Merge branch 'master' of pakal.ccg.unam.mx:larisams/gene-disease-embeddings

@@ -14,4 +14,8 @@ The main goal of this proyect is to obtain sentence embeddings of 450 abstract t
 ### Programs and commands used 
 ```Shell
 \scripts
+```
+### Results from clustering
+```Shell
+\results
 ```
\ No newline at end of file

+#Cluster:  1
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+#Cluster:  2
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\ No newline at end of file

+#Cluster:  1
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+#Cluster:  2
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\ No newline at end of file

+#Cluster:  1
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+#Cluster:  2
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+#Cluster:  3
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+#Cluster:  4
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+449_s   445
+455_s   451
\ No newline at end of file

+library(methods)
+library(cluster)
+
+# Funcion para imprimir los clusters
+print_cluster <- function(obj, filename) {
+  
+  for(cl in 1:length(obj)) {
+    
+    write.table(paste("\nCluster: ", cl, "\n"), file = filename, append = TRUE, quote = FALSE, row.names = TRUE, col.names = FALSE)
+    write.table(obj[[cl]], file = filename, append = TRUE, quote = FALSE, row.names = TRUE, col.names = FALSE, sep = "   ")
+    
+  }
+}
+###################################################################################################################################################
+# Receive arguments
+arg = commandArgs(trailingOnly = T)
+
+if (length(arg)==0) {
+  stop("Must supply input file.n", call.=FALSE)
+}
+
+################################################# Run analysis ##################################################
+vecs <- read.table(arg[1], 
+                   header = F, row.names = 1, sep = ' ', 
+                   colClasses = c("character", rep("numeric", 299)))
+
+senclus <- hclust(dist(vecs), method = 'ward.D')
+print("agglomerative coefficient: ")
+print(coef.hclust(senclus))
+
+# Guardamos la imagen del dendograma original
+png("Dendogram_ward.png", height = 608, width = 975)
+plot(senclus, hang = -1)
+dev.off()
+
+###
+# Particion en dos clusters
+png("Dendogram_2clusters.png", height = 608, width = 975)
+plot(senclus, hang = -1)
+cls2 <- rect.hclust(senclus, k=2, border = 3:4)
+dev.off()
+
+# Escribir archivo
+print_cluster(cls2, "SentenceMembership_2clusters.txt")
+
+#######
+# Particion en tres clusters
+png("Dendogram_3clusters.png", height = 608, width = 975)
+plot(senclus, hang = -1)
+cls3 <- rect.hclust(senclus, k=3, border = 3:4)
+dev.off()
+
+# Escribir archivo
+print_cluster(cls3, "SentenceMembership_3clusters.txt")
+
+#####
+# Particion en cuatro clusters
+png("Dendogram_4clusters.png", height = 608, width = 975)
+plot(senclus, hang = -1)
+cls4 <- rect.hclust(senclus, k=4, border = 3:4)
+dev.off()
+
+# Escribir archivo
+print_cluster(cls4, "SentenceMembership_4clusters.txt")
+
+
+
+

+from optparse import OptionParser
+
+# Recibir input y output
+parser = OptionParser()
+parser.add_option("-i", dest="inF",help="Input vector file. Sentence is separated by tabs from values which are sparated by simple space", metavar="PATH")
+parser.add_option("-o", dest="otF",help="output file name", metavar="PATH")
+
+(options, args) = parser.parse_args()
+if len(args) > 0:
+    parser.error("Please indicate an input directory")
+    sys.exit(1)
+
+# Asignar variables
+infile = options.inF
+outfile = options.otF
+
+# Abrir nuevo archivo
+newfile = open(outfile, 'w')
+
+# Reemplazar tab por espacio
+with open(infile) as vectors:
+	for line in vectors:
+		# Aislar el numero de articulo de sus valores
+		elements = line.rstrip().split('\t')
+
+		# Ponemos una letra para facilitar la indentificacion posterior
+		index = elements[0] + '_s'
+
+		# Armar la nueva linea
+		newline = ' '.join([index,elements[1]])
+		newline = newline + '\n'
+		newfile.write(newline)
+
+newfile.close()
\ No newline at end of file