]") |
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_Option(["-sequence","sequence"],["input"],None,1,"Sequence database USA"),_Option(["-pattern","pattern"],["input"],None,1,"Search pattern, using standard IUPAC one-letter codes") |
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_Option(["-est","est"],["input"],None,1,"EST sequence(s)"),_Option(["-genome","genome"],["input"],None,1,"Genomic sequence") |
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_Option([ [[#variable77a8ea60]], [[#variable77a8eaa0]]],["input"],None,1, [[#variable7d1068c0]]),_Option([ [[#variable50448200]], [[#variable50448e80]]],["input"],None,1, [[#variable77a8ea80]]) |
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#77a8ea60]] | "-msf" |
| 1 | 2 | [[#77a8ea60]] | "-infile" |
| 1 | 3 | [[#77a8ea60]] | "-sequence" |
| 1 | 4 | [[#77a8ea60]] | "-sequence" |
| 1 | 5 | [[#77a8ea60]] | "-est" |
| 1 | 6 | [[#77a8ea60]] | "-d" |
| 2 | 1 | [[#77a8eaa0]] | "msf" |
| 2 | 2 | [[#77a8eaa0]] | "infile" |
| 2 | 3 | [[#77a8eaa0]] | "sequence" |
| 2 | 4 | [[#77a8eaa0]] | "sequence" |
| 2 | 5 | [[#77a8eaa0]] | "est" |
| 2 | 6 | [[#77a8eaa0]] | "database" |
| 3 | 1 | [[#7d1068c0]] | "File containing sequences" |
| 3 | 2 | [[#7d1068c0]] | "infile value" |
| 3 | 3 | [[#7d1068c0]] | "seq file to use (phylip)" |
| 3 | 4 | [[#7d1068c0]] | "Sequence database USA" |
| 3 | 5 | [[#7d1068c0]] | "EST sequence(s)" |
| 3 | 6 | [[#7d1068c0]] | "The database to retrieve from." |
| 4 | 1 | [[#50448200]] | "-method" |
| 4 | 2 | [[#50448200]] | "-trout" |
| 4 | 3 | [[#50448200]] | "-method" |
| 4 | 4 | [[#50448200]] | "-pattern" |
| 4 | 5 | [[#50448200]] | "-genome" |
| 4 | 6 | [[#50448200]] | "-s" |
| 5 | 1 | [[#50448e80]] | "method" |
| 5 | 2 | [[#50448e80]] | "trout" |
| 5 | 3 | [[#50448e80]] | "method" |
| 5 | 4 | [[#50448e80]] | "pattern" |
| 5 | 5 | [[#50448e80]] | "genome" |
| 5 | 6 | [[#50448e80]] | "search_string" |
| 6 | 1 | [[#77a8ea80]] | "Choose the method to use" |
| 6 | 2 | [[#77a8ea80]] | "Create a tree file" |
| 6 | 3 | [[#77a8ea80]] | "sub. model [f,k,j,l,s]" |
| 6 | 4 | [[#77a8ea80]] | "Search pattern, using standard IUPAC one-letter codes" |
| 6 | 5 | [[#77a8ea80]] | "Genomic sequence" |
| 6 | 6 | [[#77a8ea80]] | "The id to search for." |