07-11-2009
multiple line parsing help
Hey everyone,
I'm having trouble figuring out how to reformat the following (large) file:
>Cluster 1
0 563nt, >FX2FH6V05GB01A... *
1 405nt, >FX2FH6V05F7LOL... at +/98%
>Cluster 2
0 551nt, >FX2FH6V05FTLO0... at +/98%
1 561nt, >FX2FH6V05F5F1E... *
2 343nt, >FX2FH6V05GBHRK... at +/98%
I need to reformat it so that the string in front of the asterisk is first on a line, followed by that string repeated, and the all of the other strings in the cluster. For example:
FX2FH6V05GB01A FX2FH6V05GB01A, FX2FH6V05F7LOL
FX2FH6V05F5F1E FX2FH6V05F5F1E, FX2FH6V05FTLO0, FX2FH6V05GBHRK
Some of the clusters are very large, and the string followed by the asterisk can be anywhere within that cluster. I can probably figure out how to flatten everything, but I'm not sure how to reorder the strings so that the one with the asterisk comes first.
Many thanks in advance for your advice.
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LEARN ABOUT CENTOS
cluster
CLUSTER(1) General Commands Manual CLUSTER(1)
NAME
cluster - find clusters in a graph and augment the graph with this information.
SYNOPSIS
cluster [-v?] [ -Ck ] [ -ck ] [ -o outfile ] [ files ]
DESCRIPTION
cluster takes as input a graph in DOT format, finds node clusters and augments the graph with this information. The clusters are specified
by the "cluster" attribute attached to nodes; cluster values are non-negative integers. cluster attempts to maximize the modularity of the
clustering. If the edge attribute "weight" is defined, this will be used in computing the clustering.
OPTIONS
The following options are supported:
-Ck specifies a targeted number of clusters that should be generated. The specified number k is only a suggestion and may not be real-
isable. If k == 0, the default, the number of clusters that approximately optimizes the modularity is returned.
-ck specifies clustering method. If k == 0, the default, the modularity will be used. If k == 1 modularity quality will be used.
-ooutfile
Specifies that output should go into the file outfile. By default, stdout is used.
-v Verbose mode.
EXAMPLES
Applying cluster to the following graph,
graph {
1--2 [weight=10.]
2--3 [weight=1]
3--4 [weight=10.]
4--5 [weight=10]
5--6 [weight=10]
3--6 [weight=0.1]
4--6 [weight=10.]
}
gives
graph {
node [cluster="-1"];
1 [cluster=1];
2 [cluster=1];
3 [cluster=2];
4 [cluster=2];
5 [cluster=2];
6 [cluster=2];
1 -- 2 [weight="10."];
2 -- 3 [weight=1];
3 -- 4 [weight="10."];
4 -- 5 [weight=10];
5 -- 6 [weight=10];
3 -- 6 [weight="0.1"];
4 -- 6 [weight="10."];
}
AUTHOR
Yifan Hu <yifanhu@research.att.com>
SEE ALSO
gvmap(1)
Blondel, V.D., Guillaume, J.L., Lambiotte, R., Lefebvre, E.: Fast unfolding of communities in large networks. Journal of Statistical
Mechanics: Theory and Experiment (2008), P10008.
3 March 2011 CLUSTER(1)