\n
([A-Z0-9]*:)([0-9]*)
tp53_somatic
mor
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
([A-Z0-9]*) ([0-9]*)
2
org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
([A-Z0-9]*) ([0-9]*)
2
org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
([A-Z0-9]*) ([A-Z0-9]* [A-Z0-9]*)
2
org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
2
org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
import java.util.regex.Pattern;
import java.util.regex.Matcher;
StringBuffer temp = new StringBuffer();
String information="";
// regular expression to extract only the sequence description
Pattern pattern = Pattern.compile ("(Effect) (.(.(.)*)*)*");
Matcher matcher = pattern.matcher(inputs);
while(matcher.find()){
information=matcher.group(2);
temp.append(information);
}
// Output sequence description
String result = temp.toString();
inputs
result
import java.util.regex.Pattern;
import java.util.regex.Matcher;
StringBuffer temp = new StringBuffer();
String information="";
// regular expression to extract only the sequence description
Pattern pattern = Pattern.compile ("(Type) (.(.(.)*)*)*");
Matcher matcher = pattern.matcher(inputs);
while(matcher.find()){
information=matcher.group(2);
temp.append(information);
}
// Output sequence description
String result = temp.toString();
inputs
result
Simple workflow to count the number of items in a list;
Simple workflow to count the number of items in a list
count = list.size();
list
count
(xml) list
number of elements counted
Simple workflow to count the number of items in a list;
Simple workflow to count the number of items in a list
count = list.size();
list
count
(xml) list
number of elements counted
It plots the distribution.
It plots the distribution.
From the list format into a delimited format.
,
org.embl.ebi.escience.scuflworkers.java.StringListMerge
## PiePlot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of ",xlab="Number of ",ylab="Pro")
datapoints <- as.table(summary.factor(dev_num))
#dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of ",xlab="Number of ",ylab="Number of ",pch=20)
#dist_plot <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
#,names.arg=names(datapoints)
dist_plot <- pie(datapoints, col=rainbow(length(datapoints), start=0.05, end=0.95), labels=NA, edges = 200, radius = 0.8, main="Pie Chart", clockwise=T); legend("topright", legend=row.names(datapoints), cex=1.4, bty="n", pch=18, pt.cex=1.9, col=rainbow(length(datapoints), start=0.1, end=0.8), ncol=1)
dev.off()
dev_numbers
dist_plot
Bar_Plot
## Plot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
datapoints <- as.table(summary.factor(dev_num))
#,names.arg=names(datapoints)
dist_plot <- barplot(datapoints, col=rainbow(length(dev_num)))
dev.off()
dev_numbers
dist_plot
devnum <- read.csv(textConnection(dev_inp),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
points <- as.matrix(summary.factor(dev_num))
n_list <- paste(capture.output(points), collapse="\n")
dev_inp
n_list
It plots the distribution.
It plots the distribution.
From the list format into a delimited format.
,
org.embl.ebi.escience.scuflworkers.java.StringListMerge
devnum <- read.csv(textConnection(dev_inp),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
points <- as.matrix(summary.factor(dev_num))
n_list <- paste(capture.output(points), collapse="\n")
dev_inp
n_list
## Pie Plot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of Number of Codons",xlab="Number of ",ylab="Projects")
datapoints <- as.table(summary.factor(dev_num))
#dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of Number of Codons",xlab="Number of Codons",ylab="Number of nodes",pch=20)
#dist_plot <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
#,names.arg=names(datapoints)
dist_plot <- pie(datapoints, col=rainbow(length(datapoints), start=0.05, end=0.95), labels=NA, edges = 200, radius = 0.8, main="Pie Chart", clockwise=T); legend("topright", legend=row.names(datapoints), cex=1.4, bty="n", pch=18, pt.cex=1.9, col=rainbow(length(datapoints), start=0.1, end=0.8), ncol=1)
dev.off()
dev_numbers
dist_plot
##BarPlot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
datapoints <- as.table(summary.factor(dev_num))
#,names.arg=names(datapoints)
dist_plot <- barplot(datapoints, col=rainbow(length(dev_num)))
dev.off()
dev_numbers
dist_plot
It plots the distribution.
It plots the distribution.
From the list format into a delimited format.
,
org.embl.ebi.escience.scuflworkers.java.StringListMerge
devnum <- read.csv(textConnection(dev_inp),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
points <- as.matrix(summary.factor(dev_num))
n_list <- paste(capture.output(points), collapse="\n")
dev_inp
n_list
## Plot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
datapoints <- as.table(summary.factor(dev_num))
#,names.arg=names(datapoints)
dist_plot <- barplot(datapoints, col=rainbow(length(dev_num)))
dev.off()
dev_numbers
dist_plot
## PiePlot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.matrix(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of ",xlab="Number of ",ylab="Pro")
datapoints <- as.table(summary.factor(dev_num))
#dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of ",xlab="Number of ",ylab="Number of ",pch=20)
#dist_plot <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
#,names.arg=names(datapoints)
dist_plot <- pie(datapoints, col=rainbow(length(datapoints), start=0.05, end=0.95), labels=NA, edges = 200, radius = 0.8, main="Pie Chart", clockwise=T); legend("topright", legend=row.names(datapoints), cex=1.4, bty="n", pch=18, pt.cex=1.9, col=rainbow(length(datapoints), start=0.1, end=0.8), ncol=1)
dev.off()
dev_numbers
dist_plot
It plots the distribution.
It plots the distribution.
From the list format into a delimited format.
,
org.embl.ebi.escience.scuflworkers.java.StringListMerge
## Plot distribution of numbers of Exons
## read the data
devnum2 <- read.csv(textConnection(dev_numbers2),header=FALSE,row.names=NULL)
dev_num2 <- as.vector(devnum2, mode="integer")
## plot the data
png(hist_plot, width=800);
hist_plot <- hist(dev_num2,col="red",main="Distribution of Number of Exons",xlab="Number of Exons",ylab="Projects")
dev.off()
dev_numbers2
hist_plot
Plots the distributions on a straight scale.
## Plot distribution of numbers of exons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of Number of Exons",xlab="Number of ",ylab="Projects")
datapoints <- as.table(summary.factor(dev_num))
dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of Number of Exons",xlab="Number of Exons",ylab="Number of nodes",pch=20)
#pie_ <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
dev.off()
dev_numbers
dist_plot
## PiePlot distribution of numbers of Exons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of Number of Exons",xlab="Number of ",ylab="Projects")
datapoints <- as.table(summary.factor(dev_num))
#dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of Number of Exons",xlab="Number of Exons",ylab="Number of nodes",pch=20)
#dist_plot <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
dist_plot <- pie(datapoints, col=rainbow(length(datapoints), start=0.05, end=0.95), labels=NA, edges = 200, radius = 0.8, main="Pie Chart", clockwise=T); legend("topright", legend=row.names(datapoints), cex=1.4, bty="n", pch=18, pt.cex=1.9, col=rainbow(length(datapoints), start=0.1, end=0.8), ncol=1)
dev.off()
dev_numbers
dist_plot
## BarPlot distribution of numbers of Exons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
datapoints <- as.table(summary.factor(dev_num))
dist_plot <- barplot(datapoints, col=rainbow(length(dev_num)))
dev.off()
dev_numbers
dist_plot
Plots the distribution on a log-log scale.
## LogPlot distribution of numbers of Exons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(log_plot, width=800);
datapoints <- as.vector(summary.factor(dev_num))
log_plot <- plot(datapoints,log="xy",col="blue",type="o",xlim=c(1,1000),main="Distribution of Number of Exons",xlab="Number of Exons",ylab="Number of nodes",pch=20)
dev.off()
dev_numbers
log_plot
Produces a list of the data points for plotting with other software.
##
devnum <- read.csv(textConnection(dev_nums),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
points <- as.matrix(summary.factor(dev_num))
point_list <- paste(capture.output(points), collapse="\n")
dev_nums
point_list
PNG plot of the distribution of developers to projects.
PNG graphic plot of log-log distribution of developers to projects.
List of points for plotting in other software.
It plots the distribution.
It plots the distribution.
From the list format into a delimited format.
,
org.embl.ebi.escience.scuflworkers.java.StringListMerge
## BarPlot distribution of numbers of codons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
datapoints <- as.table(summary.factor(dev_num))
dist_plot <- barplot(datapoints, col=rainbow(length(dev_num)))
dev.off()
dev_numbers
dist_plot
Plots the distributions on a straight scale.
## Plot distribution of numbers of codons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of Number of Codons",xlab="Number of ",ylab="Projects")
datapoints <- as.table(summary.factor(dev_num))
dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of Number of Codons",xlab="Number of Codons",ylab="Number of nodes",pch=20)
#pie_ <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
dev.off()
dev_numbers
dist_plot
Plots the distribution on a log-log scale.
## LogPlot distribution
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(log_plot, width=800);
datapoints <- as.vector(summary.factor(dev_num))
log_plot <- plot(datapoints,log="xy",col="blue",type="o",xlim=c(1,1000),main="Distribution of Number of Codons",xlab="Number of Codons",ylab="Numbernodes",pch=20)
dev.off()
dev_numbers
log_plot
## PiePlot distribution of numbers of codons
## read the data
devnum <- read.csv(textConnection(dev_numbers),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
## plot the data
png(dist_plot, width=800);
#png(pie_, width=800);
#dist_plot <- hist(dev_num,col="red",main="Distribution of Number of Codons",xlab="Number of ",ylab="Projects")
datapoints <- as.table(summary.factor(dev_num))
#dist_plot <- plot(datapoints,xlim=range(dev_num),col="blue",type="o",main="Distribution of Number of Codons",xlab="Number of Codons",ylab="Number of nodes",pch=20)
#dist_plot <- pie(datapoints, col=rainbow(length(dev_num), start=0.1, end=0.8), main="Pie Chart", clockwise=T)
dist_plot <- pie(datapoints, col=rainbow(length(datapoints), start=0.05, end=0.95), labels=NA, edges = 200, radius = 0.8, main="Pie Chart", clockwise=T); legend("topright", legend=row.names(datapoints), cex=1.4, bty="n", pch=18, pt.cex=1.9, col=rainbow(length(datapoints), start=0.1, end=0.8), ncol=1)
dev.off()
dev_numbers
dist_plot
Produces a list of the data points for plotting with other software.
##
devnum <- read.csv(textConnection(dev_nums),header=FALSE,row.names=NULL)
dev_num <- as.vector(devnum, mode="integer")
points <- as.matrix(summary.factor(dev_num))
point_list <- paste(capture.output(points), collapse="\n")
dev_nums
point_list
## Plot distribution of numbers of codons
## read the data
devnum2 <- read.csv(textConnection(dev_numbers2),header=FALSE,row.names=NULL)
dev_num2 <- as.vector(devnum2, mode="integer")
## plot the data
png(hist_plot, width=800);
hist_plot <- hist(dev_num2,col="red",main="Distribution of Number of Codons",xlab="Number of ",ylab="Projects")
dev.off()
dev_numbers2
hist_plot
PNG plot of the distribution of developers to projects.
PNG graphic plot of log-log distribution of developers to projects.
List of points for plotting in other software.
Get tp53 gene mutations by ids from TP53 IARC database (see http://srs.o2i.it/srs71/)
http://bioinformatics.istge.it:8080/axis/services/o2i.getP53MutationsByIds
Get tp53 ids by field label from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53IdsByField
Get any tp53 field value starting by another field value choosen from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
tp53_somatic
mid
intron
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53FieldByField
Get any tp53 field value starting by another field value choosen from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
sht
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53FieldByField
Get any tp53 field value starting by another field value choosen from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
tp53_somatic
mid
effect
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53FieldByField
Get any tp53 field value starting by another field value choosen from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
cno
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53FieldByField
Get any tp53 field value starting by another field value choosen from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
tp53_somatic
mid
typ
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53FieldByField
Get any tp53 field value starting by another field value choosen from one of the IARC TP53 databases (see srs.o2i.it/srs71/)
tp53_somatic
mid
exon
http://bioinformatics.istge.it:8080/axis/services/p53_getz_services.getP53FieldByField
Completed
getP53_Codons
getP53_Topography
Scheduled
Running
Completed
getP53_Topography
getP53_Ids
Scheduled
Running
Completed
getP53_Topography
getP53_Mut_Type
Scheduled
Running
Completed
getP53_Mut_Type
getP53_Effect
Scheduled
Running
Completed
getP53_Intron
getP53_Exon
Scheduled
Running
Completed
getP53_Effect
getP53_Intron
Scheduled
Running
Completed
getP53_Exon
getP53_Mutations
Scheduled
Running