tfscan output conversion

[Henrikki Almusa]

Hello,

I'm trying to convert tfscan to write report output (patch attached). This 
basicly should work, but it doesn't. So one problem and one test request.

Problem. For some reason this patch seems to make it hang if used more than 
one sequence. I've used -debug option and taken last 75 lines from debug to 
add as attachment (since whole thing is almost 1meg). I can't figure out what 
causes this.

Test request. Since there is now the binding factor informtion added to this 
i've put that into tail of report. However i don't get these using tfscan 
here, so i'd like someone to see what it looks like with them.

Thanks,
-- 
Henrikki Almusa
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  testing *name
  found [1] 'id'
reportWriteSeqTable jwid 10 jmin 6 tagval 'MOUSE$A21COL_02     '
reportWriteSeqTable subseq 6 seq 840 28..33
ajFeatGetNote 'acc'
  try /note="*id HS$APOE_08          "
  testing *name
  try /note="*acc R00149"
  testing *name
  found [1] 'acc'
reportWriteSeqTable jwid 9 jmin 6 tagval 'R00149'
ajFeatGetNote 'id'
  try /note="*id HS$APOE_08          "
  testing *name
  found [1] 'id'
reportWriteSeqTable jwid 10 jmin 6 tagval 'HS$APOE_08          '
reportWriteSeqTable subseq 5 seq 840 374..378
ajFeatGetNote 'acc'
  try /note="*id HS$ALBU_03          "
  testing *name
  try /note="*acc R00079"
  testing *name
  found [1] 'acc'
reportWriteSeqTable jwid 9 jmin 6 tagval 'R00079'
ajFeatGetNote 'id'
  try /note="*id HS$ALBU_03          "
  testing *name
  found [1] 'id'
reportWriteSeqTable jwid 10 jmin 6 tagval 'HS$ALBU_03          '
ajStrCut 0 0 len: 1 ibegin: 0 iend: 1
ajStrCut 0 0 len: 3 ibegin: 0 iend: 1
ajFeattableDel 80723c0
ajSeqRead: input file 'mRNA.small.twice' still there, try again
ajFeattableDel 0
seqRead: cleared
seqRead: seqin format 10 'fasta'
seqRead: one format specified
ajFileBuffNobuff mRNA.small.twice buffsize: 15
++seqRead known format 10
++seqReadFmt format 10 (fasta) 'mRNA.small.twice' feat No
ajSeqParseNcbi '>Exon_10_head_2 (copied for testing two seqs) 
'
trying ajSeqParseFasta
ajSeqParseFasta '>Exon_10_head_2 (copied for testing two seqs) 
'
result id: 'Exon_10_head_2' acc: '' desc: '(copied for testing two seqs) '
parsed id 'Exon_10_head_2' acc '' sv '' gi '' desc '(copied for testing two seqs) '
seqSetName 'Exon_10_head_2' result: 'Exon_10_head_2'
at EOF: File already read to end mRNA.small.twice
End of file - data in buffer - return ajFalse
ajFileBuffClear (0) Nobuff: Yes
 first: 15 thys->Pos: 15 thys->Size: 15 thys->Nobuff: Yes
ajFileBuffClear 'mRNA.small.twice' (0 lines)
     Y size: 15 pos: 15 removed 15 lines add to free: 0
seqReadFmt success with format 10 (fasta)
seqQueryMatch 'Exon_10_head_2' id '' acc '' Sv '' Des '' Key '' Org ''
No accession number to test
No taxonomy to test
No keyword to test
No description to test
testing sequence 'Exon_10_head_2' type 'DNA' IsNuc No IsProt No
ajSeqTypeCheckIn type 'dna' found (DNA sequence)
Remove all gaps
ajSeqIsNuc Type ''
seqTypeGapnucS test
Convert '?XUu' to 'NNTt'
ajSeqRead: open buffer  usa: 'mRNA.small.twice' returns: Yes
++keep restored 0..0 (N) 'fasta' 10
ajSeqRead: thys->Db '', seqin->Db ''
ajSeqRead: thys->Name 'Exon_10_head_2'
ajSeqRead: thys->Entryname 'Exon_10_head_2', seqin->Entryname ''
ajSeqRead: thys->Name 'Exon_10_head_2'
ajSeqSetRange (len: 840 0..0 old 0..0)
      result: (len: 840 0..0)
ajSeqallNext success
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