Bioperl: Subject: version 1.009 available

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Fri, 29 May 1998 14:58:00 +0000 (GMT)

Hello- version 1.009 has become available at

The following improvements have been made; versions 1.007 and 1.008
were never annnounced publicly. Notably, many more formats are now
supported (via ReadSeq).

Version 1.007 on 15 Mar 1998.
* Added functions that return indices instead of actual sequence data:
var_inds(), invar_inds(), gap_free_inds(), unknown_free_inds(),
special_free_inds() and no_allgap_inds() return the indices of
(in)variable, gap-free, unknown-free, gap+unknown-free and non-gap-only
columns; they are the counterparts of var_sites(), etc.
* Added remove_gaps() to return ungapped (original) sequence data
* Added equal_no_gaps() to check for equality ignoring gaps
* Added equalize_lengths() for padding a sequence bag with gaps
such that all rows have equal length (current procedure is slow)
* The default id is now ``_'' (was: ``No_Id_Given'')
* Internal functions _rowbounds() and _colbounds() now return indices
from the user's perspective, but WITHOUT substracting offset.  Instead,
all functions subtract offset after applying _rowbounds()/_colbounds()

Version 1.008 on 13 May 1998.
* Added readseq conversion support, making it possible to read and write
the following formats: MSF, Paup, PIR/Codata, ASN.1. (ASN.1 was not
parsed successfully: readseq seems to be unable to read in its own ASN.1
output). Technically, readseq is now used to parse files that have been
processed as ``raw'' before; now ``raw'' format is recognized using the
expression /^[A-Z_0-9$_GAP_SYMBOL$_UNKN_SYMBOL\s]+$/im, i.e. the file
may only have alphanumerical characters, gap and unknown-symbol, and
whitespace. If commata, etc, are detected, readseq is used for parsing.
Readseq itself seems to be unable to detect ``raw'' format in some cases,
causing weird results.
* Added Clustal support for parsing; still to be tested and documented.

Version 1.009 on 25 May 1998.
* The module can now be ``built'' in the standard way (perl Makefile.PL, etc).

Please allow me to ask one question to the `experts': is there a way to 
convince MakeMaker that the module is not in the top-level directory of
the distribution, but instead in the ``appropriate'' directory, according
to hierarchy ? E.g. MakeMaker does not accept in a directory
``Bio'', and this causes major frustration (and duplicate copies). 


P.S. I'm looking forward to meeting many of you at ISMB'98 !
(( since I'll also attend a symposium on large-scale phylogenies,, I may not arrive before Monday
early afternoon.))

best wishes,
Georg Fuellen,,
Univ. Bielefeld, Research Group in Practical Comp Science, Fax +49 521 106 6411, BioMOO:GeorgF, Fon .... 106 2903

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