tfscan output conversion

[Henrikki Almusa]

Hello,

This patch should actually print the info properly into tail. Still would like 
to confirm that though. 

But the problem still remains. So any info on why the while fails?

-- 
Henrikki Almusa
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ajFeatGetNote 'id'
  try /note="*id MOUSE$A21COL_02     "
  testing *name
  found [1] 'id'
reportWriteSeqTable jwid 10 jmin 6 tagval 'MOUSE$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          '
ajFeattableDel 80723d8
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