[Bioperl-l] Ppsearch, Prints, Prfscan troubles
Brian Osborne
b_i_osborne@hotmail.com
Wed, 20 Feb 2002 16:26:04 -0500
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bioperl-l,=20
The Parse.pm modules in these three Tools directories (PPSEARCH, PRINTS, =
PRFSCAN) all contain the statement "use SeqFeatureSet", which doesn't =
exist in 1.0. What these modules are doing is parsing the results files =
from these programs (fingerPRINTScan in the case of PRINTS) and making =
matches into SeqFeature::Generic objects, then using add_Feature to add =
the SeqFeatures to the "set". Definitely a nice use of the SeqFeature =
feature, in principle.
My guess is that there's no longer any such thing as a set of =
SeqFeatures separate from sequence objects, is that correct? Should =
these modules simply return arrays of SeqFeature::Generic objects?
I could "mess" around in this code but there appears to be no test data =
files in t/. Could the authors step in and help out? Fix the Parse.pm =
modules and/or provide some results files that I could use?
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 (<FONT size=3D1>PPSEARCH, PRINTS, PRFSCAN)</FONT><FONT =
size=3D2> all=20
contain the statement "use SeqFeatureSet", which doesn't exist in 1.0. =
What=20
these modules are doing is parsing the results files from these programs =
(fingerPRINTScan in the case of PRINTS) and making matches into=20
SeqFeature::Generic objects, then using add_Feature to add the =
SeqFeatures to=20
the "set". Definitely a nice use of the SeqFeature feature, in=20
principle.</FONT></FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>My guess is that there's no longer any =
such thing=20
as a set of SeqFeatures separate from sequence objects, is that correct? =
Should=20
these modules simply return arrays of SeqFeature::Generic =
objects?</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/. Could the authors step in and =
help out?=20
Fix the Parse.pm modules and/or provide some results files that I could=20
use?</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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