'''Replace residues on either end of a sequence with gaps.

Cut out the sections of each read which the assembler has decided are not

good enough to include in the contig and replace them with gap

'''

''' Pad ends of a read to make it fit into an alignment.

The start argument is the position of the first base of the reads sequence

in the contig it is part of. If the start value is lower than 1 (since

ACE files count from 1, not 0) we take part of the sequence off the start,

otherwise each end is padded to the length of the consensus with gaps.

'''

if start < 1:

seq = read[-1*start+1:]

else:

seq = (start-1) * '-' + read

seq = seq + (conlength-len(seq)) * '-'

"""Parse a FASTA string with lines delimited by \\n into a list of lists.

Each inner list contains a name and a sequence.

"""

out = []

line_counter = -1

for line in in_fasta.split("\n"):

if line.startswith(">"):

contig_name = line.split()[0]

contig_seq = ""

out.append([contig_name, contig_seq])

else:

out[line_counter][1] += line.rstrip()

"""Count nucleotide differences between two sequences.

Ignore difference if one of the 2 nucleotides compared is an "*".

If the total number of differences is above 'max_diff', does not count.

Return a list with: [count = 'int', remove = 'True/False']

"""

count = 0

remove = False

for i in xrange(len(seq1)):

if seq1[i] == "*" or seq2[i] == "*":

continue

elif seq1[i] != seq2[i]:

count += 1

if count > max_diff:

remove = True

"""Calculate pairwise differentiation indexes.

"""

ace_gen = Ace.parse(open(in_ace, 'r'))

with open(out_file, "w") as output_file:

while 1:

try:

contig = ace_gen.next()

except:

print "***All contigs treated***"

break

align = Alignment(Gapped(IUPAC.ambiguous_dna, "-"))

align.add_sequence(contig.name, contig.sequence)

for readn in xrange(len(contig.reads)):

clipst = contig.reads[readn].qa.qual_clipping_start

clipe = contig.reads[readn].qa.qual_clipping_end

start = contig.af[readn].padded_start

seq = cut_ends(contig.reads[readn].rd.sequence, clipst, clipe)

seq = pad_read(seq, start, len(contig.sequence))

if "pseudo" not in contig.reads[readn].rd.name:

align.add_sequence(contig.reads[readn].rd.name, seq)

sequences = read_fasta(align.format("fasta"))

contig_name = re.findall("(Contig_[0-9]+)", sequences[0][0])[0]

print "Treating", contig_name

window_len = 8 # PARAMETER

max_diff = 3 # PARAMETER

len_contig = len(sequences[0][1])

number_indexes = 0

total_indexes = 0

for seq in sequences[1:]:

try:

start = len(re.findall("^-+", seq[1])[0])

except:

start = 0

len_seq = 0

min_len_seq = 100 # PARAMETER

count = 0

for window in range(start, len_contig, window_len):

nuc_contig = sequences[0][1][window:window + window_len]

nuc_seq = seq[1][window:window + window_len]

if "-" in nuc_seq:

len_seq += len(nuc_seq.replace("-", ""))

else:

diff = count_diff(nuc_contig, nuc_seq, max_diff)

if diff[1] == False:

count += diff[0]

len_seq += window_len

len_seq -= seq.count("*")

if len_seq >= min_len_seq:

index = float(count) / len_seq

if count > 0:

number_indexes +=1

total_indexes += index

else:

index = "NA"

#output_file.write(contig_name + "\t" + str(index) + "\n")

try:

mean_index = float(total_indexes) / number_indexes

except:

mean_index = "NA"

_plateform = platform.system()

name = __program_name__

text = """

%s(1) User Commands %s(1)

\033[1mNAME\033[0m

\t%s - Calculate pairwise differentiation indexes for sequences

\tin an alignment file in ACE format.

\033[1mSYNOPSIS\033[0m

\t\033[1mpython %s.py \033[0m[\033[4mOPTION\033[0m]... [\033[4mFILE\033[0m]...

\033[1mDESCRIPTION\033[0m

\tCalculate pairwise differentiation indexes

\t%s uses Biopython to parse an ACE file and calculate, for

\teach sequence in each contig, a pairwise differentiation index. The

\tindex (P) is calculated as follows:

\tP = N/L

\twher 'N' is the number of differences between the sequence and the

\tconcensus of the contig to which it belongs and 'L' is the length of

\tthe sequence.

\033[1mOPTIONS\033[0m

\t\033[1m-h, --help\033[0m

\t\tDisplay the manual of this program

\t\033[1m-i, --input\033[0m

\t\tInput file in ACE format

\t\033[1m-o, --output\033[0m

\t\tOutput file in tab separated text format

\033[1mAUTHORS\033[0m

\t%s

%s %s %s %s(1)

"""%(name, name, name, name, name, __authors__, name, __version__, __revision_date__, name)

if _plateform != 'Windows' and "this is cool":

print text

else:

remove = ["\033[1m","\033[0m","\033[4m"]

for i in remove:

text = text.replace(i, "")

try:

opts, args = getopt.getopt(sys.argv[1:], "hi:o:s:", ["help",

"input=", "output="])

except getopt.GetoptError, e:

print "Input error. Use -h for help"

sys.exit(0)

window_length = 11

maximum_indels = 2

stars = False

for option, value in opts:

if option in ('-h', '--help'):

help()

sys.exit(0)

elif option in ('-i', '--input'):

input_ace = value

output_snpcount = input_ace.replace(".ace", "") + "_pwd.txt"

elif option in ('-o', '--output'):

output_file = value

try:

with open(input_ace) as test:

pass

except:

print "Input Error: No ACE file specified or file not found."

print "Use -h for help."

sys.exit(0)