Source code for pytransit.draw_trash

# Copyright 2015.
#   Michael A. DeJesus, Chaitra Ambadipudi, and  Thomas R. Ioerger.
#
#
#    This file is part of TRANSIT.
#
#    TRANSIT is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License.
#
#
#    TRANSIT is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with TRANSIT.  If not, see <http://www.gnu.org/licenses/>.


import view_trash
from math import *
import os
import platform

try:
    import Image
    import ImageDraw
    import ImageFont
except ImportError:
    import PIL.Image as Image
    import PIL.ImageDraw as ImageDraw
    import PIL.ImageFont as ImageFont


[docs]def normalize(X, old_min, old_max, new_min, new_max): old_range = (old_max - old_min) new_range = (new_max - new_min) if old_range == 0: return new_min else: return (((X - old_min) * new_range) / old_range) + new_min
[docs]def read_prot_table(path): orf2data = {} for line in open(path): if line.startswith("#"): continue tmp = line.strip().split("\t") orf2data[tmp[8]] = [int(tmp[1]), int(tmp[2]), tmp[3], tmp[7]] return(orf2data)
[docs]def hash_prot_genes(path): hash = {} for line in open(path): if line.startswith("#"): continue tmp = line.strip().split("\t") start, end = int(tmp[1]), int(tmp[2]) for i in range(start,end+1): #if i not in hash: # hash[i] = tmp[8] hash[i] = tmp[8] return hash
linuxFonts = [] linuxFonts.append("/usr/share/fonts/truetype/ttf-dejavu/DejaVuSans-Bold.ttf") linuxFonts.append("/usr/share/fonts/dejavu-lgc/DejaVuLGCSerifCondensed-Bold.ttf") linuxFonts.append("/usr/share/fonts/dejavu-lgc/DejaVuLGCSansCondensed-Bold.ttf") winFonts = [] winFonts.append("consolab.ttf") winFonts.append("courb.ttf") winFonts.append("arial.ttf") fontsize = 16 font = ImageFont.load_default() if platform.system() == "Linux": for fontpath in linuxFonts: if os.path.isfile(fontpath): font = ImageFont.truetype(fontpath, fontsize) break elif platform.system() == "Windows": for fontpath in winFonts: try: font = ImageFont.truetype(fontpath, fontsize) break except: pass
[docs]def draw_reads(draw, reads, ta_sites, start_x=0, start_y=0, width=400, height=100, start=0, end=500, min_read=0, max_read=500, lwd=2): TRUNC_READS = [min(rd, max_read) for rd in reads] NORM_READS = [normalize(rd, 0, max_read, 0, max_read) for rd in TRUNC_READS] new_min_w = start_x new_max_w = start_x + width #- self.padding_r new_min_h = start_y new_max_h = start_y + height for i,TA in enumerate(ta_sites): TApos = normalize(TA, start, end, new_min_w, new_max_w) if NORM_READS[i] == 0: continue read_h = normalize(NORM_READS[i], 0, max_read, new_min_h, new_max_h) # height of read line Y1 = start_y Y2 = start_y - (read_h-start_y) draw.line([(TApos, Y1), (TApos, Y2)], width=lwd, fill=(255,0,0))
[docs]def draw_ta_sites(draw, ta_sites, start_x=0, start_y=0, width=200, height=0, start=0, end=500, lwd=2): new_min_w = start_x new_max_w = start_x + width #- self.padding_r for i,TA in enumerate(ta_sites): TApos = normalize(TA, start, end, new_min_w, new_max_w) draw.line([(TApos, start_y+0), (TApos, start_y + height)], width=lwd, fill="black")
[docs]def draw_scale(draw, start_x, start_y, height, max_read): #print "scale", start_x, start_y, height MIDREAD = int(max_read/2.0) top_text_w, top_text_h = draw.textsize(str(max_read), font=font) draw.text((start_x, start_y), str(max_read), font=font, fill="black") draw.text((start_x, start_y + height/2.0), str(MIDREAD), font=font, fill="black") bottom_text_w, bottom_text_h = draw.textsize(str(MIDREAD), font=font) draw.text((start_x+bottom_text_w-(top_text_w/2.0), start_y+height), "0", font=font, fill="black")
[docs]def draw_features(draw, features, start, end, start_x, start_y, width, height): pass
[docs]def draw_genes(draw, GENES, orf2data, start, end, start_x, start_y, width, height): padding_h = 3 text_w, text_h = draw.textsize("RV0001", font=font) gene_h = height - text_h #print "GENES height", height #print "GENES text_h", text_h #print "GENES gene_h", gene_h triangle_size = 10 for gene in GENES: if gene not in orf2data: continue gene_start = orf2data[gene][0] gene_end = orf2data[gene][1] strand = orf2data[gene][2] name = orf2data[gene][3] new_min = start_x new_max = start_x + width norm_start = normalize(max(orf2data[gene][0], start), start, end, new_min, new_max) norm_end = normalize(min(orf2data[gene][1], end), start, end, new_min, new_max) #if True: # print gene, name, gene_start, gene_end, strand #, norm_start, norm_end if strand == "-": if gene_start >= start: draw.rectangle(((norm_start+triangle_size, start_y+5),(norm_end,start_y+gene_h-5)), fill="blue") #draw.polygon([(norm_start,start_y+gene_h/2.0),(norm_start, gene_h+20+5), (norm_start,ta_sites_finish_h +gene_h+10)], fill="blue" ) draw.polygon([(norm_start+triangle_size, start_y),(norm_start+triangle_size,start_y+gene_h), (norm_start,start_y+gene_h/2.0)], fill="blue" ) else: draw.rectangle(((norm_start, start_y+5),(norm_end,start_y+gene_h-5)), fill="blue") #draw.rectangle(((norm_start, start_y),(norm_end,start_y+gene_h)), fill="blue") else: if gene_end <= end: draw.rectangle(((norm_start, start_y+5),(norm_end-triangle_size, start_y+gene_h-5)), fill="blue") draw.polygon([(norm_end-triangle_size, start_y),(norm_end-triangle_size,start_y+gene_h), (norm_end,start_y+gene_h/2.0)], fill="blue" ) else: draw.rectangle(((norm_start, start_y+5),(norm_end, start_y+gene_h-5)), fill="blue") #draw.rectangle(((norm_start,start_y ),(norm_end, start_y+gene_h)), fill="blue") if name == "-": name = gene if not name.startswith("non-coding"): name_text_w, name_text_h = draw.textsize(name, font=font) if abs(norm_start-norm_end) >= name_text_w: draw.text(( norm_start + (abs(norm_start-norm_end) - name_text_w)/2.0 , start_y+gene_h+text_h), name, font=font, fill="black")
[docs]def get_dynamic_height(N): #Set rest of heights and widths read_h = 100 gene_h = 50 ta_h = 20 padding_h = 3 canvas_h = read_h*N + ta_h + gene_h + padding_h + padding_h + 80 return (canvas_h)
[docs]def draw_canvas(fulldata, hash, orf2data, labels=[], min_read=0, max_read=2000, start=1, end=500, canvas_h=-1, canvas_w=1000): temp_image = Image.new("RGB",(200, 200),"white") temp_draw = ImageDraw.Draw(temp_image) #Set main draw object N = len(fulldata) #Set Labels if not labels: labels= ["Read Counts"]*N #Get dynamic text widths #print "Labels:" max_label_w = 0 for L in labels: label_text_w, label_text_h = temp_draw.textsize(L, font=font) max_label_w = max(label_text_w, max_label_w) #print L scale_text_w, scale_text_h = temp_draw.textsize(str(max_read), font=font) #Set rest of heights and widths read_h = 100 gene_h = 50 ta_h = 20 padding_w = 3 padding_h = 3 read_w = canvas_w - (max_label_w + scale_text_w + padding_w + padding_w + 30) if canvas_h == -1: canvas_h = read_h*N + ta_h + gene_h + padding_h + padding_h + 80 image = Image.new("RGB",(canvas_w, canvas_h),"white") draw = ImageDraw.Draw(image) lwd = 2 GENES = [] TA_SITES = [] READS = [] nc_count = 1 for j,data in enumerate(fulldata): #print j temp = [] for pos,read in data: if start <= pos <= end: gene = hash.get(pos,"non-coding") if gene == "non-coding" and len(GENES) > 0 and not GENES[-1].startswith("non-coding"): gene+="_%d" % nc_count nc_count +=1 if j ==0: if gene not in GENES: GENES.append(gene) TA_SITES.append(pos) temp.append(read) READS.append(temp) #print READS #print "start", start #print "end", end #print len(READS), len(TA_SITES) #print "" #for rd in READS: # print rd #print "" start_x = max_label_w + padding_w + 21 draw.line([(start_x, 0), (start_x, canvas_h)], width=lwd, fill="black") start_y = 0 half = 100*0.5 start_x += 5 for j in range(len(fulldata)): start_y+=read_h+padding_h draw.text((10, start_y - half), labels[j], font=font, fill="black") draw_reads(draw, READS[j], TA_SITES, start_x, start_y, read_w, read_h, start, end, min_read, max_read) draw_scale(draw, start_x+read_w+padding_w+2, start_y-100+10, 70, max_read) start_y+=10 #start_x+=5 #TA sites draw.text((30, start_y),'TA Sites', font=font, fill="black") draw_ta_sites(draw, TA_SITES, start_x, start_y, read_w, ta_h, start, end) #Genes start_y += 50 draw.text((30, start_y+10),'Genes', font=font, fill="black") width = read_w draw_genes(draw, GENES, orf2data, start, end, start_x, start_y, width, gene_h) return(image)