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Generate trim files for TPF in NCBI GRC format #45

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suryasaha opened this issue May 11, 2015 · 0 comments
Open

Generate trim files for TPF in NCBI GRC format #45

suryasaha opened this issue May 11, 2015 · 0 comments
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feature
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SL3.0

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@suryasaha
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Columns for Trim curation file:

  • Taxid (value (Solanum lycopersicum)=4081)
  • AssmGrp (value=TGP)
  • AssmUnit (value=Primary)
  • Chr (values=1-12, Un)
  • TPFType (values=chromosome, contig)
  • Acc.ver
  • TrimPos (1-based; first or last base used in AGP)
  • FromEnd (values = L, H; L: trim bases with values lt TrimPos; H: trim bases with values gt TrimPos)
  • Comment

Create new classes
@suryasaha suryasaha added this to the SL3.0 milestone May 11, 2015
suryasaha added a commit that referenced this issue May 11, 2015
@suryasaha
inited for #45
ec85b51
suryasaha added a commit that referenced this issue May 11, 2015
@suryasaha
added functionality listed in #45. Need to add tests and fix validati…
0db9c00 
…on checks
suryasaha added a commit that referenced this issue May 13, 2015
@suryasaha
init for testing functionality for #45
e3000bb
suryasaha added a commit that referenced this issue May 13, 2015
@suryasaha
Cleaned up class variable names, fixed type checks and function to ge…
12e8a2c 
…t formatted trim point file. Re #45
suryasaha added a commit that referenced this issue May 13, 2015
@suryasaha
added tests to create TP lines, add to TP object, for type checks and…
f934c26 
… formatted TP file. Re #45
suryasaha added a commit that referenced this issue May 20, 2015
@suryasaha
Accepting chr number as param. Fixed dreaded off by one err when tran…
cc51283 
…slating scaffold AGP coords to chromosome space. Calling new routine get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps for TPF,SP and TP objects. Creating and writing SP object. TP object not written as no TP functionality right now. For #45 and #26
suryasaha added a commit that referenced this issue May 20, 2015
@suryasaha
Added get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps to retur…
7350df7 
…n switch point and trim point objects. Returned TP object is empty since no TP are used for tomato TPF files. Older get_tpf methods are now marked deprecated. For #26 and #45.
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