Cytoscape User Manual

This document is licensed under the Creative Commons license, 2006

Authors: The Cytoscape Collaboration

The Cytoscape project is an ongoing collaboration between:

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

Cytoscape is a project dedicated to building open-source network visualization and analysis software. A software "Core" provides basic functionality to layout and query the network and to visually integrate the network with state data. The Core is extensible through a plug-in architecture, allowing rapid development of additional computational analyses and features.

Cytoscape's roots are in Systems Biology, where it is used for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape allows the visual integration of the network with expression profiles, phenotypes, and other molecular state information, and links the network to databases of functional annotations.

The central organizing metaphor of Cytoscape is a network (graph), with genes, proteins, and molecules represented as nodes and interactions represented as links, i.e. edges, between nodes.

Cytoscape is a Java application verified to run on Linux, Windows, and Mac OS X. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 5 or later is available for the platform.

When a network is loaded, Cytoscape will look something like the image below:

The main window here has several components:

The network management and attribute browser panels are dockable tabbed panels known as CytoPanels. You can undock any of these panels by clicking on the Float Window control in the upper-right corner of the CytoPanel.

If you select this control, e.g. on the attribute browser panel, you will now have two Cytoscape windows, the main window, and a new window labeled CytoPanel 2, similar to the one shown below. Popup will be displayed when you put the mouse pointer on a cell.

Note that CytoPanel 2 now has a Dock Window control. If you select this control, the window will dock onto the main window.

Cytoscape also has an editor that enables you to build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window. The Node shapes and Edge arrows on the palette are defined by the currently used Visual Style. To edit a network, just select the Editor tab on CytoPanel 1. An example of an editor, with the palette contained in CytoPanel 1 and defined by the BioMoleculeEditor Visual Style, is shown below.

Cytoscape recognizes a number of optional command line arguments, including run-time specification of network files, attribute files, and session files. This is the output generated when the cytoscape is executed with the "-h" or "--help" flag:

usage: java -Xmx512M -jar cytoscape.jar [OPTIONS]
 -h,--help                      Print this message.
 -v,--version                 Print the version number.
 -s,--session <file>        Load a cytoscape session (.cys) file.
 -N,--network <file>     Load a network file (any format).
 -e,--edge-attrs <file>    Load an edge attributes file (edge attribute format).
 -n,--node-attrs <file>   Load a node attributes file (node attribute format).
 -m,--matrix <file>        Load a node attribute matrix file (table).
 -p,--plugin <file>         Load a plugin jar file, directory of jar files,
                                     plugin class name, or plugin jar URL.
 -P,--props <file>         Load cytoscape properties file (Java properties
                                    format) or individual property: -P name=value.
 -V,--vizmap <file>      Load vizmap properties file (Java properties format).

Any file specified for an option may be specified as either a path or as a URL. For example you can specify a network as a file (assuming that myNet.sif exists in the current working directory): cytoscape.sh -N myNet.sif. Or you can specify a network as a URL: cytoscape.sh -N http://example.com/myNet.sif.

All options described above (including plugins) can be loaded from the GUI once Cytoscape is running.

There are 4 different ways of creating networks in Cytoscape:

source  target  interaction  boolean attribute  string attribute        floating point attribute
YJR022W YNR053C pp      TRUE    abcd12371       1.2344543
YER116C YDL013W pp      TRUE    abcd12372       1.2344543
YNL307C YAL038W pp      FALSE   abcd12373       1.2344543
YNL216W YCR012W pd      TRUE    abcd12374       1.2344543
YNL216W YGR254W pd      TRUE    abcd12375       1.2344543

YJR022W YNR053C
YER116C YDL013W
YNL307C YAL038W
YNL216W YCR012W
YNL216W YGR254W

Unique ID A     Unique ID B     Alternative ID A        Alternative ID B        Aliases A       Aliases B       Interaction detection methods   First author surnames   Pubmed IDs      species A       species B       Interactor types        Source database Interaction ID  Interaction labels      Cross-references        Associated Files        Experiment files        Experiment labels       Different techniques    Different Pubmed articles       Different sources       Weight

7205    5747    TRIP6   PTK2    Q15654  Q05397-1        vv|HPRD Currently not available 14688263|15892868(Marcotte)     Mammalia        Homo sapiens    protein|protein HPRD|Marcotte   0       Thyroid hormone receptor interactor 6-FAK-|PTK2-TRIP6   NA(HPRD)|NA(Marcotte)   HPRD/02859_psimi.xml|other/ORIGINAL_DATA_MARCOTTE.txt   vv(HPRD/02859_psimi.xml)|HPRD(other/ORIGINAL_DATA_MARCOTTE.txt) 17651(ExptRef)|Marcotte 2       2       2       2

4174    7311    MCM5    UBA52   P33992  P62987  neighbouring_reaction   Currently not available 15608231(Reactome)      Homo sapiens    Homo sapiens    protein|protein Reactome        1       P33992-P62988   Reaction:68944<->Reaction:68946(Reactome)|Reaction:68946<->Reaction:68944(Reactome)     other/ORIGINAL_DATA_MARCOTTE.txt        neighbouring_reaction(other/REACTOMEhomo_sapiens.interactions.txt)      Reactome        1       1       1       1

7040    7040    TGFB1   TGFB1   P01137  P01137  nmr: nuclear magnetic resonance Currently not available 8679613 Homo sapiens    Homo sapiens    protein|protein BIND    2       TGFB1-TGFB1-    72085(BIND)     BIND/bind_taxid9606.1.psi.xml   nmr: nuclear magnetic resonance(BIND/bind_taxid9606.1.psi.xml)  NotAvailable    1       1       1       1

Cytoscape can read network/pathway files written in the following formats:

The SIF format specifies nodes and interactions only, while other formats store additional information about network layout and allow network data exchange with a variety of other network programs and data sources. Typically, SIF files are used to import interactions when building a network for the first time, since they are easy to create in a text editor or spreadsheet. Once the interactions have been loaded and network layout has been performed, the network may be saved to GML or XGMML format for interaction with other systems. All file types listed (except Excel) are text files and you can edit and view them in a regular text editor.

nodeA <relationship type> nodeB
nodeC <relationship type> nodeA
nodeD <relationship type> nodeE nodeF nodeB
nodeG
...
nodeY <relationship type> nodeZ

node1 typeA node2
node2 typeB node3 node4 node5
node0

node1 xx node2
node1 xx node2
node1 yy node2

node1 xx node1

  pp .................. protein – protein interaction
  pd .................. protein -> DNA
  (e.g. transcription factor binding upstream of a regulating gene.)

  pr .................. protein -> reaction
  rc .................. reaction -> compound
  cr .................. compound -> reaction
  gl .................. genetic lethal relationship
  pm .................. protein-metabolite interaction
  mp .................. metabolite-protein interaction

Example_1      C
Example_1      network1
network1       A        pp        B
network1       B        pp        A
Example_1      C        pp        B

Example_2      M1
Example_2      M2
M1             A
M2             B        pp        C
Example_2      A        pp        B
Example_2      M1       im        M2

Example_3      M1       im        M2
Example_3      M3       im        M1
Example_3      M2       im        M3
Example_3      C        pp        M3
Example_3      M2       pp        C
M1             A
M2             A        pp        B
M3             B        pp        C

Example_4      M1
root           M3
M1             A        pp        B
M1             B        pp        A
Example_4      C        pp        B
M3             M2
M2             D
M3             E        pp        F
M3             D        pp        F
M3             D        pp        E
Example_4      D        pp        C
Example_4      A        pp        M2
Example_4      B        pp        M3
Example_4      M2       pp        B

Example_5      M4
M4             D
M4             M3
M3             M2        pp        C
M2             M1        pp        B
M1             A
M4             C         pp        D

Interaction networks are useful as stand-alone models. However, they are most powerful for answering scientific questions when integrated with additional information. Cytoscape allows the user to add arbitrary node, edge and network information to Cytoscape as node/edge/network attributes. This could include, for example, annotation data on a gene or confidence values in a protein-protein interaction. These attributes can then be visualized in a user-defined way by setting up a mapping from data attributes to visual attributes (colors, shapes, and so on). The section on visual styles discusses this in greater detail.

FunctionalCategory
YAL001C = metabolism
YAR002W = apoptosis
YBL007C = ribosome

InteractionStrength
YAL001C (pp) YBR043W = 0.82
YMR022W (pd) YDL112C = 0.441
YDL112C (pd) YMR022W = 0.9013

attributeName (class=JavaClassName)

floatingPointAttribute
firstName = 1
secondName = 2.5

floatingPointAttribute (class=Double)
firstName = 1
secondName = 2.5

floatingPointAttribute 
firstName = 1.0
secondName = 2.5

sourceName (edgeType) targetName

sourceName edgeType targetName

listAttributeName (class=java.lang.String)
firstObjectName = (firstValue::secondValue::thirdValue)
secondObjectName = (onlyOneValue)

newlineAttr
YJL157C = This is a long\nline for a label.

In addition to normal node and edge attribute data, Cytoscape also supports importing gene expression data. Gene expression data are imported using a different file format than normal attributes; however, the resulting attributes are not treated differently by Cytoscape. Gene expression data (like attribute data) can be loaded at any time, but are (generally) only relevant once a network has been loaded.

Identifier [CommonName] value1 value2 ... valueN [pval1 pval2 ... pvalN]

GENE COMMON gal1RG gal4RG gal80R gal1RG gal4RG gal80R
YHR051W COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
YHR124W NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
YKL181W PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01
YGR072W UPF3 0.245 -0.471 0.787 4.10450e-04 7.51780e-04 1.37130e-05

GENE COMMON gal1RG gal4RG gal80R gal1RG gal4RG gal80R
YHR051W COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
YHR124W NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
YKL181W PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01

Probeset
YHR051W = probeset2
YHR124W = probeset3
YKL181W = probeset4

GENE COMMON gal1RG gal4RG gal80R gal1RG gal4RG gal80R
probeset2 COX6 -0.034 0.111 -0.304 3.75720e-01 1.56240e-02 7.91340e-06
probeset3 NDT80 -0.090 0.007 -0.348 2.71460e-01 9.64330e-01 3.44760e-01
probeset4 PRS1 -0.167 -0.233 0.112 6.27120e-03 7.89400e-04 1.44060e-01

<text> <text> cond1 cond2 ... cond1 cond2 ... [NumSigConds]

<text> <text> cond1 cond2 ...

<tab><tab>RATIOS<tab><tab>...LAMBDAS

FormalGeneName CommonGeneName ratio1 ratio2 ... [lambda1 lambda2 ...] [numSigConds]

NumSigGenes int1 int2 ...

Using Cytoscape's Editor, you can build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window. The palette contains a set of shapes (for nodes) and arrows (for edges). The shapes on the palette are defined by the current Visual Style, with Node Shape and Node Color mapping into the shape and color of a node, and Edge Target Arrow mapping into the target arrow of an edge. An example of an editor, with the palette contained in CytoPanel 1, is shown below.

To edit an existing network, just select the Editor tab in CytoPanel 1. To start editing a new network, create a new network by going to File → New → Network → Empty Network.

To add a node to a network, drag and drop a node shape from the palette onto the canvas. To connect two nodes with an edge, drag and drop an arrow shape onto a node on the canvas. This node becomes the source node of the edge. Move the cursor and a rubber-banded line will follow the cursor. As the cursor passes over another node, that node is highlighted and the rubber-banded line will snap to a connection point on that second node. Click the mouse while over this node and the connection will be established.

You can abort the drawing of the edge by clicking on an empty spot on the palette.

Note that if you change the Visual Style, the palette used by the current network view will also change to be consistent with the mappings in the new Visual Style.

There is also an Edit → Connect Selected Nodes option that, when chosen, creates a clique amongst the selected nodes.

The editor provides accelerators for adding nodes and edges. Control-clicking at a position on the canvas creates a node at that position. The NODE_TYPE attribute of the node will be the same as the NODE_TYPE of the node most recently added, defaulting back to the original visual style. In this manner, you can use control-clicking as a kind of "stamp" to add multiple nodes of the same type to the network. Control-clicking on a node on the canvas starts an edge with its source at that node. Move the cursor and a rubber-banded line will follow the cursor. As the cursor passes over another node, that node is highlighted and the rubber-banded line will snap to a connection point on that second node. Control-click the mouse again and the connection will be established. The EDGE_TYPE attribute of the edge will be the same as the EDGE_TYPE of the edge most recently added, defaulting back to the original visual style. You can abort the drawing of the edge by control-clicking on an empty spot on the palette.

You can delete nodes and edges by selecting a number of nodes and edges, then selecting Edit → Delete Selected Nodes and Edges. You can recover any nodes and edges deleted from a network by going to Edit → Undo. However, note that this will restore all nodes and edges that were previously deleted from the network, not just those deleted by the most recent delete operation.

Annotations in Cytoscape are stored as a set of ontologies (e.g. the Gene Ontology, or GO). An ontology consists of a set of controlled vocabulary terms that annotate the objects. For example, using the Gene Ontology, the Saccharomyces Cerevisiae CDC55 gene has a biological process described as “protein biosynthesis”, to which GO has assigned the number 6412 (a GO ID).

GO 8150 biological_process
 GO 7582 physiological processes
   GO 8152 metabolism
    GO 44238 primary metabolism
      GO 19538 protein metabolism
        GO 6412 protein biosynthesis

Graphical View of GO Term 6412: protein biosynthesis

Cytoscape can use this ontology DAG (Directed Acyclic Graph) to annotate objects in networks. The Ontology Server (originally called "BioDataServer") is a Cytoscape feature which allows you to load, navigate, and assign annotation terms to nodes and edges in a network. Cytoscape 2.4 now has an enhanced GUI for loading ontology and associated annotation, enabling you to load both local and remote files.

format-version: 1.2
date: 27:11:2006 17:12
saved-by: midori
auto-generated-by: OBO-Edit 1.002
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
default-namespace: gene_ontology
remark: cvs version: $Revision: 5.49 $

[Term]
id: GO:0000001
name: mitochondrion inheritance
namespace: biological_process
def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
synonym: "mitochondrial inheritance" EXACT []
is_a: GO:0048308 ! organelle inheritance
is_a: GO:0048311 ! mitochondrion distribution

[Term]
id: GO:0000002
name: mitochondrial genome maintenance
namespace: biological_process
def: "The maintenance of the structure and integrity of the mitochondrial genome." [GOC:ai]
is_a: GO:0007005 ! mitochondrion organization and biogenesis

SGD     S000003916      AAD10           GO:0006081      SGD_REF:S000042151|PMID:10572264        ISS             P       aryl-alcohol dehydrogenase (putative)        YJR155W gene    taxon:4932      20020902        SGD
SGD     S000005275      AAD14           GO:0008372      SGD_REF:S000069584      ND              C       aryl-alcohol dehydrogenase (putative)        YNL331C gene    taxon:4932      20010119        SGD

node_1 pp node_2
node_3 pp node_1
node_2 pp node_3

node_1  OA_0000232
node_2  OA_0000441
node_3  OA_0000702

node_1 (pp) node_2  MI:0445
node_3 (pp) node_1  MI:0046
node_2 (pp) node_3  MI:0346

LinkOut provides a mechanism to link nodes and edges to external web resources within Cytoscape. Right-clicking on a node or edge in Cytoscape view opens a popup menu with a list of web links.

The external links are specified in a linkout.props file which is included in the cytoscape.jar file. The defaults include a number of links such as Entrez, SGD, iHOP, and Google, as well as a number of species-specific links. In addition to the default links, users can customize the LinkOut menu by adding (or removing) links by editing the linkout properties (found under Edit → Preferences → Properties...).

External links are listed as ‘key’-‘value’ pairs in the linkout.props file where key specifies the name of the link and value is the search URL. The LinkOut menus are organized in a hierarchical structure that is specified in the key. Linkout key terms specific for nodes start with the keyword nodelinkouturl, for edges this is edgelinkouturl.

For example, the following entry:

nodelinkouturl.Model Organism DB.SGD (yeast)=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=%ID%

places the SGD link under the yeast submenu. This link will appear in Cytoscape as:

In a similar fashion one can added new submenus.

The %ID% string in the URL is a place-holder for the node label. When the popup menu is generated this marker is substituted with the node label. In the above example, the generated SGD link for the YIM1 protein is:

http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=YIM1

If you want to query based on a different attribute you currently need to specify a different Node Label using the VizMapper.

For edges the mechanism is much the same; however here the placeholders %ID1% and %ID2% reflect the source and target node label respectively.

Currently there is no mechanism to check whether the constructed URL query is correct and if the node label is meaningful. Similarly, there is no ID mapping between various identifiers. For example, a link to NCBI Entrez from a network that uses ensembl gene identifiers as node labels will produce a link to Entrez using ensembl ID, which results in an incorrect link. It is the user's responsibility to ensure that the node label that is used as the search term in the URL link will result in a meaningful link.

cytoscape.sh -P new_linout.props

cytoscape.sh -P nodelinkouturl.yeast.SGD=http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%

Cytoscape is built with a number of open source third-party Java libraries. The Cytoscape team gratefully acknowledges the following libraries:

This product includes software developed by the Apache Software Foundation (http://www.apache.org/).

This product includes software developed by the JDOM Project (http://www.jdom.org/).

One-step installation of the Cytoscape software is accomplished using the InstallAnywhere product from ZeroG Software, Inc. (http://zerog.com)

Handlers for the following format still exist in Cytoscape as legacy code, however we strongly recommend using the new formats (OBO + Gene Association) described in the previous section, since they are easier to download directly from the Gene Ontology project and use directly. Currently, users have no access to an import interface for this old format.

(curator=GO) (type=all)
0003673 = Gene_Ontology
0003674 = molecular_function [partof: 0003673 ]
0008435 = anticoagulant [isa: 0003674 ]
0016172 = antifreeze [isa: 0003674 ]
0016173 = ice nucleation inhibitor [isa: 0016172 ]
0016209 = antioxidant [isa: 0003674 ]
0045174 = glutathione dehydrogenase (ascorbate) [isa: 0009491 0015038 0016209 0016672 ]
0004362 = glutathione reductase (NADPH) [isa: 0015038 0015933 0016209 0016654 ]
0017019 = myosin phosphatase catalyst [partof: 0017018 ]
...

(curator=KEGG) (type=Metabolic Pathways)
90001 = Metabolism
80001 = Carbohydrate Metabolism [isa: 90001 ]
80003 = Lipid Metabolism [isa: 90001 ]
80002 = Energy Metabolism [isa: 90001 ]
80004 = Nucleotide Metabolism [isa: 90001 ]
80005 = Amino Acid Metabolism [isa: 90001 ]
80006 = Metabolism of Other Amino Acids [isa: 90001 ]
80007 = Metabolism of Complex Carbohydrates [isa: 90001 ]
...

(species=Saccharomyces cerevisiae) (type=Biological Process) (curator=GO)
YMR056C = 0006854
YBR085W = 0006854
YJR155W = 0006081
...

(species=Mycobacterium tuberculosis) (type=Metabolic Pathways) (curator=KEGG)
RV0761C = 10
RV0761C = 71
RV0761C = 120
RV0761C = 350
RV0761C = 561
RV1862 = 10
...

ontology=goOntology.txt
annotation=yeastBiologicalProcess.txt
annotation=yeastMolecularFunction.txt
annotation=yeastCellularComponent.txt

 gunzip go-YYYYMM-termdb.xml.gz
 python parseGoTermsToFlatFile.py go-YYYYMM-termdb.xml > goOntology.txt

SPTR    O00115  DRN2_HUMAN              GO:0003677      PUBMED:9714827  TAS             F       Deoxyribonuclease II precursor  IPI00010348     protein taxon:9606              SPTR
SPTR    O00115  DRN2_HUMAN              GO:0004519      GOA:spkw        IEA             F       Deoxyribonuclease II precursor  IPI00010348     protein taxon:9606        20020425      SPTR
SPTR    O00115  DRN2_HUMAN              GO:0004531      PUBMED:9714827  TAS             F       Deoxyribonuclease II precursor  IPI00010348     protein taxon:9606              SPTR
...

(species=Homo sapiens) (type=Molecular Function) (curator=GO)
IPI00010348 = 0003677
IPI00010348 = 0004519
IPI00010348 = 0004531
...

(species=Homo sapiens) (type=Biological Process) (curator=GO)
NP_001366 = 0006259
NP_001366 = 0006915
NP_005289 = 0007186
NP_647593 = 0006899
...

SP      O00115  IPI00010348             ENSP00000222219;        NP_001366;              BAA28623;AAC77366;AAC35751;AAC39852;BAB55598;AAB51172;AAH10419; 2960,DNASE2     1777,DNASE2
SP      O00116  IPI00010349             ENSP00000324567;ENSP00000264167;        NP_003650;              CAA70591;       327,AGPS        8540,AGPS
SP      O00124  IPI00010353             ENSP00000265616;ENSP00000322580;        NP_005662;              BAA18958;BAA18959;AAH20694;             7993,D8S2298E
...

python parseAssignmentsToFlatFileFromGoaProject.py gene_association.goa_human xrefs.goa

# parseGoTermToFlatFile.py:  translate a GO XML ontology file into a simpler
#  Cytoscape flat file
#-----------------------------------------------------------------------------------
# RCS: $Revision: 1.3 $   $Date: 2003/05/18 00:38:43 $
#-----------------------------------------------------------------------------------
import re, pre, sys
#-----------------------------------------------------------------------------------
def flatFilePrint (id, name, isaIDs, partofIDs):
  isa = ''
  if (len (isaIDs) > 0):
    isa = '[isa: '
    for isaID in isaIDs:
      isa += isaID
      isa += ' '
    isa += ']'
  partof = ''
  if (len (partofIDs) > 0):
    partof = '[partof: '
    for partofID in partofIDs:
      partof += partofID
      partof += ' '
    partof += ']'
  result = '~np~%~/np~s = ~np~%~/np~s ~np~%~/np~s ~np~%~/np~s' ~np~%~/np~ (id, name, isa, partof)
  result = result.strip ()
  if (result == 'isa = isa' or result == 'partof = partof'):
    print >> sys.stderr, 'meaningless term: ~np~%~/np~s' ~np~%~/np~ result
  else:
    print result
#-----------------------------------------------------------------------------------
if (len (sys.argv) != 2):
  print 'usage:  ~np~%~/np~s <someFile.xml>' ~np~%~/np~ sys.argv [0]
  sys.exit ();
inputFilename = sys.argv [1];
print >> sys.stderr,  'reading ~np~%~/np~s...' ~np~%~/np~ inputFilename
text = open (inputFilename).read ()
print >> sys.stderr,  'read ~np~%~/np~d characters' ~np~%~/np~ len (text)
regex = '<go:term .*?>(.*?)</go:term>';
cregex = pre.compile (regex, re.DOTALL)   # . matches newlines
m = pre.findall (cregex, text)
print >> sys.stderr, 'number of go terms: ~np~%~/np~d' ~np~%~/np~ len (m)
regex2 = '<go:accession>GO:(.*?)</go:accession>.*?<go:name>(.*?)</go:name>'
cregex2 = re.compile (regex2, re.DOTALL)
regex3 = '<go:isa\s*rdf:resource="http://www.geneontology.org/go#GO:(.*?)"\s*/>'
cregex3 = re.compile (regex3, re.DOTALL)
regex4 = '<go:part-of\s*rdf:resource="http://www.geneontology.org/go#GO:(.*?)"\s*/>'
cregex4 = re.compile (regex4, re.DOTALL)
goodElements = 0
badElements = 0
print '(curator=GO) (type=all)'
for term in m:
  m2 = re.search (cregex2, term)
  if (m2):
    goodElements += 1;
    id = m2.group (1)
    name = m2.group (2)
    isaIDs = []
    m3 = re.findall (cregex3, term);
    for ref in m3:
      isaIDs.append (ref)
    m4 = re.findall (cregex4, term);
    partofIDs = []
    for ref in m4:
      partofIDs.append (ref)
    flatFilePrint (id, name, isaIDs, partofIDs)
  else:
    badElements += 1;
    print >> sys.stderr, 'no match to m2...'
    print >> sys.stderr, "---------------\n~np~%~/np~s\n------------------" ~np~%~/np~ term
print >> sys.stderr,  'goodElements ~np~%~/np~d' ~np~%~/np~ goodElements
print >> sys.stderr, 'badElements ~np~%~/np~d' ~np~%~/np~ badElements
#--------------------------------------

import sys
#-----------------------------------------------------------------------------------
def fixCanonicalName (rawName):
# for instance, trim 'YBR085W|ANC3' to 'YBR085W'
  bar = rawName.find ('|')
  if (bar < 0):
    return rawName
  return rawName [:bar]
#-----------------------------------------------------------------------------------
def fixGoID (rawID):
  bar = rawID.find (':') + 1
  return rawID [bar:]
#-----------------------------------------------------------------------------------
def readGoaXrefFile (filename):
  lines = open (filename).read().split ('\n')
  result = {}
  for line in lines:
    if (len (line) < 10):
      continue
    tokens = line.split ('\t')
    ipi = tokens [2]
    np = tokens [5]
    semicolon = np.find (';')
    if (semicolon >= 0):
      np = np [:semicolon]
    if (len (ipi) > 0 and len (np) > 0):
      result [ipi] = np
  return result
#-----------------------------------------------------------------------------------
if (len (sys.argv) != 3):
  print 'error!  parse   <gene_associations file from GO> <goa xrefs file> '
  sys.exit ()
associationFilename = sys.argv [1];
xrefsFilename = sys.argv [2]
species = 'Homo sapiens'
ipiToNPHash = readGoaXrefFile (xrefsFilename)
tester = 'IPI00099416'
print 'hash size: ~np~%~/np~d' ~np~%~/np~ len (ipiToNPHash)
print 'test map: ~np~%~/np~s -> NP_054861: ~np~%~/np~s ' ~np~%~/np~ (tester, ipiToNPHash [tester])
bioproc = open ('bioproc.txt', 'w')
molfunc = open ('molfunc.txt', 'w')
cellcomp = open ('cellcomp.txt', 'w')
bioproc.write ('(species=~np~%~/np~s) (type=Biological Process) (curator=GO)\n' ~np~%~/np~ species)
molfunc.write ('(species=~np~%~/np~s) (type=Molecular Function) (curator=GO)\n' ~np~%~/np~ species);
cellcomp.write ('(species=~np~%~/np~s) (type=Cellular Component) (curator=GO)\n' ~np~%~/np~ species);
lines=open(associationFilename).read().split('\n')
sys.stderr.write ('found ~np~%~/np~d lines\n' ~np~%~/np~ len (lines))

for line in lines:
  if (line.find ('!') == 0 or len (line) < 2):
    continue
  tokens = line.split ('\t')
  goOntology = tokens [8]
  goIDraw = tokens [4]
  goID = goIDraw.split (':')[1]
  ipiName = fixCanonicalName (tokens [10])
  if (len (ipiName) < 1):
    continue


  if (not ipiToNPHash.has_key (ipiName)):
    continue
  refseqName = ipiToNPHash [ipiName]
  printName = refseqName
  #printName = ipiName
  if (ipiName == tester):
    print '~np~%~/np~s (~np~%~/np~s) has go term ~np~%~/np~s' ~np~%~/np~ (tester, printName, goID)
  if (goOntology == 'C'):
    cellcomp.write ('~np~%~/np~s = ~np~%~/np~s\n' ~np~%~/np~ (printName, goID))
  elif (goOntology == 'P'):
    bioproc.write ('~np~%~/np~s = ~np~%~/np~s\n' ~np~%~/np~ (printName, goID))
  elif (goOntology == 'F'):
    molfunc.write ('~np~%~/np~s = ~np~%~/np~s\n' ~np~%~/np~ (printName, goID))
#-----------------------------------------------------------------------------------

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