[Biopython-dev] [Biopython - Feature #3341] (New) Improve SffIO to parse 3 extra lines present in some SFF files ("Run Name:, Analysis Name:, Full Path:)"

[redmine at redmine.open-bio.org]

Issue #3341 has been reported by Martin Mokrejš.

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Feature #3341: Improve SffIO to parse 3 extra lines present in some SFF files ("Run Name:, Analysis Name:, Full Path:)"
https://redmine.open-bio.org/issues/3341

Author: Martin Mokrejš
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


Some file have extra 3 lines per each record in the SFF file. One such file is already in biopython test data:
biopython/Tests/Roche/E3MFGYR02_random_10_reads.sff
biopython/Tests/Roche/paired.sff

The three lines "Run Name:, Analysis Name:, Full Path:" are not parsed into the object and later on, are not written out. Hence, sff round trip read in -> write out breaks (biopython-1.58). These three lines somehow do not appear in every SFF file, and so far I haven't seen these in files extracted from SRA. Seems these only appear in original Roche SFF files.


>E3MFGYR02JWQ7T
  Run Prefix:   R_2008_01_09_16_16_00_
  Region #:     2
  XY Location:  3946_2103

  Run Name:       R_2008_02_08_17_05_24_build11_mlabrecque_100707593662420SV11007SID4607RunID24947331
  Analysis Name:  /data/2008_02_08/R_2008_02_08_17_05_24_build11_mlabrecque_100707593662420SV11007SID4607RunID24947331/D_2008_02_08_23_45_24_d41_AnalysisPipe
  Full Path:      /data/R_2008_02_08_17_05_24_build11_mlabrecque_100707593662420SV11007SID4607RunID24947331/D_2008_02_08_23_45_24_d41_AnalysisPipe

  Read Header Len:  32
  Name Length:      14
  # of Bases:       265
  Clip Qual Left:   5
  Clip Qual Right:  264
  Clip Adap Left:   0
  Clip Adap Right:  0




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