reads = SeqIO.parse(fileName, 'fasta')

prots = []

dna = []

for read in reads:

# there are sequence from markers other than COI. Filter those out

# if read.description.find("COI-5P") == -1:

# print "ignoring %s " % read.description

# continue

sequence = read.seq.ungap("-")

translation = sequence.translate(table=9)

if translation.count("*"):

hasGoodTr = False

# find other possible reading frames or die trying

for frame in [1,2]:

s = sequence[frame:]

t = s.translate(table=9)

if not t.count("*"):

sequence = s

translation = t

hasGoodTr = True

break

if not hasGoodTr:

print "\n\n\n\n"

print "****** seqeuence %s contains a stop in its translation" % read.id

print "\n\n\n\n"

print translation

sys.exit(0)

dna.append(SeqRecord.SeqRecord(id=read.id, seq=sequence, name=""))

prots.append(SeqRecord.SeqRecord(id=read.id, seq=translation, name=""))

print "Writing %s sequences for file %s" % (len(prots), fileName)

SeqIO.write(dna, open(os.path.join(outDir,os.path.splitext(os.path.basename(fileName))[0]+".fna"), 'w'), 'fasta')

import sys

if len(seq1) != len(seq2):

# TODO CHANGE TO EXCEPTION

print "Seqeunces are not of the same length"

sys.exit(0)

start = 0

end = len(seq1)

# find true start

for x in range(len(seq1)):

if seq1[x] != '-':

start = x

break

for x in range(len(seq2)):

if seq2[x] != '-':

if start < x:

start = x

break

for x in range(len(seq1))[::-1]:

if seq1[x] != '-':

end = x

break

for x in range(len(seq2))[::-1]:

if seq2[x] != '-':

if start > x:

end = x

break

dist = sum([1 for x in range(start, end+1) if seq1[x] != seq2[x] ])

print seq1.id, seq2.id, start, end, dist

# TODO: move this top

ali = AlignIO.read(outPal2NalFile, 'clustal')

distMatrix = np.zeros((len(ali), len(ali)))

for pair in itertools.combinations(range(len(ali)), 2):

distMatrix[pair[0], pair[1]] = computeDist(ali[pair[0]], ali[pair[1]])

print distMatrix

myAvg = np.average(distMatrix)

myStd = np.std(distMatrix)

myMax = distMatrix[np.unravel_index(distMatrix.argmax(), distMatrix.shape)]

# fill diagonal with max to ignore z

np.fill_diagonal(distMatrix, distMatrix.max())

myMin = distMatrix[np.unravel_index(distMatrix.argmin(), distMatrix.shape)]

# assumes that nucleotide and amino acid files have the smae name scheme except for extension

# faa versus fna

baseName = os.path.splitext(os.path.basename(myFileProt))[0]

myFileDna = os.path.join(os.path.dirname(myFileProt), baseName+".fna")

protAliOutFile = os.path.join(outDir, baseName+".aln")

pal2nalOutFile = os.path.join(outDir, baseName+".pal2nal")

sequences = SeqIO.to_dict(SeqIO.parse(myFileProt, 'fasta'))

if len(sequences) == 1:

# nothing to align, just write to files and continute to next file

SeqIO.write(sequences.values(), open( protAliOutFile, 'w'), 'clustal')

sequences = SeqIO.to_dict(SeqIO.parse(myFileDna, 'fasta'))

SeqIO.write(sequences.values(), open(pal2nalOutFile, 'w'), 'clustal')

print "Single seq file, exiting"

return

clustalWCmd = ['/Users/mahdi/programs/clustalw-2.1-macosx/clustalw2', '-ALIGN',

'-INFILE=%s' % myFileProt, '-TYPE=PROTEIN', '-OUTFILE=%s' % protAliOutFile, '-OUTORDER=INPUT']

# mafftCmd = ['mafft-linsi', '--amino', '--clustalout', myFileProt , '>', protAliOutFile]

pal2nalcmd = ['perl', '/Users/mahdi/programs/pal2nal.v14/pal2nal.pl', protAliOutFile, myFileDna, '-codontable', '9', ]

with open(os.devnull, 'w') as fnull, open(pal2nalOutFile, 'w') as out:

subprocess.call(clustalWCmd, stderr=fnull, stdout=fnull)

subprocess.call(pal2nalcmd, stdout=out)

hmmerCmd = ["/Users/mahdi/programs/hmmer-3.1b2-macosx-intel/binaries/hmmbuild",

"-O", '/tmp/effectiveAli', "%s.hmm" % proteinAliFName, "%s" % proteinAliFName]

hmmLogo = ["/Users/mahdi/programs/hmmer-3.1b2-macosx-intel/binaries/hmmlogo", "%s.hmm" % proteinAliFName]

aminoAcids = ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y"]

print hmmerCmd

with open(os.devnull, 'w') as fnull, open("%s.logo" % proteinAliFName, 'w') as logoFile:

subprocess.call(hmmerCmd, stderr=fnull, stdout=fnull)

subprocess.call(hmmLogo, stderr=fnull, stdout=logoFile)

concensusLine = ""

for line in open('/tmp/effectiveAli','r'):

line = line.rstrip()

if line[0:4] == "#=GC":

concensusLine += line.split()[2]

effectiveCols = [x for x in range(len(concensusLine)) if concensusLine[x]=='x']

logoFile = open("%s.logo" % proteinAliFName, 'r')

logoFile.readline()

logoFile.readline()

probs ={}

for line in logoFile:

line = line.rstrip()

data = line.split()

colNum = data[0].replace(":", "")

if data[0][0] not in ['0','1','2','3','4','5','6','7','8','9']:

break

total = sum([float(x) for x in data[1:-2]])

print line

normalizedPro = [float(x)/total for x in data[1:-2]]

probs[int(colNum)] = dict(zip(aminoAcids, normalizedPro))

# Quick and VERY slow

# convert o matrix and operate directly on it

ali = AlignIO.read(aliFName, 'clustal')

scores = {}

for seqNumRemove in range(len(ali)):

newSeqs = AlignIO.MultipleSeqAlignment([])

aliWithValidCols = AlignIO.MultipleSeqAlignment([])

for seqNum in range(len(ali)):

if seqNum != seqNumRemove:

newSeqs.append(ali[seqNum])

aliWithValidCols = newSeqs[:,validCols[0]:validCols[0]+1]

querySeq = ali[seqNumRemove, validCols[0]:validCols[0]+1]

for col in validCols[1:]:

aliWithValidCols += newSeqs[:,col:col+1]

querySeq += ali[seqNumRemove, col:col+1]

AlignIO.write(aliWithValidCols, open("/tmp/tempPartialAli", 'w'), 'clustal')

SeqIO.write(querySeq, open('/tmp/querySeq', 'w'), 'fasta')

print "seq %s out of %s completed" % (seqNumRemove, len(ali))

print "running hmmer and gathering stats"

hmmBuildCmd = ["/Users/mahdi/programs/hmmer-3.1b2-macosx-intel/binaries/hmmbuild", "/tmp/tempPartialAli.hmm", "/tmp/tempPartialAli"]

hmmScanCmd = ["/Users/mahdi/programs/hmmer-3.1b2-macosx-intel/binaries/hmmscan",

"/tmp/tempPartialAli.hmm", "/tmp/querySeq"]

hmmPressCmd = ["/Users/mahdi/programs/hmmer-3.1b2-macosx-intel/binaries/hmmpress",

"/tmp/tempPartialAli.hmm"]

with open(os.devnull, 'w') as fnull, open("/tmp/alResult", 'w') as out:

subprocess.call(hmmBuildCmd, stdout=fnull)

subprocess.call(hmmPressCmd, stderr=fnull, stdout=fnull)

subprocess.call(hmmScanCmd, stderr=fnull, stdout=out)

print hmmBuildCmd

print hmmScanCmd

search = SearchIO.parse("/tmp/alResult", "hmmer3-text").next()

bScore = search.hsps[0].bitscore

scores[search.id] = bScore