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fixed circulize.py for compatibility with python 3 #61

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fixed circulize.py for compatibility with python 3 #61

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80 changes: 40 additions & 40 deletions misc_scripts/circules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def write_clipped(seq_header, seq_seq, start, end, prefix):
l = str(end - start)

#writing out clipped sequence
print "clip points: %i - %i - length: %s -> writing sequence to '%s.circular.%s.fasta'\n" %(start, end, l, prefix, l)
print("clip points: %i - %i - length: %s -> writing sequence to '%s.circular.%s.fasta'\n" %(start, end, l, prefix, l))
sequence = seq_seq[start:end]
out = open(prefix+'.circular.'+l+'.fasta','w')
out.write(">%s_ciruclar_%s\n%s\n" %(seq_header, str(l), sequence))
Expand All @@ -43,11 +43,11 @@ def write_clipped(seq_header, seq_seq, start, end, prefix):

def roll_over(seq_seq, new_start, prefix):

print "new start coordinate: %s -> writing sequence to '%s.roll.%s.fasta'\n" %(new_start, prefix, new_start)
print("new start coordinate: %s -> writing sequence to '%s.roll.%s.fasta'\n" %(new_start, prefix, new_start))
sequence = seq_seq[new_start-1:]+seq_seq[:new_start-1]
out = open(prefix+'.rolled.'+str(new_start)+'.fasta', 'w')
out.write(">%s_s%s_l%s\n%s\n" %(prefix, new_start, len(sequence), sequence))
out.close()
out.close()

parser = argparse.ArgumentParser(description=DESCRIPTION, prog='circules.py',
formatter_class=argparse.RawDescriptionHelpFormatter,
Expand Down Expand Up @@ -89,10 +89,10 @@ def roll_over(seq_seq, new_start, prefix):
args = parser.parse_args()

if len(sys.argv) < 2: #if the script is called without any arguments display the usage
print
print "%s\n" %DESCRIPTION
print()
print("%s\n" %DESCRIPTION)
parser.print_usage()
print
print()
sys.exit(1)

if '-' in args.kmer:
Expand All @@ -113,37 +113,37 @@ def roll_over(seq_seq, new_start, prefix):
seqs[current]+=l.strip().upper()

if len(seqs) > 1:
print "\nThe file '%s' contains %i sequences. The circules script is currently designed to only handle a single fasta sequence at a time - Sorry!\n" %(args.fasta, len(seqs))
print("\nThe file '%s' contains %i sequences. The circules script is currently designed to only handle a single fasta sequence at a time - Sorry!\n" %(args.fasta, len(seqs)))
sys.exit()

print "%s\n" %DESCRIPTION
print("%s\n" %DESCRIPTION)

print "\n###########################\n\nProcessing sequence of length %s" %len(seqs[seqs.keys()[0]])
print("\n###########################\n\nProcessing sequence of length %s" %len(seqs[list(seqs.keys())[0]]))

if args.newstart_roll:
print "\n####################\n## Result output ##\n####################\n"
print "\n'Rolling' circular sequence to new start coordinate .."
roll_over(seqs[seqs.keys()[0]], args.newstart_roll, args.prefix)
print ""
print("\n####################\n## Result output ##\n####################\n")
print("\n'Rolling' circular sequence to new start coordinate ..")
roll_over(seqs[list(seqs.keys())[0]], args.newstart_roll, args.prefix)
print("")
sys.exit()


if args.extract_by_coordinates:
if not ',' in args.extract_by_coordinates:
print "Expecting clipping coordinates delimited by comma (','), e.g. '-c 50,1567'"
print("Expecting clipping coordinates delimited by comma (','), e.g. '-c 50,1567'")
sys.exit()
print "\n####################\n## Result output ##\n####################\n"
print "\nExtracting sequence by coordinates .."
print("\n####################\n## Result output ##\n####################\n")
print("\nExtracting sequence by coordinates ..")
clips = args.extract_by_coordinates.split(",")
write_clipped(seqs.keys()[0], seqs[seqs.keys()[0]], clips[0], clips[1], args.prefix)
print ""
write_clipped(list(seqs.keys())[0], seqs[list(seqs.keys())[0]], clips[0], clips[1], args.prefix)
print("")
sys.exit()

for k in range(kmers[0],kmers[1],kmers[2]):
clips = {}
repeats = {}
for s in seqs:
print "\nCollecting %s-mers .." %k,
print("\nCollecting %s-mers .." %k, end=' ')
i=0
while i <= (len(seqs[s])-k):
kmer = str(seqs[s][i:i+k])
Expand All @@ -158,7 +158,7 @@ def roll_over(seq_seq, new_start, prefix):
kmer = str(seqs[s][i:i+k])
skip = 0
# print "%i %s" %(i, kmer)
for pos in reversed(range(len(kmer))):
for pos in reversed(list(range(len(kmer)))):
# print pos,kmer[pos]
if not kmer[pos] in 'acgtACGT':
# print "%i\tambiguous" %pos
Expand All @@ -172,10 +172,10 @@ def roll_over(seq_seq, new_start, prefix):
dic[kmer].append(i)
# print "\tok"
i+=1
print "Done!"
print("Done!")


print "Evaluating %s-mers .." %k,
print("Evaluating %s-mers .." %k, end=' ')

for s in seqs:
test = {}
Expand Down Expand Up @@ -203,11 +203,11 @@ def roll_over(seq_seq, new_start, prefix):

i+=1

print "Done!\n"
print("Done!\n")

if repeats:

print "\n###################\n## Repeat report ##\n###################"
print("\n###################\n## Repeat report ##\n###################")
tandem = {}
for kmer in repeats:
repeats[kmer] = sorted(list(set(repeats[kmer])))
Expand Down Expand Up @@ -274,7 +274,7 @@ def roll_over(seq_seq, new_start, prefix):
block_start_end_coordinates = {}

minstep = int(sorted(tandem[m[0]][2])[0])
coordinates = range(m[0],m[1]+1)
coordinates = list(range(m[0],m[1]+1))

if minstep >= k:
m[1]+=k-1
Expand All @@ -295,25 +295,25 @@ def roll_over(seq_seq, new_start, prefix):
motif = seqs[s][m[0]:m[1]+1]
if not motif in motifs_by_regions:
motifs_by_regions[motif] = []
print "\nmotif '%s', found multiple times in the following region(s) (start - end coordinate):" %seqs[s][m[0]:m[1]+1]
print("\nmotif '%s', found multiple times in the following region(s) (start - end coordinate):" %seqs[s][m[0]:m[1]+1])


for b in sorted(block_start_end_coordinates):
# print b,block_start_end_coordinates[b]
start = block_start_end_coordinates[b][0]
end = block_start_end_coordinates[b][1]
print "%i - %i (%i x)" %(start, end, (end-start)/(m[1]-m[0]+1))
print("%i - %i (%i x)" %(start, end, (end-start)/(m[1]-m[0]+1)))
# print seqs[s][start:end+1]
# print len(seqs[s])
motifs_by_regions[motif].append([start,end])


print "\n########################\n## Circularity report ##\n########################"
print("\n########################\n## Circularity report ##\n########################")
nothing = True
if len(clips) >= 1:
print "\nFound %i candidate(s) for circularity supported by duplicated %i-mers:" %(len(clips), k)
print("\nFound %i candidate(s) for circularity supported by duplicated %i-mers:" %(len(clips), k))
for l in sorted(clips):
print "\t- suggested clip points %i - %i (length %s; supported by %i duplicted %i-mers); extract by adding '-l %i' or '-c %s,%s' to your command" %(int(clips[l][0][0]), int(clips[l][0][1]), l, len(clips[l])/2, k, l, clips[l][0][0], clips[l][0][1])
print("\t- suggested clip points %i - %i (length %s; supported by %i duplicted %i-mers); extract by adding '-l %i' or '-c %s,%s' to your command" %(int(clips[l][0][0]), int(clips[l][0][1]), l, len(clips[l])/2, k, l, clips[l][0][0], clips[l][0][1]))
nothing = False


Expand All @@ -326,24 +326,24 @@ def roll_over(seq_seq, new_start, prefix):
if motifs_by_regions[m][i][1] == len(seqs[s]):
primes.append(i)
if len(primes) == 2:
print "\nFound motif '%s' at terminal positions (see 'Repeat report' above), which could indicate circularity." %m
print("\nFound motif '%s' at terminal positions (see 'Repeat report' above), which could indicate circularity." %m)
start_clip = motifs_by_regions[m][primes[0]][1]
end_clip = motifs_by_regions[m][primes[1]][1]
print "\t- suggested clip points: %s - %s (length %s); extract the clipped sequence by adding '-c %s,%s' to your command" %(start_clip, end_clip, end_clip-start_clip, start_clip, end_clip)
print "\n\tThis will remove the repeated motif from the 5' end of the sequence.\n\tThe correct length can currently not be determined unambiguously because of the repeat. Longer reads could resolve this.\n"
print("\t- suggested clip points: %s - %s (length %s); extract the clipped sequence by adding '-c %s,%s' to your command" %(start_clip, end_clip, end_clip-start_clip, start_clip, end_clip))
print("\n\tThis will remove the repeated motif from the 5' end of the sequence.\n\tThe correct length can currently not be determined unambiguously because of the repeat. Longer reads could resolve this.\n")
sys.exit()

if nothing:
print "\nDid not find any candidates for circularity using k = %s\n" %k
print("\nDid not find any candidates for circularity using k = %s\n" %k)
sys.exit()

print ""
print("")



if args.extract_by_length:
print "\n####################\n## Result output ##\n####################\n"
print "Extracting by expected length .."
print("\n####################\n## Result output ##\n####################\n")
print("Extracting by expected length ..")

if args.length_tolerance_absolute:
minlength = args.extract_by_length - args.length_tolerance_absolute
Expand All @@ -355,15 +355,15 @@ def roll_over(seq_seq, new_start, prefix):
minlength = args.extract_by_length
maxlength = minlength

print "specified length: %s (tolerance: %s - %s) - Evaluating candidate lengths" %(args.extract_by_length, minlength, maxlength)
print("specified length: %s (tolerance: %s - %s) - Evaluating candidate lengths" %(args.extract_by_length, minlength, maxlength))
for l in sorted(clips):
if l <= maxlength and l >= minlength:
pass
else:
del(clips[l])

if clips:
print "\nFound candidates in the expected length range"
print("\nFound candidates in the expected length range")
for s in seqs:
for l in sorted(clips):
write_clipped(s, seqs[s], clips[l][0][0], clips[l][0][1], args.prefix)
Expand All @@ -383,4 +383,4 @@ def roll_over(seq_seq, new_start, prefix):
# out.write(">test_%s\n%s\n" %(str(l),sequence))
# out.close()
else:
print "\nDid not find any candidates in the specified length range\n"
print("\nDid not find any candidates in the specified length range\n")