[Bioperl-l] Final 0.6.2 checks/merges

[Ewan Birney]

I have extract from Peter his final list of checks/merges. This looks long
but alot of these have already happened. I have assigned these to go to
either myself or Jason and we will work on these tomorrow.

There are a list of things to merge from the branch ---> head, which is
relevant to hilmar for leading us to 0.7 branching point sometime later
this year.


Anyway here is the list. If branch-aware people want to jump in a take
stuff off mine/jason's hands, let me know. Otherwise Jason and I will just
plough through these




Bio/PrimarySeqI.pm

Ewan : initiator codon / stop codon handling only if sequence is a full
CSD (F) 

Bio/Seq.pm

Ewan:  use can("entire_seq") instead of can("seq") in add_SeqFeature (F) -
not
   merged

Ewan:  added feature_count() method, used in SeqIO::embl (F)



Bio/SimpleAlign.pm

Ewan: read_MSF changed to make initial whitespace on an alignment line
optional. (F)
Ewan: write_MSF changed to write out 2 blank lines to MSF file, not
stdout. (B)


Bio/UnivAln.pm
Jason: fixed test for empty list of parameters in _initialize (B)


Bio/Index/AbstractSeq.pm
Jason: in fetch(), only set display_id if $seq is defined. (B)


Bio/Index/Fasta.pm
Jason: change handling of main indexing loop (B)
Jason: add last record to index (B)

Bio/Root/Utilities.pm
Jason: in create_filehandle(), check for (not ref $client), instead of
(not $client) (B)


Bio/SeqFeature/FeaturePair.pm
Jason: has_tag and each_tag_value implementation added. (F)

Bio/SeqIO/embl.pm

Ewan:

 o seq->accession($acc) changed to $seq->accession_number (F)
 o handle absence of Feature Table when reading/writing sequences - in
   next_seq() and write_seq() (F)
 o use $seq->seq() to set sequence, instead of making a new
   PrimarySeq and setting set->primary_seq() (BF)
 o can('accession_number') rather than can('accession') in write_seq (F)
 o check that $line is defined in _write_line_EMBL_regex (B)
 o return '' if @lines is empty in _write_line_EMBL_regex (B)
 o set $s to '' if !defined in _write_line_EMBL_regex (B)

Bio/SeqIO/fasta.pm

Jason: deal with FASTA entries with > in description (B)

Bio/SeqIO/genbank.pm

Hilmar's call: substantial rewrite by Hilmar Lapp


Bio/SeqIO/swiss.pm

?? Leaving branch broken.



Bio/Tools/pSW.pm
Ewan: o updated to use new-style BioPerl ->seq() method (F)
Ewan: o use Bio::LocatableSeq instead of Bio::Seq (F)


Ewan:

scripts/bpfetch.pl
 o allow output in Swissprot format (from indexed Swissprot files) (F)
scripts/bpindex
 o allow the indexing of Swissprot files (F)







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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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