R: graphs, part2

load data from data frame:

col1 col2 weight
ничего космос 1.0
first two columns consider to be vertex names, third - weight
data<-read.table("/home/bliss/Study/Bauman/Magistr&Disser/Data/dat.txt",header=T,sep="\t")
gr<-graph.data.frame(as.data.frame(data),directed=T)


get vertex id by value: which(V(gr)$name=="космос")
get edge weight using vertex names: E(gr, P=c(which(V(gr)$name=="голубой")-1,which(V(gr)$name=="платок")-1))$weight
Vertex idx starts from 0, not 1!

R: working with graphs

use igraph


library(igraph)
create empty graph: graph.empty()
create graph with edges (1,2); (2,3); (5,6): graph(c(1,2,2,3,5,6), directed=TRUE)
get nodes number:  vcount(graph)
get edges number: ecount(graph)
add/delete edges: add.edges; delete.edges

Shortest paths: http://igraph.sourceforge.net/doc/R/shortest.paths.html

shortest.paths(graph, v=V(graph), mode = c("all", "out", "in"),
      weights = NULL, algorithm = c("automatic", "unweighted",
                                    "dijkstra", "bellman-ford",
                                    "johnson"))
get.shortest.paths(graph, from, to=V(graph), mode = c("all", "out",
      "in"), weights = NULL)
get.all.shortest.paths(graph, from, to = V(graph), mode = c("all", "out", "in")) 
average.path.length(graph, directed=TRUE, unconnected=TRUE)
path.length.hist (graph, directed = TRUE, verbose = igraph.par("verbose")) 

Python Regular Expressions

E.g. we'd like to parse such html-code using regexp:
 <tr><td><font color="#bbbbbb">5587  </font></td><td>изумление</td><td>S</td><td>13.98</td><td>20.65</td>
## <td>#N/A</td><td>#N/A</td><td>#N/A</td><td>#N/A</td><td>#N/A</td><td>#N/A</td><td>#N/A</td><td></td></tr>


The code will be:

rows=re.finditer('(\<tr.+?tr\>)',html) ##nejadnyi (v otlichie ot .+ ischet stroki ne maxim dliny)
for row in rows:
cells=re.finditer('(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)(\<td.+?td\>)',row.groups()[0])


Round brackets '(', ')' means group, you may iterate or name them.
\ - read as it is
.+ - find any string (any symbols), finds string with maximum length and takes a lot of sources
.+? - find any string (any symbols), not maximum length , better one to parse constructions like
<tr>...</tr>..<tr>...</tr>







'(\<tr.+tr\>)', finds  ({<tr>...</tr>..<tr>...</tr>}), only one
'(\<tr.+?tr\>)', finds  ({<tr>...</tr>},{<tr>...</tr>})



Primitive function to remove html tags:
def remove_tags(html): pattern=re.compile('<.*?>')  
result=pattern.sub("",html)  
return result

Find string that doesn't contain symbol (e.g. '{'):
re.finditer('({[^}]+})', str)

Apache error log

Directory: /var/log/apache2/error.log