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xmatchview.py
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#!/usr/bin/env python3
# xmatchview.py
# Visualizing genome synteny
# Rene L Warren 2005-2020
import sys
import os
import getopt
import re
import csv
# import Image ## https://stackoverflow.com/questions/17451711/typeerror-when-resizing-an-image-with-pil-in-python
from PIL import Image
from PIL import ImageDraw
from PIL import ImageFont
from PIL import ImageEnhance
from PIL import PSDraw
import subprocess
#---------------------------------------------
def checkFile(file):
print("Checking input %s" % file)
if not os.path.exists(file):
print("File %s" % file + " is not valid")
sys.exit(1)
else:
print("exists.")
#---------------------------------------------
def readGFF(file,scale):
feature = {}
(start,end) = (0,0)
with open(file) as fd:
rd = csv.reader(fd, delimiter="\t", quotechar='"')
for row in rd:
id = row[0]
start = float(int(row[3])/scale)
end = float(int(row[4])/scale)
print("__%s__ - __%s__ <<<<<" % (start,end))
color = row[9]
if color == None:
color = "yellow"
if id not in feature:
feature[id] = {}
if start not in feature[id]:
feature[id][start] = {}
if 'end' not in feature[id][start]:
feature[id][start]['end'] = ""
if 'color' not in feature[id][start]:
feature[id][start]['color'] = ""
feature[id][start]['end'] = end
feature[id][start]['color'] = color
print("INITIALIZED %s : %i,%i with %s" %(row[0],start,end,color))
return feature
#---------------------------------------------
def readPAF(paf_file,mismatch,block_length,reference,query,scale):
(nocdt,match)=({},{})
ctline = 0
xmatch_obj=open(paf_file, 'r')
for line in xmatch_obj:
### reverse matches qryname qrystart qryend orient hitname hitstart hitend match block
### 1 2 3 4 5 6 7 8
rev_regex = re.compile("(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\-\s+(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)")
rm = rev_regex.match(line)
###forward matches
fwd_regex = re.compile("(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\+\s+(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)")
fm = fwd_regex.match(line)
if rm != None:
ctline = 1
#print "GR: %s" % line
#print "REVERSE: %s %s %s %s %s %s %s %s" % (rm.group(1), rm.group(2), rm.group(3), rm.group(4), rm.group(5), rm.group(6), rm.group(7), rm.group(8))
alignLen = float(rm.group(6)) - float(rm.group(5)) + 1
percentMis = 100 * float(( alignLen - float(rm.group(7))) / alignLen )
#print "=== %.2f === %.2f ===" % (alignLen,percentMis)
#sys.exit(1)
(primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(str(rm.group(1)), float(rm.group(2)), float(rm.group(3)), str(rm.group(4)), float(rm.group(6)), float(rm.group(5))) ### order of 5 and 6 is important to plot alignments in different colors
if (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
else:
if primary_match in query and secondary_match in reference: #RLW after reading FASTA for each
startFirstMatchS = startFirstMatch + query[primary_match]['offset'] #RLW
endFirstMatchS = endFirstMatch + query[primary_match]['offset'] #RLW
startSecondMatchS = startSecondMatch + reference[secondary_match]['offset'] #RLW
endSecondMatchS = endSecondMatch + reference[secondary_match]['offset'] #RLW
####no autovivification in python
if primary_match not in nocdt:
nocdt[primary_match]={}
if secondary_match not in nocdt[primary_match]:
nocdt[primary_match][secondary_match]={}
if startFirstMatchS not in nocdt[primary_match][secondary_match]:
nocdt[primary_match][secondary_match][startFirstMatchS]={}
if endFirstMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]={}
if startSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]={}
if endSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]={}
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]=percentMis
if percentMis > mismatch:
continue #will not display alignment lines below threshold
elif (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
elif (endFirstMatch - startFirstMatch) < block_length:
continue #will skip smaller alignment
else:
if primary_match in query and secondary_match in reference:
startFirstMatch = (startFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
endFirstMatch = (endFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
startSecondMatch = (startSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
endSecondMatch = (endSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
print("%i-%i :: %i-%i" % (startFirstMatch,endFirstMatch,startSecondMatch,endSecondMatch))
if primary_match not in match:
match[primary_match]={}
if secondary_match not in match[primary_match]:
match[primary_match][secondary_match]={}
if startFirstMatch not in match[primary_match][secondary_match]:
match[primary_match][secondary_match][startFirstMatch]={}
if endFirstMatch not in match[primary_match][secondary_match][startFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch]={}
if startSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]={}
if endSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]={}
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]=percentMis
###forward matches
elif fm != None:
ctline = 1
#print "GF: %s" % line
#print "FORWARD: %s %s %s %s %s %s %s %s" % (fm.group(1), fm.group(2), fm.group(3), fm.group(4), fm.group(5), fm.group(6), fm.group(7), fm.group(8))
alignLen = float(fm.group(6)) - float(fm.group(5)) + 1
percentMis = 100 * float(( alignLen - float(fm.group(7))) / alignLen )
#percentMis2 = 100 * float((float(fm.group(8)) - float(fm.group(7))) / float(fm.group(8)))
#print "=== %.2f === %.2f === %.2f" % (alignLen,percentMis,percentMis2)
#sys.exit(1)
(primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(str(fm.group(1)), float(fm.group(2)), float(fm.group(3)), str(fm.group(4)), float(fm.group(5)), float(fm.group(6)))
if (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
else:
if primary_match in query and secondary_match in reference: #RLW after reading FASTA for each
startFirstMatchS = startFirstMatch + query[primary_match]['offset'] #RLW
endFirstMatchS = endFirstMatch + query[primary_match]['offset'] #RLW
startSecondMatchS = startSecondMatch + reference[secondary_match]['offset'] #RLW
endSecondMatchS = endSecondMatch + reference[secondary_match]['offset'] #RLW
####no autovivification in python
if primary_match not in nocdt:
nocdt[primary_match]={}
if secondary_match not in nocdt[primary_match]:
nocdt[primary_match][secondary_match]={}
if startFirstMatchS not in nocdt[primary_match][secondary_match]:
nocdt[primary_match][secondary_match][startFirstMatchS]={}
if endFirstMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]={}
if startSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]={}
if endSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]={}
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]=percentMis
if percentMis > mismatch:
continue #will not display alignment lines below threshold
elif (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
elif (endFirstMatch - startFirstMatch) < block_length:
continue #will skip smaller alignment
else:
if primary_match in query and secondary_match in reference:
startFirstMatch = (startFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
endFirstMatch = (endFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
startSecondMatch = (startSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
endSecondMatch = (endSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
print("%i-%i :: %i-%i" % (startFirstMatch,endFirstMatch,startSecondMatch,endSecondMatch))
if primary_match not in match:
match[primary_match]={}
if secondary_match not in match[primary_match]:
match[primary_match][secondary_match]={}
if startFirstMatch not in match[primary_match][secondary_match]:
match[primary_match][secondary_match][startFirstMatch]={}
if endFirstMatch not in match[primary_match][secondary_match][startFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch]={}
if startSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]={}
if endSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]={}
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]=percentMis
#else:
#print "NO RE:%s" % line
xmatch_obj.close()
if ctline == 0 :
print("There are no alignments to plot. Make sure your file %s is reporting alignments -- fatal." % paf_file)
sys.exit(1)
return nocdt, match
#---------------------------------------------
def readCrossMatch(crossmatch_file,mismatch,block_length,reference,query,scale):
(nocdt,match)=({},{})
ctline = 0
xmatch_obj=open(crossmatch_file, 'r')
for line in xmatch_obj:
# Query start end R Ref end start
# 10 8.70 0.00 0.00 JN039333.1_Picea_abies 440 462 (2149) C KT263970.1_Picea_sitchensis (1851) 524 502
# start end
# 16 4.55 0.00 0.00 JN039333.1_Picea_abies 484 505 (2106) KT263970.1_Picea_sitchensis 341 362 (2013)
###reverse matches s.i. qry
rev_regex = re.compile("(\s+)?\d+\s+(\S+)\s+\S+\s+\S+\s+(\S+)\s+(\S+)\s+(\S+)\s+\S+\s+C\s+(\S+)\s+\S+\s+(\S+)\s+(\S+)")
rm = rev_regex.match(line)
###forward matches
fwd_regex = re.compile("(\s+)?\d+\s+(\S+)\s+\S+\s+\S+\s+(\S+)\s+(\S+)\s+(\S+)\s+\S+\s+(\S+)\s+(\S+)\s+(\S+)\s+\S+")
fm = fwd_regex.match(line)
if rm != None and rm.group(3) != "0" and rm.group(6) != "0":
ctline = 1
#print "GR: %s" % line
#print "REVERSE: %s %s %s %s %s %s %s" % (rm.group(1), rm.group(2), rm.group(3), rm.group(4), rm.group(5), rm.group(6), rm.group(7))
#(percentMis, primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(float(rm.group(1)), rm.group(2), float(rm.group(3)), float(rm.group(4)), rm.group(5), float(rm.group(6)), float(rm.group(7)))
(percentMis, primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(float(rm.group(2)), rm.group(3), float(rm.group(4)), float(rm.group(5)), rm.group(6), float(rm.group(7)), float(rm.group(8)))### has to be in this order to plot reverse align in diff color
if (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
else:
if primary_match in query and secondary_match in reference: #RLW after reading FASTA for each
startFirstMatchS = startFirstMatch + query[primary_match]['offset'] #RLW
endFirstMatchS = endFirstMatch + query[primary_match]['offset'] #RLW
startSecondMatchS = startSecondMatch + reference[secondary_match]['offset'] #RLW
endSecondMatchS = endSecondMatch + reference[secondary_match]['offset'] #RLW
####no autovivification in python
if primary_match not in nocdt:
nocdt[primary_match]={}
if secondary_match not in nocdt[primary_match]:
nocdt[primary_match][secondary_match]={}
if startFirstMatchS not in nocdt[primary_match][secondary_match]:
nocdt[primary_match][secondary_match][startFirstMatchS]={}
if endFirstMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]={}
if startSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]={}
if endSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]={}
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]=percentMis
if percentMis > mismatch:
continue #will not display alignment lines below threshold
elif (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
elif (endFirstMatch - startFirstMatch) < block_length:
continue #will skip smaller alignment
else:
if primary_match in query and secondary_match in reference:
startFirstMatch = (startFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
endFirstMatch = (endFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
startSecondMatch = (startSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
endSecondMatch = (endSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
print("%i-%i :: %i-%i" % (startFirstMatch,endFirstMatch,startSecondMatch,endSecondMatch))
if primary_match not in match:
match[primary_match]={}
if secondary_match not in match[primary_match]:
match[primary_match][secondary_match]={}
if startFirstMatch not in match[primary_match][secondary_match]:
match[primary_match][secondary_match][startFirstMatch]={}
if endFirstMatch not in match[primary_match][secondary_match][startFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch]={}
if startSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]={}
if endSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]={}
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]=percentMis
###forward matches
elif fm != None and fm.group(3) != "0" and fm.group(6) != "0":
ctline = 1
#print "GF: %s" % line
#print "FORWARD: %s %s %s %s %s %s %s" % (fm.group(1), fm.group(2), fm.group(3), fm.group(4), fm.group(5), fm.group(6), fm.group(7))
# (percentMis, primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(float(fm.group(1)), fm.group(2), float(fm.group(3)), float(fm.group(4)), fm.group(5), float(fm.group(6)), float(fm.group(7)))
(percentMis, primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(float(fm.group(2)), fm.group(3), float(fm.group(4)), float(fm.group(5)), fm.group(6), float(fm.group(7)), float(fm.group(8)))
if (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
else:
if primary_match in query and secondary_match in reference: #RLW after reading FASTA for each
startFirstMatchS = startFirstMatch + query[primary_match]['offset'] #RLW
endFirstMatchS = endFirstMatch + query[primary_match]['offset'] #RLW
startSecondMatchS = startSecondMatch + reference[secondary_match]['offset'] #RLW
endSecondMatchS = endSecondMatch + reference[secondary_match]['offset'] #RLW
####no autovivification in python
if primary_match not in nocdt:
nocdt[primary_match]={}
if secondary_match not in nocdt[primary_match]:
nocdt[primary_match][secondary_match]={}
if startFirstMatchS not in nocdt[primary_match][secondary_match]:
nocdt[primary_match][secondary_match][startFirstMatchS]={}
if endFirstMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]={}
if startSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]={}
if endSecondMatchS not in nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS]:
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]={}
nocdt[primary_match][secondary_match][startFirstMatchS][endFirstMatchS][startSecondMatchS][endSecondMatchS]=percentMis
if percentMis > mismatch:
continue #will not display alignment lines below threshold
elif (primary_match == secondary_match) and (startSecondMatch == startFirstMatch) and (endSecondMatch == endFirstMatch):
print("Exact match over full coordinates, ignoring...")
elif (endFirstMatch - startFirstMatch) < block_length:
continue #will skip smaller alignment
else:
if primary_match in query and secondary_match in reference:
startFirstMatch = (startFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
endFirstMatch = (endFirstMatch/scale) + query[primary_match]['offset_len'] #RLW
startSecondMatch = (startSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
endSecondMatch = (endSecondMatch/scale) + reference[secondary_match]['offset_len'] #RLW
print("%i-%i :: %i-%i" % (startFirstMatch,endFirstMatch,startSecondMatch,endSecondMatch))
if primary_match not in match:
match[primary_match]={}
if secondary_match not in match[primary_match]:
match[primary_match][secondary_match]={}
if startFirstMatch not in match[primary_match][secondary_match]:
match[primary_match][secondary_match][startFirstMatch]={}
if endFirstMatch not in match[primary_match][secondary_match][startFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch]={}
if startSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]={}
if endSecondMatch not in match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch]:
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]={}
match[primary_match][secondary_match][startFirstMatch][endFirstMatch][startSecondMatch][endSecondMatch]=percentMis
#else:
#print "NO RE:%s" % line
xmatch_obj.close()
if ctline == 0 :
print("There are no alignments to plot. Make sure your file %s is reporting alignments -- fatal." % crossmatch_file)
sys.exit(1)
return nocdt, match
#---------------------------------------------
def generateCoords(nocdt, size, leap, protein):
freq={}
pos_range=list(range(0,size,leap))
for pos in pos_range:
print("%i out of %i" % (pos,size))
for query in nocdt:
for comparison in nocdt[query]:
start1_dict=list(nocdt[query][comparison].keys())
start1_dict.sort()
for start1 in start1_dict:
end1_dict=list(nocdt[query][comparison][start1].keys())
end1_dict.sort()
for end1 in end1_dict:
start2_dict=list(nocdt[query][comparison][start1][end1].keys())
start2_dict.sort()
for start2 in start2_dict:
end2_dict=list(nocdt[query][comparison][start1][end1][start2].keys())
end2_dict.sort()
for end2 in end2_dict:
(ss,ee) = (start2,end2)
if protein:
size_ref = end2 - start2
buffer = ((size_ref - (size_ref/3)) / 2)
ss = start2 + buffer
ee = end2 - buffer
if((pos >= ss and pos <= ee) or (pos >= ee and pos <= ss)):
current_mismatch=float(nocdt[query][comparison][start1][end1][start2][end2])
if pos not in freq:
freq[pos]={}
if current_mismatch not in freq[pos]:
freq[pos][current_mismatch]=int(0)
freq[pos][current_mismatch]=freq[pos][current_mismatch]+1
return freq
#---------------------------------------------
def findOccurences(s, ch):
return [i for i, letter in enumerate(s) if letter == ch]
#---------------------------------------------
def readFasta(file, scale):
(head_match, previous_contig,seq_length) = (None,None,0)
L1={}
order=[]#RLW
npos={} #RLW
zpos={}
tot_length = 0 #RLW
file_obj = open(file, 'r')
for line in file_obj:
head_match_regex = re.compile('>(\S+)')
head_match = head_match_regex.match(line)
if head_match != None:
if (head_match != previous_contig and previous_contig != None):
(seq_length, scale)=(int(seq_length), int(scale))
if previous_contig not in L1:#RLW
L1[previous_contig]={} #RLW
L1[previous_contig]['scaled_len'] = float(seq_length/scale) #RLW
L1[previous_contig]['offset_len'] = float(tot_length/scale) #RLW first ID will be offset at 0 as it should
L1[previous_contig]['offset'] = tot_length #RLW
L1[previous_contig]['npos'] = npos
L1[previous_contig]['zpos'] = zpos
print("NPOS: (Ns or Zs only tracked on 1-line sequences)")
print(npos)
order.append(previous_contig) #RLW
print("%s length = %i bp, scaled to %.0f pixels" % (previous_contig,seq_length,L1[previous_contig]['scaled_len'])) #RLW
tot_length += seq_length #RLW
seq_length = 0 #resets the sequence length
previous_contig = head_match.group(1)
else:
seq_subset_regex = re.compile('(.*)', re.I)
seq_subset = seq_subset_regex.match(line)
if seq_subset != None:
seq_length += len(seq_subset.group(1))
npos=findOccurences(seq_subset.group(1).upper(), "N")
zpos=findOccurences(seq_subset.group(1).upper(), "Z")
(seq_length, scale)=(int(seq_length), int(scale))
if previous_contig not in L1: #RLW
L1[previous_contig]={} #RLW
L1[previous_contig]['scaled_len'] = float(seq_length/scale) #RLW
L1[previous_contig]['offset_len'] = float(tot_length/scale) #RLW
L1[previous_contig]['offset'] = tot_length #RLW
L1[previous_contig]['npos'] = npos
L1[previous_contig]['zpos'] = zpos
print("NPOS: (Ns or Zs only tracked on 1-line sequences)")
print(npos)
order.append(previous_contig) #RLW
print("%s length = %i bp, scaled to %.0f pixels" % (previous_contig,seq_length,L1[previous_contig]['scaled_len'])) #RLW
tot_length += seq_length #RLW
file_obj.close()
scaled_tot_len = float(tot_length/scale) #RLW
print("Total length = %i bp, scaled to : %.0f pixels " % (tot_length,scaled_tot_len)) #RLW
return (order, L1, tot_length) #RLW tot_length
#---------------------------------------------
def initColor(alpha):
color={}
#allocate colors
color["white"] = (255,255,255,255)
color["black"] = (0,0,0,255)
color["swamp"] = (150,150,30,255)
color["blue"] = (0,102,204,255)
color["yellow"] = (255,255,0,255)
color["cyan"] = (0,255,255,255)
color["purple"] = (255,0,255,alpha)
color["green"] = (100,250,25,255)
color["lime"] = (57,255,20,255)
color["red"] = (250,25,75,255)
color["sarin"] = (255,66,0,255)
color["forest"] = (25,175,0,255)
color["dirtyred"] = (200,0,120,255)
color["navy"] = (0,0,150,alpha)
color["dirtyyellow"] = (200,200,75,255)
color["grey"] = (153,153,153,255)
color["lightgrey"] = (220,220,220,355)
color["salmon"] = (255,153,153,alpha)
color["lightblue"] = (153,204,255,alpha)
color["orange"] = (255,153,51,255)
color["beige"] = (222,184,135,255)
return color
#---------------------------------------------
def initGraph():
data={}
#default data points
data['width']=2400
data['height']=1200
data['ref_y']=300 #250
data['mis_bar']=50
data['query_y']=70
data['x']=50
data['xlabel']=110
data['bar_thick']=20
data['query_thick']=15
data['reference_thick']=15
data['x_legend']=600
data['y_legend']=750
data['x_legend_picto']=100
data['tick_up']=25
data['tick_down']=40
return data
#---------------------------------------------
def drawRectangle(draw,start,end,y,thickness,bar_color,text,font,text_color):
draw.rectangle((start,y,end,y+thickness), bar_color)
#---------------------------------------------
def drawRefText(draw,start,end,y,thickness,bar_color,text,font,text_color):
#draw.text((start-80, y-2), text, font=font, fill=text_color)###position of SEQUENCE label
draw.text((start+2, y-25), text, font=font, fill=text_color)###position of SEQUENCE label
draw.line((start,y-21,start,y-1),text_color,width=1)
draw.line((end,y-21,end,y-1),text_color,width=1)
#---------------------------------------------
def drawQryText(draw,start,end,y,thickness,bar_color,text,font,text_color):
#draw.text((start-80, y-2), text, font=font, fill=text_color)###position of SEQUENCE label
draw.text((start+2, y+17), text, font=font, fill=text_color)###position of SEQUENCE label
draw.line((start,y+thickness+1,start,y+thickness+20),text_color,width=1)
draw.line((end,y+thickness+1,end,y+thickness+20),text_color,width=1)
#---------------------------------------------
def plotFrequency(freq,size,scale,draw,color,data,leap):
pos_range=list(range(0,size,leap))
for pos in pos_range:
if pos in freq:
freq_list=freq[pos]
previous=data['mis_bar']
identity_range=list(range(99,-1,-1))## RESTRICT SI AXIS was 9
for id in identity_range:
cumul=int(0)
for freq_keys in freq_list:
if id >= freq_keys:
cumul += freq_list[freq_keys]
if cumul<1:
color_now="white"
elif cumul==1:
color_now="blue"
elif cumul==2:
color_now="cyan"
elif cumul==3:
color_now="green"
elif cumul==4:
color_now="orange"
elif cumul>=5:
color_now="dirtyred"
#elif cumul==6:
# color_now="salmon"
#elif cumul==7:
# color_now="orange"
#elif cumul>=8:
# color_now="yellow"
extension=((200-(2*id))+data['mis_bar']) #RESTRICT SI AXIS y was 20
compressed=(pos/scale)+data['x'] #x
if color_now != "white":
#print "%i, %i, %i, %i %s" % (compressed,previous,compressed,extension,color_now)
draw.line((compressed,previous,compressed,extension),color[color_now])
previous = extension
#---------------------------------------------
def drawRelationship(reference_list, order_ref, query_list, order_qry, match_list, scale, mismatch, block_length, alignment_file, freq, reflength, leap, format, formatdict, protein, alpha, refgff, qrygff, qrylength, fontpath):
scaled_reflength=int(reflength/scale)
###Initialize new graph
data=initGraph()
###Get colors
color=initColor(alpha)
###Set Font
arialfont = fontpath + "/arial.ttf"
pilfont = fontpath + "/helvR14.pil"
#default all font sizes to default (it is quite small, you must provide a valid path for best results)
font_18=ImageFont.load_default()
font_20=ImageFont.load_default()
fontb_20=ImageFont.load_default()
fontbi_20=ImageFont.load_default()
fontb_22=ImageFont.load_default()
font_24=ImageFont.load_default()
fontb_24=ImageFont.load_default()
if os.path.exists(arialfont): ### Will check for truetype first, they look better
###Set Font (truetype)
font_18=ImageFont.truetype(fontpath + "/arial.ttf",18)
font_20=ImageFont.truetype(fontpath + "/arial.ttf",20)
fontb_20=ImageFont.truetype(fontpath + "/arialbd.ttf",20)
fontbi_20=ImageFont.truetype(fontpath + "/arialbi.ttf",20)
fontb_22=ImageFont.truetype(fontpath + "/arialbd.ttf",22)
font_24=ImageFont.truetype(fontpath + "/arial.ttf",24)
fontb_24=ImageFont.truetype(fontpath + "/arialbd.ttf",24)
elif os.path.exists(pilfont): ### Will settle for PIL font, if ttf do not exist. Otherwise, sticking with default.
###Set font (pil) (sizes are limited, made to be compatible with TT fonts)
font_18=ImageFont.load_path(fontpath + "/helvR14.pil")
font_20=ImageFont.load_path(fontpath + "/helvR18.pil")
fontb_20=ImageFont.load_path(fontpath + "/helvB18.pil")
fontbi_20=ImageFont.load_path(fontpath + "/helvBO18.pil")
fontb_22=ImageFont.load_path(fontpath + "/helvB24.pil")
font_24=ImageFont.load_path(fontpath + "/helvR24.pil")
fontb_24=ImageFont.load_path(fontpath + "/helvB24.pil")
###Define Image
back = Image.new("RGBA", (data['width'],data['height']),(0,0,0,0))
bdraw = ImageDraw.Draw(back)
poly = Image.new("RGBA", (data['width'],data['height']))
draw = ImageDraw.Draw(poly)
###Draw Legend
date=subprocess.getstatusoutput("date")
###Picto Legend
bdraw.text((data['x_legend_picto']+280,data['y_legend']), "Legend", font=fontb_24, fill=color['black'])
y_legend = data['y_legend']+30
bdraw.text((data['x_legend_picto'],y_legend), "Frequency Repeated", font=fontbi_20, fill=color['black'])
####
bdraw.text((data['x_legend'],y_legend), "Mismatch threshold : %i %%" % mismatch, font=font_20, fill=color['black'])
bdraw.text((data['x_legend'],y_legend+20), "Minimum block length : %i bp" % block_length, font=font_20, fill=color['black'])
bdraw.text((data['x_legend'],y_legend+40), "Scale (pixel:bp) 1:%i" % scale, font=font_20, fill=color['black'])
#bdraw.text((data['x_legend'],y_legend+60), "%s" % date[1], font=font_20, fill=color['black'])
####
y_legend+=25
bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['blue'])
bdraw.text((data['x_legend_picto']+25,y_legend), "Single copy", font=font_20, fill=color['black'])
y_legend+=25
bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['cyan'])
bdraw.text((data['x_legend_picto']+25,y_legend), "2X", font=font_20, fill=color['black'])
y_legend+=25
bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['green'])
bdraw.text((data['x_legend_picto']+25,y_legend), "3X", font=font_20, fill=color['black'])
y_legend+=25
bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['orange'])
bdraw.text((data['x_legend_picto']+25,y_legend), "4X", font=font_20, fill=color['black'])
y_legend+=25
bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['dirtyred'])
bdraw.text((data['x_legend_picto']+25,y_legend), "5X and over", font=font_20, fill=color['black'])
y_legend+=25
#bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['salmon'])
#bdraw.text((data['x_legend_picto']+25,y_legend), "6X", font=font_20, fill=color['black'])
#y_legend+=25
#bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['orange'])
#bdraw.text((data['x_legend_picto']+25,y_legend), "7X", font=font_20, fill=color['black'])
#y_legend+=25
#bdraw.rectangle((data['x_legend_picto'],y_legend,data['x_legend_picto']+20,y_legend+20), outline=color['black'], fill=color['yellow'])
#bdraw.text((data['x_legend_picto']+25,y_legend), "8X and over", font=font_20, fill=color['black'])
y_legend+=40
bdraw.text((data['x_legend_picto'],y_legend), "Collinear Blocks", font=fontbi_20, fill=color['black'])
y_legend+=30
bdraw.polygon((data['x_legend_picto']-5,y_legend,data['x_legend_picto'],y_legend+25,data['x_legend_picto']+25,y_legend+25,data['x_legend_picto']+20,y_legend), outline=color['navy'], fill=color['lightblue'])
bdraw.text((data['x_legend_picto']+30,y_legend), "Direct", font=font_20, fill=color['black'])
y_legend+=30
bdraw.polygon((data['x_legend_picto']-5,y_legend,data['x_legend_picto']+25,y_legend+25,data['x_legend_picto']-5,y_legend+25,data['x_legend_picto']+25,y_legend), outline=color['purple'], fill=color['salmon'])
bdraw.text((data['x_legend_picto']+30,y_legend), "Inverted", font=font_20, fill=color['black'])
y_legend+=40
bdraw.text((data['x_legend_picto'],y_legend), "Other", font=fontbi_20, fill=color['black'])
y_legend+=30
bdraw.rectangle((data['x_legend_picto']-5,y_legend+5,data['x_legend_picto']+25,y_legend+7), fill=color['red'])
bdraw.text((data['x_legend_picto']+30,y_legend), "Mismatch threshold", font=font_20, fill=color['black'])
y_legend+=30
bdraw.rectangle((data['x_legend_picto']-5,y_legend,data['x_legend_picto']+25,y_legend+(data['reference_thick']/2)), outline=color['black'], fill=color['yellow'])
bdraw.text((data['x_legend_picto']+30,y_legend), "Sequence features", font=font_20, fill=color['black'])
y_legend+=30
bdraw.rectangle((data['x_legend_picto']+5,y_legend,data['x_legend_picto']+10,y_legend+data['reference_thick']), outline=color['red'], fill=color['red'])
bdraw.text((data['x_legend_picto']+30,y_legend), "Ambiguous bases (Ns)", font=font_20, fill=color['black'])
y_legend+=30
####Draw Reference
for ref in order_ref: #RLW
scaled_offset_len = 0 #RLW
if ref in reference_list: #RLW
scaled_offset_len = reference_list[ref]['offset_len'] #RLW
init_coord=int(data['x']+scaled_offset_len) #RLW
last_coord=int(data['x']+scaled_offset_len+reference_list[ref]['scaled_len']) #RLW
### draw top rectangle for REFERENCE
drawRectangle(bdraw, init_coord, last_coord,data['ref_y'],data['reference_thick'],color['black'],ref,fontb_20,color['black'])
drawRefText(bdraw, init_coord, last_coord,data['ref_y'],data['reference_thick'],color['black'],ref,fontb_20,color['black'])
###DRAW histo
x_range=list(range(data['x'], last_coord, 100))
### draw kbp scale
if reflength >= 10000:
for position in x_range:
base_number=int(((position-data['x'])*scale)/1000)
bdraw.rectangle((position,data['tick_up'],position+2,data['tick_down']),color['black'])
bdraw.text((position-5, data['tick_up']-25), "%i" % base_number, font=font_20, fill=color['black'])
else:
for position in x_range:
base_number=(position-data['x']) * scale
base_number=float(base_number)
base_number=base_number/1000
bdraw.rectangle((position,data['tick_up'],position+2,data['tick_down']),color['black'])
#print "%i %i %i >>> %.2f <<< %i,%i" % (data['x'],position,scale,base_number,data['x_legend_picto'],position)
bdraw.text((position-5, data['tick_up']-25), "%.1f" % base_number, font=font_24, fill=color['black'])
bdraw.text((data['x']+scaled_reflength+60,data['tick_up']-25), "kbp", font=fontb_24, fill=color['black'])
###Mismatch Axis
#identity=int(0)
identity = int(0) ### RESTRICT SI AXIS was 90
grid_range=list(range(data['mis_bar'], data['ref_y']-30, 20))
###Draw grid
for grid in grid_range:
bdraw.rectangle((data['x'],grid,data['x']+scaled_reflength+5,grid+2),color['lightgrey'])
bdraw.text((data['x']+scaled_reflength+10, grid-7), "%i " % identity, font=font_18, fill=color['black'])
identity += 10 ### RESTRICT SI AXIS was 1
###Draw grid metric
bdraw.text((data['x']+scaled_reflength+60, 150), "% Identity", font=font_18, fill=color['black'])
###Draw Repeat Frequency
plotFrequency(freq,reflength,scale,bdraw,color,data,leap)
###Draw Threshold
threshold_line= data['mis_bar'] + (200-(2*mismatch))
draw.rectangle((data['x'],threshold_line,data['x']+scaled_reflength+5,threshold_line+2), color['red'])
###Draw Query & Collinear blocks
(current_position, LCB)=(data['x'], 10)
####Draw Query (only if not in reference list)
decay = 350
for qry in order_qry: #RLW
scaled_offset_len = 0 #RLW
if qry in query_list: #RLW
scaled_offset_len = query_list[qry]['offset_len'] #RLW
init_coord=int(data['x']+scaled_offset_len) #RLW
last_coord=int(data['x']+scaled_offset_len+query_list[qry]['scaled_len']) #RLW
### draw bottom rectangle for QUERY
if qry not in order_ref: ### only draw if query not same as ref ##### REMOVE WHEN THEY HAVE SAME NAMES
drawRectangle(bdraw, init_coord, last_coord,data['ref_y']+decay,data['query_thick'],color['black'],qry,fontb_20,color['black'])
drawQryText(bdraw, init_coord, last_coord,data['ref_y']+decay,data['query_thick'],color['black'],qry,fontb_20,color['black'])
plotflag = 0
###Draw blocks and relationships
for match in match_list:
allhit=match_list[match]
for hit in allhit:
start1_list=allhit[hit]
stop=current_position + query_list[match]['offset_len']
#if match != hit:
# drawRectangle(bdraw,current_position,stop,data['ref_y']+decay,data['query_thick'],color['black'], hit, fontb_20, color['black'])
s1_list_sort=list(start1_list.keys())
s1_list_sort.sort()
for start1 in s1_list_sort:
end1_list=start1_list[start1]
e1_list_sort=list(end1_list.keys())
e1_list_sort.sort()
for end1 in e1_list_sort:
start2_list=end1_list[end1]
s2_list_sort=list(start2_list.keys())
s2_list_sort.sort()
for start2 in s2_list_sort:
end2_list=start2_list[start2]
e2_list_sort=list(end2_list.keys())
e2_list_sort.sort()
for end2 in e2_list_sort:
if start2 > end2:
outline_color="purple"
fill_color="salmon"
else:
outline_color="navy"
fill_color="lightblue"
###draw ORF on upper
size_qry = end1 - start1
size_ref = end2 - start2
buf_ref = ((size_ref - (size_ref/3)) / 2)
buf_qry = ((size_qry - (size_qry/3)) / 2)
ss1 = start1 + buf_qry
ee1 = end1 - buf_qry
ss2 = start2 + buf_ref
ee2 = end2 - buf_ref
print("%s (%i-%i) hits %s :: mismatch %.2f target(%i) block %i target (%i) " % (match,start1,end1,hit,end2_list[end2],mismatch,size_ref,block_length))
if match == hit:### COMPARE 1 SEQUENCE AGAINST ITSELF
print("SAME QUERY AND HIT NAME...WILL COMPARE AGAINST ITSELF");
if start1 <= start2:
repeat_size = start2 - start1
size_chunk = int(decay * repeat_size / scaled_reflength)
print("%i %i %i" % (size_chunk, repeat_size, scaled_reflength))
size_chunk += 50
if protein:
if end2_list[end2] <= mismatch: ###does it pass the mismatch cutoff?
ss1 = int(ss1)
ss2 = int(ss2)
bdraw.rectangle((data['x']+ss1,data['ref_y']+data['reference_thick']+7,data['x']+ee1,data['ref_y']+data['reference_thick']+17), outline=color["black"], fill=color["red"])###REF1
bdraw.rectangle((data['x']+ss2,data['ref_y']+data['reference_thick']+7,data['x']+ee2,data['ref_y']+data['reference_thick']+17), outline=color["black"], fill=color["red"])###REF2
draw.arc((data['x']+ss1,data['ref_y']+data['reference_thick']+15-size_chunk,data['x']+ss2,data['ref_y']+data['reference_thick']+17+size_chunk),360,180, color[outline_color])
back.paste(poly, mask=poly)
del draw
poly = Image.new("RGBA", (data['width'],data['height']))
draw = ImageDraw.Draw(poly)
plotflag = 1
else:
if end2_list[end2] <= mismatch: ###does it pass the mismatch cutoff?
start1 = int(start1)
start2 = int(start2)
draw.rectangle((data['x']+start1,data['ref_y'],data['x']+end1,data['ref_y']+data['reference_thick']), outline=color[outline_color], fill=color[fill_color])###REF LEFT REPEAT COLINEAR BLOCKS
draw.rectangle((data['x']+start2,data['ref_y'],data['x']+end2,data['ref_y']+data['reference_thick']), outline=color[outline_color], fill=color[fill_color])###REF RIGHT REPEAT COLINEAR BLOCKS
draw.arc((data['x']+start1,data['ref_y']+data['reference_thick']-size_chunk,data['x']+start2,data['ref_y']+data['reference_thick']+size_chunk),360,180, color[outline_color])###DRAW ARC AT REPEAT EDGE ONLY
back.paste(poly, mask=poly)
del draw
poly = Image.new("RGBA", (data['width'],data['height']))
draw = ImageDraw.Draw(poly)
plotflag = 1
else : #COMPARE
if protein:
if end2_list[end2] <= mismatch: ###does it pass the mismatch cutoff?
draw.polygon((data['x']+ss1,data['ref_y']+data['reference_thick']+17,data['x']+ss2,data['ref_y']+decay-17,data['x']+ee2,data['ref_y']+decay-17,data['x']+ee1,data['ref_y']+data['reference_thick']+17), outline=color[outline_color], fill=color[fill_color])
draw.rectangle((data['x']+ss1,data['ref_y']+data['reference_thick']+7,data['x']+ee1,data['ref_y']+data['reference_thick']+17), outline=color["black"], fill=color["red"]) ###REF
draw.rectangle((data['x']+ss2,data['ref_y']+decay-17,data['x']+ee2,data['ref_y']+decay-7), outline=color["black"], fill=color["red"])###QRY
back.paste(poly, mask=poly)
del draw
poly = Image.new("RGBA", (data['width'],data['height']))
draw = ImageDraw.Draw(poly)
plotflag = 1
else:
if end2_list[end2] <= mismatch: ###does it pass the mismatch cutoff?
draw.polygon((data['x']+start2,data['ref_y']+data['reference_thick'],data['x']+start1,data['ref_y']+decay,data['x']+end1,data['ref_y']+decay,data['x']+end2,data['ref_y']+data['reference_thick']), outline=color[outline_color], fill=color[fill_color])
draw.rectangle((data['x']+start2,data['ref_y'],data['x']+end2,data['ref_y']+data['reference_thick']), outline=color[outline_color], fill=color[fill_color]) ###REF COLINEAR BLOCKS
draw.rectangle((data['x']+start1,data['ref_y']+decay,data['x']+end1,data['ref_y']+decay+data['reference_thick']), outline=color[outline_color], fill=color[fill_color])###QRY COLINEAR BLOCKS
back.paste(poly, mask=poly)
del draw
poly = Image.new("RGBA", (data['width'],data['height']))
draw = ImageDraw.Draw(poly)
plotflag = 1
#if plotflag==0:
# print "It looks like there is nothing to plot, try increasing -m 99 -- FATAL"
# sys.exit(1)
#enhancer = ImageEnhance.Sharpness(im)
#for i in range(8):
# factor = i / 4.0
# enhancer.enhance(factor).show("Sharpness %f" % factor)
### draw features on reference
for ref in order_ref:
scaled_offset_len = 0 #RLW
if ref in reference_list: #RLW
scaled_offset_len = reference_list[ref]['offset_len'] #RLW
if ref in refgff:
for scaledexstart in refgff[ref]:
exstart = data['x'] + scaledexstart + scaled_offset_len
exend = data['x'] + refgff[ref][scaledexstart]['end'] + scaled_offset_len
draw.rectangle((exstart,data['ref_y'],exend,data['ref_y']+(data['reference_thick']/2)),outline=refgff[ref][scaledexstart]['color'], fill=refgff[ref][scaledexstart]['color'])###features/exons
if 'npos' in reference_list[ref]:
for nstart in reference_list[ref]['npos']: ### draw Ns
nstart = data['x'] + (nstart/scale) + scaled_offset_len
draw.line((nstart,data['ref_y']+1,nstart,data['ref_y']+data['reference_thick']-1),color['red'],width=1)###reference
if 'zpos' in reference_list[ref]: ### draw Zs
for nstart in reference_list[ref]['zpos']:
nstart = data['x'] + (nstart/scale) + scaled_offset_len
draw.line((nstart,data['ref_y']+1,nstart,data['ref_y']+data['reference_thick']-1),color['lime'],width=1)
### draw features on query
for qry in order_qry:
if qry not in order_ref: ### only draw if query not same as ref
scaled_offset_len = 0 #RLW
if qry in query_list: #RLW
scaled_offset_len = query_list[qry]['offset_len'] #RLW
if qry in qrygff:
for scaledexstart in qrygff[qry]:
exstart = data['x'] + scaledexstart + scaled_offset_len
exend = data['x'] + qrygff[qry][scaledexstart]['end'] + scaled_offset_len
draw.rectangle((exstart,data['ref_y']+decay+(data['reference_thick']/2)+1,exend,data['ref_y']+decay+data['reference_thick']),outline=qrygff[qry][scaledexstart]['color'], fill=qrygff[qry][scaledexstart]['color'])###features/exons
if 'npos' in query_list[qry]: ### draw Ns
for nstart in query_list[qry]['npos']:
nstart = data['x'] + (nstart/scale) + scaled_offset_len
draw.line((nstart,data['ref_y']+decay+1,nstart,data['ref_y']+decay+data['reference_thick']-1),color['red'],width=1)
if 'zpos' in query_list[qry]: ### draw Zs
for nstart in query_list[qry]['zpos']:
nstart = data['x'] + (nstart/scale) + scaled_offset_len
draw.line((nstart,data['ref_y']+decay+1,nstart,data['ref_y']+decay+data['reference_thick']-1),color['lime'],width=1)
#### FINAL IMAGE PROCESSING
back.paste(poly, mask=poly)
file = "xmv-" + alignment_file + "_m" + str(mismatch) + "_b" + str(block_length) + "_r" + str(leap) + "_c" + str(scale) + "." + format
print("Saving %s..." % file)
back.save(open(file, 'wb'), formatdict[format])
print("done.")
return file
#---------------------------------------------
def main():
opts, args = getopt.getopt(sys.argv[1:], "x:s:q:m:r:c:b:f:p:e:y:a:")
(ref_gff_file, qry_gff_file, alignment_file, reference_file, query_file, format, fontpath)=(None,None,None,None,None,"png","")
(mismatch, block_length, scale, leap, protein, alpha)=(0,0,0,0,0,255)
(reference, reflength)=([],[])
formatdict = {'png':'PNG','gif':'GIF','tiff':'TIFF','jpeg':'JPEG'}
for o, v in opts:
if o == "-x":
alignment_file=str(v)
if o == "-s":
reference_file=str(v)
if o == "-q":
query_file=str(v)
if o == "-m":
mismatch=int(v)
if o == "-b":
block_length=int(v)
if o == "-c":
scale=int(v)
if o == "-r":
leap=int(v)
if o == "-f":
format=str(v)
if o == "-e":
ref_gff_file=str(v)
if o == "-y":
qry_gff_file=str(v)