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gff draw

muti_gff_draw.py

@@ -0,0 +1,37 @@
+import csv
+from pathlib import Path
+import sys
+def features_draw(gff_list,out_script):
+	with open(gff_list) as IN,open(out_script,'w') as OUT:
+		OUT.write("from dna_features_viewer import GraphicFeature, GraphicRecord\n\n")
+		filenames = IN.readlines()
+		for name in filenames:
+			name = name.strip()
+			features_name =Path(name).stem
+			OUT.write("features_"+features_name+"=[\n")
+			with open(name) as GFFFILE:
+				gff = csv.reader(GFFFILE,delimiter='\t')
+				start,end = [],[]
+				strand = ""
+				for gfftext in gff:
+					strand = gfftext[6]
+					if gfftext[2] in ["CDS","exon"]:
+						start.append(int(gfftext[3]))
+						end.append(int(gfftext[4]))
+				start.sort()
+				end.sort()
+				tmp_number = start[0] #init
+				start = [i-tmp_number for i in start] #init
+				end = [i-tmp_number for i in end] #init
+				for double_pos in zip(start,end):
+					feature = "GraphicFeature(start={}, end={}, strand={}1, color='#ccccff'),".format(double_pos[0],double_pos[1],strand)
+					OUT.write("\t"+feature+"\n")
+			OUT.write("]\n")
+			OUT.write("record = GraphicRecord(sequence='',sequence_length={},features=features_{})\n".format(end[-1]+1,features_name))
+			OUT.write("ax, _ = record.plot(figure_width=15)\nrecord.plot_sequence(ax)\n")
+			OUT.write("ax.figure.savefig('{}.pdf', bbox_inches='tight')\n".format(features_name))
+
+if (len(sys.argv)==3):
+	features_draw(sys.argv[1],sys.argv[2])
+else:
+	print("Usage: python gff.list features_draw.py")