[Bioperl-guts-l] bioperl commit

Jason Stajich jason at pub.open-bio.org
Sat Jul 10 12:28:49 EDT 2004


jason
Sat Jul 10 12:28:49 EDT 2004
Update of /home/repository/bioperl/bioperl-live/t/data
In directory pub.open-bio.org:/tmp/cvs-serv12828/t/data

Modified Files:
	mutations.xml polymorphism.xml 
Log Message:
handle diffs okay for either XML::Writer pre 0.5 and >= 0.5

bioperl-live/t/data mutations.xml,1.3,1.4 polymorphism.xml,1.2,1.3
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/data/mutations.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/bioperl/bioperl-live/t/data/mutations.xml	2001/10/09 15:11:18	1.3
+++ /home/repository/bioperl/bioperl-live/t/data/mutations.xml	2004/07/10 16:28:49	1.4
@@ -1,4 +1,3 @@
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G&gt;A" trivname="E2K">
     <DNA number="1" start="4" end="4" length="1" isMutation="1">
         <label>point</label>
@@ -29,7 +28,6 @@
         <allele_mut>K</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+14T&gt;A" trivname="L5X">
     <DNA number="1" start="14" end="14" length="1" isMutation="1">
         <label>point</label>
@@ -57,7 +55,6 @@
         <allele_mut>*</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G&gt;A" trivname="E2K">
     <DNA number="1" start="4" end="4" length="1" isMutation="1">
         <label>point</label>
@@ -88,7 +85,6 @@
         <allele_mut>K</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100delATCCAG" trivname="I34del-2">
     <DNA number="1" start="100" end="105" length="6" isMutation="1">
         <label>deletion</label>
@@ -118,7 +114,6 @@
         <allele_mut></allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101delT" trivname="I34delX172">
     <DNA number="1" start="101" end="101" length="1" isMutation="1">
         <label>deletion</label>
@@ -149,7 +144,6 @@
         <allele_mut>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101insGGGCCC" trivname="I34ins+2">
     <DNA number="1" start="101" end="101" length="0" isMutation="1">
         <label>insertion</label>
@@ -180,7 +174,6 @@
         <allele_mut>RAL</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100insG" trivname="I34ins81X">
     <DNA number="1" start="100" end="100" length="0" isMutation="1">
         <label>insertion</label>
@@ -211,7 +204,6 @@
         <allele_mut>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100AT&gt;GGGCCC" trivname="I34ins82X">
     <DNA number="1" start="100" end="101" length="2" isMutation="1">
         <label>complex</label>
@@ -242,7 +234,6 @@
         <allele_mut>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.-1G&gt;A">
     <DNA number="1" start="-1" end="-1" length="1" isMutation="1">
         <label>point</label>
@@ -265,7 +256,6 @@
         <region>5'UTR</region>
     </RNA>
 </seqDiff>
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+2766T&gt;C">
     <DNA number="1" start="2766" end="2766" length="1" isMutation="1">
         <label>point</label>
@@ -288,7 +278,6 @@
         <region>3'UTR</region>
     </RNA>
 </seqDiff>
-
 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+12165A&gt;G">
     <DNA number="1" start="12165" end="12165" length="1" isMutation="1">
         <label>point</label>
@@ -312,7 +301,6 @@
         <region dist="-1">3'UTR</region>
     </RNA>
 </seqDiff>
-
 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+4G&gt;T" trivname="V2F">
     <DNA number="1" start="4" end="4" length="1" isMutation="1">
         <label>point</label>
@@ -344,7 +332,6 @@
         <allele_mut>F</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+1168G&gt;T" trivname="D34Y">
     <DNA number="1" start="1168" end="1168" length="1" isMutation="1">
         <label>point</label>
@@ -376,7 +363,6 @@
         <allele_mut>Y</allele_mut>
     </AA>
 </seqDiff>
-
 <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.-4C&gt;G">
     <DNA number="1" start="-4" end="-4" length="1" isMutation="1">
         <label>point</label>

===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/data/polymorphism.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/bioperl/bioperl-live/t/data/polymorphism.xml	2001/08/03 11:18:09	1.2
+++ /home/repository/bioperl/bioperl-live/t/data/polymorphism.xml	2004/07/10 16:28:49	1.3
@@ -1,4 +1,3 @@
-
 <seqDiff id="M20132" moltype="rna" offset="362" sysname="[c.+4G|A|T;c.+31C|A]" trivname="[E2|K|X;Q11|K]">
     <DNA number="1.1" start="4" end="4" length="1" isMutation="0">
         <label>point</label>



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