Sigcleave and report

[Gary Williams, Tel 01223 494522]

It looks as if the same problem affects restrict:
The text in the tail of the report is not cleared.
For example the second sequence in the list has no hits, but the
fragments from the first sequence are reported again.

Gary

% restrict @list -enz acci -site 4 stdout -frag 
Finds restriction enzyme cleavage sites
########################################
# Program: restrict
# Rundate: Thu May 20 16:34:01 2004
# Report_format: table
# Report_file: stdout
########################################

#=======================================
#
# Sequence: AY582533     from: 1   to: 3846
# HitCount: 2
#
# Minimum cuts per enzyme: 1
# Maximum cuts per enzyme: 2000000000
# Minimum length of recognition site: 4
# Blunt ends allowed
# Sticky ends allowed
# DNA is linear
# Ambiguities allowed
#
#=======================================

  Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev
3primerev
   1773    1778 AccI        GTMKAC             1774   1776        
.         .
   2018    2023 AccI        GTMKAC             2019   2021        
.         .

#---------------------------------------
#
# Fragment lengths:
#     1827
#     1774
#     245                  
#
#---------------------------------------
#=======================================
#
# Sequence: AY582532     from: 1   to: 4635
# HitCount: 0
#
# Minimum cuts per enzyme: 1
# Maximum cuts per enzyme: 2000000000
# Minimum length of recognition site: 4
# Blunt ends allowed
# Sticky ends allowed
# DNA is linear
# Ambiguities allowed
#
#=======================================

  Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev
3primerev

#---------------------------------------
#
# Fragment lengths:
#     1827
#     1774
#     245
#
#---------------------------------------  



Henrikki Almusa wrote:
> 
> Hello,
> 
> There was a bug in sigcleave. The tail text "No scores over " is left in tail
> after printing report without any hits. If there is multiple sequences in
> input file and sequence later have hits, then same text appears in report
> with hits as well.
> 
> However it seems that there is no function like "ajReportClearTail" so it's
> fixed by putting empty AjPString in there after writing a report. Would it be
> useful functions to clear header and tail? If not then, I'll put this to
> emboss-submit as is.
> 
> --
> Henrikki Almusa
> 
>   ------------------------------------------------------------------------
>                                Name: sigcleave_tail_fix.patch
>    sigcleave_tail_fix.patch    Type: text/x-diff
>                            Encoding: 7bit

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk