[Bioperl-l] PPSEARCH, PRINTS, PRFSCAN troubles
Brian Osborne
b_i_osborne@hotmail.com
Wed, 20 Feb 2002 13:01:20 -0500
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bioperl-l,=20
The Parse.pm modules in these three Tools directories all contain the =
statement "use SeqFeatureSet", which doesn't exist in bioperl-live, as =
you know. What these modules are attempting to do is parse the results =
files from these programs (fingerPRINTScan in the case of PRINTS) and =
make matches into SeqFeature::Generic objects, then use add_Feature to =
add the SeqFeatures to the "set". Definitely a nice use of the =
SeqFeature feature, in principle.
I could "mess" around in this code but there appears to be no test data =
files in t/, I could be mistaken of course. Could the authors step in =
and help out? Fix the Parse.pm modules and/or provide some results =
files?
Thank you,
Brian O.
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<DIV><FONT face=3DArial size=3D2>bioperl-l, </FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>The Parse.pm modules in these three =
Tools=20
directories all contain the statement "use SeqFeatureSet", which doesn't =
exist=20
in bioperl-live, as you know. What these modules are attempting to do is =
parse=20
the results files from these programs (fingerPRINTScan in the case of =
PRINTS)=20
and make matches into SeqFeature::Generic objects, then use add_Feature =
to add=20
the SeqFeatures to the "set". Definitely a nice use of the SeqFeature =
feature,=20
in principle.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I could "mess" around in this code but =
there=20
appears to be no test data files in t/, I could be mistaken of course. =
Could the=20
authors step in and help out? Fix the Parse.pm modules and/or provide =
some=20
results files?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thank you,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Brian O.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV></BODY></HTML>
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