[Bioperl-l] problem help me...........please

Sat May 13 05:17:58 UTC 2006

hello
I am very happy to see the prompt reply from the group members..
As you all suggested  to attach the required files ..
So I have attached all the three file first the input file,secod I have saved the error I was getting into a error file and third the programme file..
Actully in error file I want to know some thing .
I am putting here one error line,
## no of nodes = Bio::Seq::RichSeq=HASH(0x11aa700) ##
what this stand for
Second thing I want to get the connected graph as I have.
which type of connected grph I explain you by example..
Let there are five object in such a way.
A connected to B
A connected to C
B connected to C
D connected to C
E connected to A
I want to create a whole link in betwwen all five.

Please help me I am not getting the result

with Regards
SAURABH MAHESHWARI
M.Sc. (BIOINFORMATICS)
JAMIA MILLIA ISLAMIA
NEW DELHI
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sample.dip
Type: application/octet-stream
Size: 5794 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20060513/77476ca5/attachment-0008.obj>
-------------- next part --------------
bash-2.05b$ perl from.pl
Bio::Graph::ProteinGraph=HASH(0x1182e70)
Bio::Graph::ProteinGraph=HASH(0x1182e70)->nodes
the unconnected nodes are =subgraph=Bio::Graph::SimpleGraph=HASH(0x11e2160)

graph density=0.00826446280991736

no of Connected components=60

please enter the protein-id whom you want to remove from the network
XMECF2

no of edges=61

no of nodes=122

enter the protein  whose interactions is to be find XMECF2
XMECF2
 interacts with map{->object_id()}

no of nodes = Bio::Seq::RichSeq=HASH(0x11aa700) Bio::Seq::RichSeq=HASH(0x11d1850
) Bio::Seq::RichSeq=HASH(0x11bd4c0) Bio::Seq::RichSeq=HASH(0x11c2fd0) Bio::Seq::
RichSeq=HASH(0x11aa7f0) Bio::Seq::RichSeq=HASH(0x1198340) Bio::Seq::RichSeq=HASH
(0x11d81a0) Bio::Seq::RichSeq=HASH(0x11ca320) Bio::Seq::RichSeq=HASH(0x11b5e40)
Bio::Seq::RichSeq=HASH(0x1190e00) Bio::Seq::RichSeq=HASH(0x11c1350) Bio::Seq::Ri
chSeq=HASH(0x11b2e20) Bio::Seq::RichSeq=HASH(0x11cb360) Bio::Seq::RichSeq=HASH(0
x1198250) Bio::Seq::RichSeq=HASH(0x11d0240) Bio::Seq::RichSeq=HASH(0x11c8f20) Bi
o::Seq::RichSeq=HASH(0x11b4ef0) Bio::Seq::RichSeq=HASH(0x119f7a0) Bio::Seq::Rich
Seq=HASH(0x11c2ee0) Bio::Seq::RichSeq=HASH(0x11dba20) Bio::Seq::RichSeq=HASH(0x1
1e2300) Bio::Seq::RichSeq=HASH(0x11b2f10) Bio::Seq::RichSeq=HASH(0x11b4b90) Bio:
:Seq::RichSeq=HASH(0x11d4df0) Bio::Seq::RichSeq=HASH(0x11d4b80) Bio::Seq::RichSe
q=HASH(0x11d8e70) Bio::Seq::RichSeq=HASH(0x11a1270) Bio::Seq::RichSeq=HASH(0x11c
b5d0) Bio::Seq::RichSeq=HASH(0x11d5cc0) Bio::Seq::RichSeq=HASH(0x11d32a0) Bio::S
eq::RichSeq=HASH(0x11b4c80) Bio::Seq::RichSeq=HASH(0x119e0c0) Bio::Seq::RichSeq=
HASH(0x11b7ed0) Bio::Seq::RichSeq=HASH(0x11ad490) Bio::Seq::RichSeq=HASH(0x1196e
60) Bio::Seq::RichSeq=HASH(0x119b7f0) Bio::Seq::RichSeq=HASH(0x11cef60) Bio::Seq
::RichSeq=HASH(0x11b7b70) Bio::Seq::RichSeq=HASH(0x11dd330) Bio::Seq::RichSeq=HA
SH(0x11da8c0) Bio::Seq::RichSeq=HASH(0x11a9f70) Bio::Seq::RichSeq=HASH(0x119b700
) Bio::Seq::RichSeq=HASH(0x119a550) Bio::Seq::RichSeq=HASH(0x11ba910) Bio::Seq::
RichSeq=HASH(0x11e0b30) Bio::Seq::RichSeq=HASH(0x11d3030) Bio::Seq::RichSeq=HASH
(0x11c62d0) Bio::Seq::RichSeq=HASH(0x11abb20) Bio::Seq::RichSeq=HASH(0x11d5bd0)
Bio::Seq::RichSeq=HASH(0x11b03c0) Bio::Seq::RichSeq=HASH(0x119e1b0) Bio::Seq::Ri
chSeq=HASH(0x11aa060) Bio::Seq::RichSeq=HASH(0x11a5700) Bio::Seq::RichSeq=HASH(0
x11a81e0) Bio::Seq::RichSeq=HASH(0x1196b00) Bio::Seq::RichSeq=HASH(0x11c1260) Bi
o::Seq::RichSeq=HASH(0x11a2800) Bio::Seq::RichSeq=HASH(0x11c63c0) Bio::Seq::Rich
Seq=HASH(0x11b60b0) Bio::Seq::RichSeq=HASH(0x11b93b0) Bio::Seq::RichSeq=HASH(0x1
1a4490) Bio::Seq::RichSeq=HASH(0x11ded50) Bio::Seq::RichSeq=HASH(0x11bbcd0) Bio:
:Seq::RichSeq=HASH(0x1194780) Bio::Seq::RichSeq=HASH(0x11aedd0) Bio::Seq::RichSe
q=HASH(0x11cd300) Bio::Seq::RichSeq=HASH(0x11a14e0) Bio::Seq::RichSeq=HASH(0x11c
4630) Bio::Seq::RichSeq=HASH(0x11a43a0) Bio::Seq::RichSeq=HASH(0x11a80f0) Bio::S
eq::RichSeq=HASH(0x11bbbe0) Bio::Seq::RichSeq=HASH(0x11d5960) Bio::Seq::RichSeq=
HASH(0x11c8e30) Bio::Seq::RichSeq=HASH(0x11cd3f0) Bio::Seq::RichSeq=HASH(0x11dd4
20) Bio::Seq::RichSeq=HASH(0x11cee70) Bio::Seq::RichSeq=HASH(0x11dbb10) Bio::Seq
::RichSeq=HASH(0x119a460) Bio::Seq::RichSeq=HASH(0x11aaa60) Bio::Seq::RichSeq=HA
SH(0x11d1760) Bio::Seq::RichSeq=HASH(0x11cb6c0) Bio::Seq::RichSeq=HASH(0x11c7530
) Bio::Seq::RichSeq=HASH(0x11deae0) Bio::Seq::RichSeq=HASH(0x11c4720) Bio::Seq::
RichSeq=HASH(0x119f890) Bio::Seq::RichSeq=HASH(0x11a6c40) Bio::Seq::RichSeq=HASH
(0x11ad130) Bio::Seq::RichSeq=HASH(0x11e23f0) Bio::Seq::RichSeq=HASH(0x11d2f40)
Bio::Seq::RichSeq=HASH(0x1194640) Bio::Seq::RichSeq=HASH(0x11d8f60) Bio::Seq::Ri
chSeq=HASH(0x11d0150) Bio::Seq::RichSeq=HASH(0x119d070) Bio::Seq::RichSeq=HASH(0
x11a5610) Bio::Seq::RichSeq=HASH(0x11aa2d0) Bio::Seq::RichSeq=HASH(0x11b94a0) Bi
o::Seq::RichSeq=HASH(0x11bd5b0) Bio::Seq::RichSeq=HASH(0x11c0ff0) Bio::Seq::Rich
Seq=HASH(0x11a6b50) Bio::Seq::RichSeq=HASH(0x119cf80) Bio::Seq::RichSeq=HASH(0x1
1baa00) Bio::Seq::RichSeq=HASH(0x11c7620) Bio::Seq::RichSeq=HASH(0x119fb00) Bio:
:Seq::RichSeq=HASH(0x11a2a70) Bio::Seq::RichSeq=HASH(0x11b1960) Bio::Seq::RichSe
q=HASH(0x11ab8b0) Bio::Seq::RichSeq=HASH(0x11e0c20) Bio::Seq::RichSeq=HASH(0x11a
d3a0) Bio::Seq::RichSeq=HASH(0x1197fe0) Bio::Seq::RichSeq=HASH(0x11b1870) Bio::S
eq::RichSeq=HASH(0x11a2b60) Bio::Seq::RichSeq=HASH(0x1192750) Bio::Seq::RichSeq=
HASH(0x11c9190) Bio::Seq::RichSeq=HASH(0x11e08c0) Bio::Seq::RichSeq=HASH(0x11dd6
90) Bio::Seq::RichSeq=HASH(0x11da7d0) Bio::Seq::RichSeq=HASH(0x11aece0) Bio::Seq
::RichSeq=HASH(0x11d80b0) Bio::Seq::RichSeq=HASH(0x11ca0b0) Bio::Seq::RichSeq=HA
SH(0x1196bf0) Bio::Seq::RichSeq=HASH(0x11b7de0) Bio::Seq::RichSeq=HASH(0x11b02d0
)
Can't call method "isa" on an undefined value at /usr/local/bioxapps/bioperl/lib
rary//Bio/Graph/ProteinGraph.pm line 477, <STDIN> line 2.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: from.pl
Type: application/octet-stream
Size: 2723 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20060513/77476ca5/attachment-0009.obj>