def validateInputs(msa, tree=None): # Check for existence and proper FASTA formatting of input MSA try: msaHandle = open(msa, "rU") except: print '** HYPNO input error: Given MSA file location does not exist or is not accessible: '+msa sys.exit(1) try: AlignIO.parse(msaHandle, "fasta").next() except: print '** HYPNO input error: improper MSA file format, must be aligned FASTA or a2m format: '+msa sys.exit(1) if tree: try: treeHandle = open(tree, "rU") except: print '** HYPNO input error: Given tree file location does not exist or is not accessible: '+tree sys.exit(1) try: Phylo.read(treeHandle, "newick") except: print '** HYPNO input error: improper tree file format, must be Newick format: '+msa sys.exit(1) if not internet_connected(): print '** HYPNO connection error: Please connect to the internet to enable HYPNO remote database queries.' sys.exit(1) return 0
def main():
args = get_args()
# iterate through all the files to determine the longest alignment
files = get_files(args.nexus)
old_names = set()
for f in files:
for align in AlignIO.parse(f, 'nexus'):
for seq in list(align):
old_names.update([seq.name])
#pdb.set_trace()
name_map = abbreviator(old_names)
for count, f in enumerate(files):
new_align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
#filename = os.path.basename(f)
#chromo_name = filename.split('.')[0]
for align in AlignIO.parse(f, 'nexus'):
for seq in list(align):
new_seq_name = name_map[seq.name]
new_align.add_sequence(new_seq_name, str(seq.seq))
#pdb.set_trace()
outf = os.path.join(args.output, os.path.split(f)[1])
try:
AlignIO.write(new_align, open(outf, 'w'), 'nexus')
except ValueError:
pdb.set_trace()
print count
def GetExec():
Recs = os.listdir(os.getcwd())
newList=[]
j = 0
listdata=dict()
k = 0
while k < len(Recs):
try:
(name, ext) = os.path.splitext(Recs[k])
typo = ''
if ext in [".txt",".fas",".fasta"]:
IORec = AlignIO.parse(Recs[k],'fasta')
typo = 'fasta'
elif ext in [".aln"]:
IORec = AlignIO.parse(Recs[k],'clustal')
typo = 'clustal'
aNum = 1
for align in IORec:
newList.append([align,name])
NumSeqs = 0
for rec in align:
NumSeqs += 1
listdata[j] = str(Recs[k]),aNum, NumSeqs,align.get_alignment_length(),str(typo)
j += 1
aNum += 1
except IOError, e:
print e
k += 1
def check_AlignIO_to_EMBOSS(self, in_filename, in_format, skip_formats=(),
alphabet=None):
"""Can Bio.AlignIO write files seqret can read back?"""
if alphabet:
old_aligns = list(AlignIO.parse(in_filename, in_format, alphabet))
else:
old_aligns = list(AlignIO.parse(in_filename, in_format))
formats = ["clustal", "phylip"]
if len(old_aligns) == 1:
formats.extend(["fasta", "nexus"])
for temp_format in formats:
if temp_format in skip_formats:
continue
# PHYLIP is a simple format which explicitly supports
# multiple alignments (unlike FASTA).
try:
new_aligns = list(emboss_piped_AlignIO_convert(old_aligns,
temp_format,
"phylip"))
except ValueError as e:
# e.g. ValueError: Need a DNA, RNA or Protein alphabet
# from writing Nexus files...
continue
try:
self.assertTrue(compare_alignments(old_aligns, new_aligns))
except ValueError as err:
raise ValueError("Disagree on file %s %s in %s format: %s"
% (in_format, in_filename, temp_format, err))
def check_simple_write_read(alignments, indent=" "):
# print indent+"Checking we can write and then read back these alignments"
for format in test_write_read_align_with_seq_count:
records_per_alignment = len(alignments[0])
for a in alignments:
if records_per_alignment != len(a):
records_per_alignment = None
# Can we expect this format to work?
if not records_per_alignment and format not in test_write_read_alignment_formats:
continue
print(indent + "Checking can write/read as '%s' format" % format)
# Going to write to a handle...
handle = StringIO()
try:
c = AlignIO.write(alignments, handle=handle, format=format)
assert c == len(alignments)
except ValueError as e:
# This is often expected to happen, for example when we try and
# write sequences of different lengths to an alignment file.
print(indent + "Failed: %s" % str(e))
# Carry on to the next format:
continue
# First, try with the seq_count
if records_per_alignment:
handle.flush()
handle.seek(0)
try:
alignments2 = list(AlignIO.parse(handle=handle, format=format, seq_count=records_per_alignment))
except ValueError as e:
# This is BAD. We can't read our own output.
# I want to see the output when called from the test harness,
# run_tests.py (which can be funny about new lines on Windows)
handle.seek(0)
raise ValueError("%s\n\n%s\n\n%s" % (str(e), repr(handle.read()), repr(alignments2)))
simple_alignment_comparison(alignments, alignments2, format)
if format in test_write_read_alignment_formats:
# Don't need the seq_count
handle.flush()
handle.seek(0)
try:
alignments2 = list(AlignIO.parse(handle=handle, format=format))
except ValueError as e:
# This is BAD. We can't read our own output.
# I want to see the output when called from the test harness,
# run_tests.py (which can be funny about new lines on Windows)
handle.seek(0)
raise ValueError("%s\n\n%s\n\n%s" % (str(e), repr(handle.read()), repr(alignments2)))
simple_alignment_comparison(alignments, alignments2, format)
if len(alignments) > 1:
# Try writing just one Alignment (not a list)
handle = StringIO()
SeqIO.write(alignments[0], handle, format)
assert handle.getvalue() == alignments[0].format(format)
def initialize_data(self):
self.motif1 = Motif(self.m1_file)
motif = open(self.m1_file, 'r')
for each in AlignIO.parse(motif, "fasta"):
self.motif1.add_promoter(each)
motif.close()
self.motif2 = Motif(self.m2_file)
motif = open(self.m2_file, 'r')
for each in AlignIO.parse(motif, "fasta"):
self.motif2.add_promoter(each)
motif.close()
def getStuff(workAlignment, geneName):
speciesList = []
global speciesList
def rmDot(string):
#Removes dots
return string.split(".")[0]
def makeMatrix(species):
#Makes the matrix that things can be stored in.
stuffDict = {}
for i in species:
stuffDict[i] = {}
for j in species:
stuffDict[i][j] = 0
return stuffDict
for i in AlignIO.parse(workAlignment, "maf"):
#Creates a list of species to be used in a matrix.
for q in xrange(len(str(i.get_column(0)))):
if rmDot(list(i)[q].id) not in speciesList:
speciesList.append(rmDot(list(i)[q].id))
#runs the makeMatrix functionto create dictOfCOunts, which will hold all of the counts.
dictOfCounts = makeMatrix(speciesList)
dictOfSames = makeMatrix(speciesList)
for i in AlignIO.parse(workAlignment, "maf"):
#Loops through each block in the alignment.i is an Object that can be turned into a list or string and has several deprecated functions (which I use).
columnDict = {}
for j in xrange(i.get_alignment_length()):
#creates columnDict, a dictionary that contains a apecies name and a letter
global columnDict
column = i.get_column(j)
if '-' or "n" or "N" not in column:
y = 0
for k in column:
columnDict[rmDot(list(i)[y].id)] = k
y = y + 1
for g in columnDict:
#Populates dictOfCounts
for h in columnDict:
if columnDict[h] != columnDict[g]:
dictOfCounts[g][h]= dictOfCounts[g][h] + 1
else:
dictOfSames[g][h] = dictOfSames[g][h] + 1
def fileWriter(path, data):
pickle.dump(data, open(path, "wb"))
fileWriter("data/" + geneName + "Diffs", dictOfCounts)
fileWriter("data/" + geneName + "Sames", dictOfSames)
fileWriter("data/emptyMatrix", makeMatrix(speciesList))
def convert_alignments(in_file, out_file, new_type):
"""converts a nexus alignment into a phylip alignment and writes to new file"""
alignments = AlignIO.parse(open(in_file, 'r'), "nexus")
for alignment in alignments:
handle = open(out_file, "a")
AlignIO.write(alignment, handle, new_type)
handle.close()
def test_seqtmatchall_piped(self):
"""seqmatchall with pair output piped to stdout."""
cline = SeqmatchallCommandline(cmd=exes["seqmatchall"],
sequence="Fasta/f002",
aformat="pair", wordsize=9,
auto=True, stdout=True)
self.assertEqual(str(cline),
exes["seqmatchall"] + " -auto -stdout"
+ " -sequence=Fasta/f002"
+ " -wordsize=9 -aformat=pair")
# Run the tool,
child = subprocess.Popen(str(cline),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
child.stdin.close()
# Check we could read it's output
for align in AlignIO.parse(child.stdout, "emboss"):
self.assertEqual(len(align), 2)
self.assertEqual(align.get_alignment_length(), 9)
# Check no error output:
self.assertEqual(child.stderr.read(), "")
self.assertEqual(0, child.wait())
child.stdout.close()
child.stderr.close()
def convert(infile, type, outtype, outfile): """Make AlignIO call to convert using the specified parameters""" from Bio import AlignIO ifh = AlignIO.parse(infile, type) AlignIO.write(ifh, outfile, outtype)
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
# Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
# TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "genbank"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def parsexmfa(xmfa, r1, r2, ref):
"""
"""
print("parsing...")
r1 = r1
r2 = r2
consensusdict = {}
gapfill = 0
totalgaps = 0
alignment = AlignIO.parse(open(xmfa), "mauve")
for aln in alignment: # each alignment block
header = []
if len(aln) > 1:
for record in aln:
header.append(record.id)
for rec in header:
if r1 in rec:
pos = rec.split("/")[1]
pos = pos.replace("-", ":")
alignarr = np.array([list(r) for r in aln], np.character)
sense, gap, fill = makesense(alignarr, header, r1, r2, ref)
gapfill += fill
totalgaps += gap
consensusdict[pos] = sense
print("total gaps: {}\n total gaps filled: {}".format(totalgaps, gapfill))
return(consensusdict)
def align(hom):
'''Takes in a homologue from getHomologues() and
aligns all of the sequences that it contains'''
with tempfile.NamedTemporaryFile() as temp_file:
uid_map = {}
for species in hom['species']:
temp = hom['species'][species][0]
temp_file.write('>' + str(temp['uid']) + '\n')
temp_file.write(temp['seq'] + '\n')
temp_file.write('\n')
uid_map[temp['uid']] = species
align_io_temp_file = StringIO.StringIO()
cline = ClustalwCommandline("clustalw", infile=temp_file.name, align='true',output='PHYLIP')
align_io_temp_file.write(cline)
alignments = AlignIO.parse(align_io_temp_file, 'phylip')
for alignment in alignments:
#TODO: Don't throw out data here
#get the first protien for the species
temp = hom[uid_map[alignment.id]]['species'][0]
#clear out all others since we only currently want one
hom[uid_map[alignment.id]]['species'] = []
#stick in the aligned sequence
temp['seq'] = str(alignment.seq)
#re append the protien
hom[uid_map[alignment.id]]['species'].append(temp)
seq_len = False
for species in hom['species']:
if not seq_len:
seq_len = len(hom['species'][species][0]['seq'])
if len(hom['species'][species][0]['seq']) != seq_len:
raise Exception("ALIGNMENT ERROR")
return hom
def main():
global args
print "doop"
d = "/home/nabil/IGORwork/safe.ALL.MAF"
for multiple_alignment in AlignIO.parse(d, "maf"):
print "new m"
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
# Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "fasta"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def main():
args = get_args()
# iterate through all the files to determine the longest alignment
files = get_files(args.input)
all_taxa = set([])
for count, f in enumerate(files):
#new_align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
new_align = MultipleSeqAlignment([], generic_dna)
for align in AlignIO.parse(f, 'nexus'):
for seq in list(align):
#pdb.set_trace()
fname = os.path.splitext(os.path.basename(f))[0]
new_seq_name = re.sub("^{}_*".format(fname), "", seq.name)
all_taxa.add(new_seq_name)
seq.id = new_seq_name
seq.name = new_seq_name
new_align.append(seq)
assert len(all_taxa) == args.taxa, "Taxon names are not identical"
outf = os.path.join(args.output, os.path.split(f)[1])
try:
AlignIO.write(new_align, open(outf, 'w'), 'nexus')
except ValueError:
pdb.set_trace()
print count
print "Taxon names in alignments: {0}".format(','.join(list(all_taxa)))
def remove_duplicate_sequences_and_sequences_missing_too_much_data(self, output_filename,remove_identical_sequences = 0):
taxa_to_remove = []
if remove_identical_sequences < 1:
taxa_to_remove = self.taxa_missing_too_much_data()
else:
taxa_to_remove = self.taxa_of_duplicate_sequences() + self.taxa_missing_too_much_data()
with open(self.input_filename) as input_handle:
with open(output_filename, "w+") as output_handle:
alignments = AlignIO.parse(input_handle, "fasta")
output_alignments = []
number_of_included_alignments = 0
for alignment in alignments:
for record in alignment:
if record.id not in taxa_to_remove:
output_alignments.append(record)
number_of_included_alignments += 1
if number_of_included_alignments <= 1:
sys.exit("Not enough sequences are left after removing duplicates.Please check you input data.")
AlignIO.write(MultipleSeqAlignment(output_alignments), output_handle, "fasta")
output_handle.close()
input_handle.close()
return taxa_to_remove
def test_needle_piped2(self):
"""needle with asis trick, and nucleotide FASTA file, output piped to stdout."""
# TODO - Support needle in Bio.Emboss.Applications
# (ideally with the -auto and -filter arguments)
# Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAA"
cline = exes["needle"]
cline += " -asequence asis:" + query
cline += " -bsequence Fasta/f002"
cline += " -auto" # no prompting
cline += " -filter" # use stdout
# Run the tool,
child = subprocess.Popen(str(cline),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
child.stdin.close()
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse("Fasta/f002", "fasta"),
AlignIO.parse(child.stdout, "emboss"),
local=False)
# Check no error output:
self.assertEqual(child.stderr.read(), "")
self.assertEqual(0, child.wait())
child.stdout.close()
child.stderr.close()
def check_bootstrap(self, filename, format, align_type="d"):
""" check we can use fseqboot to pseudosample an alignment
The align_type type argument is passed to the commandline object to
set the output format to use (from [D]na,[p]rotein and [r]na )
"""
self.assert_(os.path.isfile(filename), "Missing %s" % filename)
cline = FSeqBootCommandline(exes["fseqboot"],
sequence = filename,
outfile = "test_file",
seqtype = align_type,
reps = 2,
auto = True, filter = True)
return_code = run_command(cline)
if return_code != 0:
raise ValueError("Return code %s from:\n%s" \
% (return_code, str(cline)))
# the resultant file should have 2 alignments...
bs = list(AlignIO.parse(open("test_file", "r" ), format))
self.assertEqual(len(bs), 2)
# ..and each name in the original alignment...
a_names = [s.name.replace(" ", "_") for s in
AlignIO.read(open(filename, "r"), format)]
# ...should be in each alignment in the bootstrapped file
for a in bs:
self.assertEqual(a_names, [s.name.replace(" ", "_") for s in a])
def filter_out_alignments_with_too_much_missing_data(input_filename, output_filename, filter_percentage,verbose):
input_handle = open(input_filename, "rU")
output_handle = open(output_filename, "w+")
alignments = AlignIO.parse(input_handle, "fasta")
output_alignments = []
taxa_removed = []
number_of_included_alignments = 0
for alignment in alignments:
for record in alignment:
number_of_gaps = 0
number_of_gaps += record.seq.count('n')
number_of_gaps += record.seq.count('N')
number_of_gaps += record.seq.count('-')
sequence_length = len(record.seq)
if sequence_length == 0:
taxa_removed.append(record.id)
print "Excluded sequence " + record.id + " because there werent enough bases in it"
elif((number_of_gaps*100/sequence_length) <= filter_percentage):
output_alignments.append(record)
number_of_included_alignments += 1
else:
taxa_removed.append(record.id)
print "Excluded sequence " + record.id + " because it had " + str(number_of_gaps*100/sequence_length) +" percentage gaps while a maximum of "+ str(filter_percentage) +" is allowed"
if number_of_included_alignments <= 1:
sys.exit("Too many sequences have been excluded so theres no data left to work with. Please increase the -f parameter")
AlignIO.write(MultipleSeqAlignment(output_alignments), output_handle, "fasta")
output_handle.close()
input_handle.close()
return taxa_removed
def load(cls, filename, schema=None):
try:
return [AlignmentExt.from_msa(msa) for msa in
AlignIO.parse(filename, cls.schema(filename, schema))]
except Exception, e:
print 'Unable to load alignments from: %s\n%s' % (filename, str(e))
return None
def check_convert(in_filename, in_format, out_format, alphabet=None):
# Write it out using parse/write
handle = StringIO()
aligns = list(AlignIO.parse(in_filename, in_format, None, alphabet))
try:
count = AlignIO.write(aligns, handle, out_format)
except ValueError:
count = 0
# Write it out using convert passing filename and handle
handle2 = StringIO()
try:
count2 = AlignIO.convert(in_filename, in_format, handle2, out_format, alphabet)
except ValueError:
count2 = 0
assert count == count2
assert handle.getvalue() == handle2.getvalue()
# Write it out using convert passing handle and handle
handle2 = StringIO()
try:
with open(in_filename) as handle1:
count2 = AlignIO.convert(handle1, in_format, handle2, out_format, alphabet)
except ValueError:
count2 = 0
assert count == count2
assert handle.getvalue() == handle2.getvalue()
def split_family_seqs():
alis_dir = cfg.dataPath('rfam/family_alis/')
meta_dir = cfg.dataPath('rfam/family_metas/')
fopen = open(cfg.dataPath('rfam/Rfam.seed'))
alis = aio.parse(fopen,'stockholm')
while 1:
infos = {}
start = fopen.tell()
while 1:
l = fopen.readline()
if l == '': break
if l[0] == '#':
ukey = str(l[5:7])
infos.update( [(ukey, infos.get(ukey,'') + l[8:])])
else:
if l.strip() != '': break
fopen.seek(start)
ali = alis.next()
if not ali:
break
rfname = infos['AC'].strip()
alifile = open(os.path.join(alis_dir, rfname+'.fa'),'w')
metafile = open(os.path.join(meta_dir, rfname+'.pickle'),'w')
aio.write(ali, alifile, 'fasta')
pickle.dump(infos, metafile)
alifile.close()
metafile.close()
def _iterate_via_AlignIO(handle, format, alphabet):
"""Iterate over all records in several alignments (PRIVATE)."""
from Bio import AlignIO
for align in AlignIO.parse(handle, format, alphabet=alphabet):
for record in align:
yield record
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
#Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
#TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"genbank"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
#Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"fasta"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
def __init__(self, file_name=None, data = None, format='fasta'):
if file_name:
super(Alignment, self).__init__(AlignIO.read(file_name, format))
elif data:
super(Alignment, self).__init__(AlignIO.parse(StringIO(data), format))
else:
super(Alignment, self).__init__([])
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
# Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
# EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
# TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "swiss"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def taxit_create(taxit_executable_loc,
aln_fasta,
hmm_file,
tree_file,
tree_stats,
pfam_acc,
output_location,
aln_stockholm):
'''
Calls taxit
'''
#taxit create --clobber --aln-fasta ./PF14424.dedup.fasta --profile ./PF14424.wholefam.hmm --tree-file ./PF14424.dedup.nh --locus PF14424 --package-name PF14424.pplacer
cmd = taxit_executable_loc \
+ " create --clobber" \
+ " --aln-fasta " + aln_fasta \
+ " --profile " + hmm_file \
+ " --tree-file " + tree_file \
+ " --tree-stats " + tree_stats \
+ " --locus " + pfam_acc \
+ " --package-name " + output_location
raw_data = subprocess.check_call(cmd, shell=True)
input_handle = open(aln_fasta, "rU")
output_handle = open(aln_stockholm, "w")
alignments = AlignIO.parse(input_handle, "fasta")
AlignIO.write(alignments, output_handle, "stockholm")
output_handle.close()
input_handle.close()
def emboss_piped_AlignIO_convert(alignments, old_format, new_format):
"""Run seqret, returns alignments (as a generator)."""
# Setup, this assumes for all the format names used
# Biopython and EMBOSS names are consistent!
cline = SeqretCommandline(exes["seqret"],
sformat=old_format,
osformat=new_format,
auto=True, # no prompting
filter=True)
# Run the tool,
child = subprocess.Popen(str(cline),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
try:
AlignIO.write(alignments, child.stdin, old_format)
except Exception as err:
child.stdin.close()
child.stderr.close()
child.stdout.close()
raise
child.stdin.close()
child.stderr.close()
# TODO - Is there a nice way to return an iterator AND
# automatically close the handle?
try:
aligns = list(AlignIO.parse(child.stdout, new_format))
except Exception as err:
child.stdout.close()
raise
child.stdout.close()
return aligns
def combine_fastas(self, leaf_node_filename, internl_node_filename,
output_file):
with open(output_file, 'w') as output_handle:
# print out leafnodes as is
with open(leaf_node_filename, 'r') as input_handle:
alignments = AlignIO.parse(input_handle, "fasta")
AlignIO.write(alignments, output_handle, "fasta")
input_handle.closed
with open(internl_node_filename, 'r') as input_handle:
alignments = AlignIO.parse(input_handle, "fasta")
output_alignments = []
for alignment in alignments:
for record in alignment:
record.id = self.internal_node_prefix + str(record.id)
record.description = ''
output_alignments.append(record)
AlignIO.write(MultipleSeqAlignment(output_alignments),
output_handle, "fasta")
input_handle.closed
output_handle.closed
def trim_sequences(filepath: str) -> List:
record = list(AlignIO.parse(filepath, "msf"))
result_record = []
for rec, num in zip(record[1:], range(len(record[1:]))):
canonical_ = rec[0]
canonical_len = len(canonical_.seq)
result = percent_id_calc(canonical_, rec[1], f"{rec[0].id[:7]}_{num}",
canonical_len)
if result:
result_record.append(result)
return result_record
def get_alignment_sequences_amount(input_path):
input_format = get_format(input_path)
if input_format == "fasta":
alignment = SeqIO.parse(open(input_path), input_format)
else:
alignment = AlignIO.parse(open(input_path), input_format)
seq_num = 0
while True:
try:
record = next(alignment)
seq_num += 1
except:
return seq_num
def seq_trimmer(self):
needle_record = list(AlignIO.parse(self.out_dir / "water.fasta",
"msf"))
self.result_record = []
for rec in needle_record[1:]:
reference_seq = rec[0]
seq_parser = IdenticalSequencesParser(reference_seq, rec[1],
self.id_score)
result = seq_parser.highly_identical_seqs()
if result:
self.result_record.append(result)
def are_sequence_names_unique(self):
with open(self.input_filename) as input_handle:
alignments = AlignIO.parse(input_handle, "fasta")
sequence_names = []
for alignment in alignments:
for record in alignment:
sequence_names.append(record.name)
if [k for k, v in list(Counter(sequence_names).items()) if v > 1
] != []:
return False
input_handle.close()
return True
def main():
args = get_args()
nexus_files = get_files(args.input)
taxa = get_all_taxon_names(nexus_files)
taxa_to_keep = get_samples_to_run(args, taxa)
for count, align_file in enumerate(nexus_files):
new_align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))
for align in AlignIO.parse(align_file, "nexus"):
for taxon in list(align):
if taxon.name in taxa_to_keep:
new_align.add_sequence(taxon.name, str(taxon.seq))
outf = os.path.join(args.output, os.path.basename(align_file))
AlignIO.write(new_align, open(outf, 'w'), 'nexus')
print count
def maf(in_maf, out_paf):
maf_f = None
try:
with open(out_paf, "w") as paf:
maf_f = AlignIO.parse(in_maf, "maf")
for grp in maf_f:
seqs = []
for seq in grp:
seqs.append(seq)
matches = 0
for i in range(0, len(seqs[0])):
if seqs[0][i] == seqs[1][i]:
matches += 1
tannots = seqs[0].annotations
qannots = seqs[1].annotations
tlen = tannots["srcSize"]
tstart = tannots["start"]
tend = tstart + tannots["size"]
if tannots["strand"] == -1:
tstart = tlen - tstart
tend = tlen - tend
qlen = qannots["srcSize"]
qstart = qannots["start"]
qend = qannots["start"] + qannots["size"]
if qannots["strand"] == -1:
qstart = qlen - qstart
qend = qlen - qend
strand = "+" if tannots["strand"] == qannots["strand"] else "-"
paf.write(
"{qname}\t{qlen}\t{qstart}\t{qend}\t{strand}\t{tname}\t{tlen}\t{tstart}\t{tend}\t{matches}\t"
"{block_len}\t255\n".format(
tname=seqs[0].id,
tlen=tlen,
tstart=tstart,
tend=tend,
qname=seqs[1].id,
qlen=qlen,
qstart=qstart if strand == "+" else qend,
qend=qend if strand == "+" else qstart,
strand=strand,
matches=matches,
block_len=tannots["size"]))
except:
traceback.print_exc()
if maf_f is not None:
maf_f.close()
return False
else:
maf_f.close()
return True
def convert_nexus_to_format(dataset_as_nexus, dataset_format):
"""
Converts nexus format to Phylip and Fasta using Biopython tools.
:param dataset_as_nexus:
:param dataset_format:
:return:
"""
fake_handle = StringIO(dataset_as_nexus)
nexus_al = AlignIO.parse(fake_handle, 'nexus')
tmp_file = make_random_filename()
AlignIO.write(nexus_al, tmp_file, dataset_format)
dataset_as_fasta = read_and_delete_tmp_file(tmp_file)
return dataset_as_fasta
def parse_alignment(self, f):
alignments = AlignIO.parse(f, 'clustal')
for msa in alignments:
self.length = msa.get_alignment_length()
self.hydropathies = get_average_hydropathies(msa,
window=self.window,
kernel=self.kernel)
self.amphipathicities = get_average_amphipathicities(
msa, window=self.window)
self.similarities = get_similarities(msa)
self.tmcenters = get_tmcenters(msa)
#what's the worst that can happen???
return msa
def load_alignments(alignmentfiles, format):
alignments = []
for file in alignmentfiles:
try:
for alignment in AlignIO.parse(file, format=format):
logger.debug("loaded alignment of length {} from {}".format(
len(alignment), file))
alignments.append(alignment)
except ValueError as e:
logger.error("Cannot parse input file {}: {}".format(file, e))
raise
logger.info("Successfully loaded {} alignments from {} input files".format(
len(alignments), len(alignmentfiles)))
return alignments
def usePhyMLForBranchLengths(alignmentFasta, newicktree):
#converts the alignment file in FASTA to PHYLIP format
alnFastaInFH = getInputTempFile(alignmentFasta)
alnPhylipOutFH = getOutputTempFile()
input_handle = open(alnFastaInFH.name, "rU")
output_handle = open(alnPhylipOutFH.name, "w")
alignments = AlignIO.parse(input_handle, "fasta")
AlignIO.write(alignments, output_handle, "phylip")
input_handle.close()
output_handle.close()
treeInFH = getInputTempFile(newicktree)
#removes the output files to be created if they already exist
if os.path.exists(alnPhylipOutFH.name + "_phyml_stats.txt"):
os.system("rm %s_phyml_stats.txt" % (alnPhylipOutFH.name))
if os.path.exists(alnPhylipOutFH.name + "_phyml_tree.txt"):
os.system("rm %s" % (alnPhylipOutFH.name + "_phyml_tree.txt"))
#spawns a process and executes all the correct input keys when prompted
child = pexpect.spawn("phyml")
child.expect(". Enter the sequence file name >")
child.sendline(alnPhylipOutFH.name)
child.sendline("D")
child.sendline("+")
child.sendline("+")
child.sendline("O")
child.sendline("U")
child.sendline("Y")
child.expect(". Enter the name of the input tree file >")
child.sendline(treeInFH.name)
#checks for how long the calculation has been going for, if it has stalled, then the process will be halted
argc = 0
startTime = time.time()
B = True
while child.isalive() and B:
argc += 1
if argc % 1000 == 0:
newTime = time.time() - startTime
if newTime > 60.0:
B = False
Ret = None
if B:
Ret = open(alnPhylipOutFH.name + "_phyml_tree.txt", "r").read()
#returns the branch lengthed tree if the process was successful
return [B, Ret]
def convert_fasta_to_phylip(input_path, output_path, blank=False):
if blank:
intermediata_path = input_path.replace(".fas", ".translated_fasta")
names_translator_path = input_path.replace(".fas", ".names_map")
res = convert_sequences_names(input_path, intermediata_path, names_translator_path, src="FastML")
input_handle = open(intermediata_path, "rU")
else:
input_handle = open(input_path, "rU")
output_handle = open(output_path, "w")
alignments = AlignIO.parse(input_handle, "fasta")
AlignIO.write(alignments, output_handle, "phylip-relaxed")
input_handle.close()
output_handle.close()
return 0
def runPhyML(aln, phymlOpt, geneDir):
"""
Function converting fasta file to phylip and running PhyML.
@param1 aln: Path
@param2 geneDir: Gene directory
@return outPhy: Path to PhyML results file
"""
# convert to Phylip format and replace eventual "!" symbols (relic from using MACSE)
origin = os.getcwd()
os.chdir(geneDir)
outPhy = aln.split("/")[-1].split(".")[0]+".phylip"
#aln = aln.split("/")[-1]
tmp = aln.split("/")[-1].split(".")[0]+".tmp"
logger = logging.getLogger("main.tree")
with open(aln, "rU") as aln2:
laln = aln2.read().replace("!", "N")
aln2.close()
with open(tmp, "w") as temp:
temp.write(laln)
temp.close()
input_handle = open(tmp, "rU")
output_handle = open(outPhy, "w")
alignments = AlignIO.parse(input_handle, "fasta")
AlignIO.write(alignments, output_handle, "phylip-relaxed")
output_handle.close()
input_handle.close()
os.remove(tmp)
# PhyML
if phymlOpt != "":
try:
opt=phymlOpt.split("ALN ")[1]
logger.debug("phyml -i {:s} {}".format(outPhy, opt))
cmd("phyml -i {:s} {}".format(outPhy, opt), False)
except:
logger.info("PhyML couldn't run with the provided info {}, running with default options.".format(phymlOpt))
cmd("phyml -i {:s} -v e -b -2".format(outPhy), False)
else:
logger.debug("phyml -i {:s} -v e -b -2".format(outPhy))
cmd("phyml -i {:s} -v e -b -2".format(outPhy), False)
os.chdir(origin)
return(geneDir+outPhy)
def hssp3_file_to_phylip(hssp3_file_name, phylip_file_name, chain_id,
master_sequence):
"""Reads a HSSP file in stockholm format and writes a new msa file in phylip-sequential format
only containing the given chain"""
alignments = list(AlignIO.parse(hssp3_file_name, format='stockholm'))
for align in alignments:
if align[0].name[4] == '/':
chain = align[0].name[5].upper()
if chain == chain_id:
align[0].id = align[0].name = align[0].description = 'MASTER'
#align[0].seq = align[0].seq.ungap('-')
AlignIO.write(align,
phylip_file_name,
format='phylip-sequential')
def check_EMBOSS_to_AlignIO(self, filename, old_format, skip_formats=()):
"""Check AlignIO can read seqret's conversion of the file."""
self.assertTrue(os.path.isfile(filename), filename)
old_aligns = list(AlignIO.parse(filename, old_format))
formats = ["clustal", "phylip", "ig", "msf"]
if len(old_aligns) == 1:
formats.extend(["fasta", "nexus"])
for new_format in formats:
if new_format in skip_formats:
continue
handle = emboss_convert(filename, old_format, new_format)
try:
new_aligns = list(AlignIO.parse(handle, new_format))
except Exception: # TODO - Which exceptions?
handle.close()
raise ValueError("Can't parse %s file %s in %s format." %
(old_format, filename, new_format))
handle.close()
try:
self.assertTrue(compare_alignments(old_aligns, new_aligns))
except ValueError as err:
raise ValueError("Disagree on %s file %s in %s format: %s" %
(old_format, filename, new_format, err))
def parse_output(file, output):
"""Parses seq-gen output (phylip) into fasta file(s)
"""
assert file
assert output
strio = StringIO.StringIO(output)
phylip = list(AlignIO.parse(strio, 'phylip-sequential'))
if len(phylip) > 1:
for i, msa in enumerate(phylip):
AlignIO.write(msa, '%i.%s' % (i, file), 'fasta')
else:
AlignIO.write(phylip[0], file, 'fasta')
def pairwisealign(seq1, seq2, **kwargs):
"""
Globally align two sequences.
:param seq1: Sequence 1
:type seq1: str
:param seq2: Sequence 2
:type seq2: str
:parm AA: True if protein sequences, false otherwise.
:param gapopen: The cost for opening a gap.
:param gapextend: The cost for extending a gap.
:returns: Sequence 1 aligned, sequence 2 aligned
:rtype: tuple
"""
if kwargs['AA']:
flag1 = '-sprotein1'
flag2 = '-sprotein2'
matrix = 'EBLOSUM62'
else:
flag1 = '-snucleotide1'
flag2 = '-snucleotide2'
matrix = 'EDNAFULL'
outfile = tempfile.NamedTemporaryFile()
callstr = 'stretcher -outfile=%s -asequence=asis:%s \
-bsequence=asis:%s -gapopen=%s -gapextend=%s -aformat fasta \
-datafile %s %s %s' % (outfile.name, seq1, seq2, kwargs['gapopen'],
kwargs['gapextend'], matrix, flag1, flag2)
status, output = getstatusoutput(callstr)
if status == 0:
result = AlignIO.parse(outfile, 'fasta')
alignmentobj = result.next()
outfile.close()
getoutput('rm %s' % outfile.name)
else:
print output
print "There was an error in pairwisealign.\
Is stretcher installed? See above output and check out" , \
outfile.name
print callstr
outfile.close()
raise SystemError
return alignmentobj[0].seq._data, alignmentobj[1].seq._data
def remove_similars(ident):
"""Remove sequences with desired % identity"""
# Input multi-seq FASTA format
validated_sequence, validated_id = [], []
for record in SeqIO.parse("../input.fasta", "fasta"):
validated_sequence.append(record.seq)
validated_id.append(record.id.split(" ")[0])
remove_id = []
for i in range(0, len(validated_sequence) - 1):
if len(validated_sequence[i]) > 10:
if validated_id[i] not in remove_id:
for j in range(i + 1, len(validated_sequence)):
if len(validated_sequence[j]) > 10:
needle_cline = NeedleCommandline(
asequence="asis:" + validated_sequence[i],
bsequence="asis:" + validated_sequence[j],
gapopen=10,
gapextend=0.5,
outfile='stdout')
stdout, stderr = needle_cline()
alignment = AlignIO.parse(StringIO(stdout), "emboss")
for needle_records in alignment:
query = list(needle_records[0].seq)
subject = list(needle_records[1].seq)
matches = [
h for h, k in zip(query, subject) if h == k
]
while '-' in matches:
matches.remove('-')
similarity = (float(len(matches)) /
len(query)) * 100
if similarity >= ident:
remove_id.append(validated_id[j])
remove_id = list(set(remove_id))
else:
remove_id.append(validated_id[i])
remove_id = list(set(remove_id))
records = (r for r in SeqIO.parse("../input.fasta", "fasta")
if r.id.split(" ")[0] not in remove_id)
SeqIO.write(records, "input2.fasta", "fasta")
os.rename("input2.fasta", "../output.fasta")
def main():
import sys
from Bio import AlignIO
if len(sys.argv) != 5:
sys.exit('python3 %s <in.mfa> <out.mfa> <inFormat> <outFormat>' %
(sys.argv[0]))
inFile = sys.argv[1]
outFile = sys.argv[2]
inFormat = sys.argv[3]
outFormat = sys.argv[4]
alignments = AlignIO.parse(inFile, inFormat)
AlignIO.write(alignments, outFile, outFormat)
def align(genes):
path = config.get_binary_path('mafft')
if not path:
raise exceptions.BinaryNotFound('MAFFT binary was not found')
with tempfile.NamedTemporaryFile(mode='w+t', suffix='.fasta') as tmp:
utils.write_genome(genes, tmp)
tmp.flush()
mafft_cmd = MafftCommandline(path, input=tmp.name, quiet=True)
stdout, _ = mafft_cmd()
records = AlignIO.parse(StringIO(stdout), "fasta")
try:
alignments = next(records)
except StopIteration:
return {}
return utils.records_to_dict(alignments)
def parse_many_alignments(infiles, fmt='fasta'):
"""
Iterate either over multiple files, or over one single file split by '//'
"""
current = ''
if not infiles or (len(infiles) == 1
and infiles[0] in ('-', '/dev/stdin')):
for line in stdin:
if line.startswith('//'):
yield AlignIO.read(StringIO(current), fmt)
current = ''
else:
current += line
else:
for infile in infiles:
yield from AlignIO.parse(infile, fmt)
def main(args=None):
if args is None:
args = argv[1:]
parser = ArgumentParser(description='convert stockholm file to FASTA')
parser.add_argument('STOCKHOLMFILE', type=FileType('r'))
ns = parser.parse_args(args)
alignments = AlignIO.parse(ns.STOCKHOLMFILE, 'stockholm')
AlignIO.write(alignments, stdout, 'fasta')
if ns.STOCKHOLMFILE != stdin:
ns.STOCKHOLMFILE.close()
return 0
def convertFasta2Phylip(instring, outstring):
"""
:param instring: in fasta
:param outstring: out phylip handle
:return: basic phylip
"""
input_handle = open(instring, "rU")
output_handle = open(outstring, "w")
alignments = AlignIO.parse(input_handle, "fasta")
AlignIO.write(alignments, output_handle, "phylip")
output_handle.close()
input_handle.close()
def _createObjectBasedOnFile(self, filePath):
if not _BioAvailable:
return filePath
conversionResult = []
file = open(filePath, 'rU')
fileFormatName = u2py_internals.detectFormat(filePath)
if fileFormatName in Serializer._seqRecordsFileFormats:
conversionResult = list(SeqIO.parse(file, fileFormatName))
self.createdFiles[filePath] = conversionResult
elif fileFormatName in Serializer._msaFileFormats:
conversionResult = list(AlignIO.parse(file, fileFormatName))
self.createdFiles[filePath] = conversionResult
else:
conversionResult = filePath
file.close()
return conversionResult
def hash_sequences(self):
sequence_hash_to_taxa = defaultdict(list)
with open(self.input_filename) as input_handle:
alignments = AlignIO.parse(input_handle, "fasta")
for alignment in alignments:
for record in alignment:
sequence_hash = hashlib.md5()
sequence_hash.update(str(record.seq).encode('utf-8'))
hash_of_sequence = sequence_hash.digest()
sequence_hash_to_taxa[hash_of_sequence].append(record.id)
if self.verbose:
print("Sample " + str(record.id) + " has a hash of " +
str(hash_of_sequence))
input_handle.close()
return sequence_hash_to_taxa
def main():
# parse command line options
usage = "%prog [options] bpg_accession"
opt_parser = OptionParser(usage=usage)
(options, args) = opt_parser.parse_args()
if len(args) != 1:
opt_parser.error('Incorrect number of arguments')
if len(args[0]) < 10 or args[0][0:3] != 'bpg':
opt_parser.error('Argument must be a bpg accession like bpg0123456')
bpg_accession = args[0]
try:
family_id = int(bpg_accession[3:])
except ValueError:
opt_parser.error('Argument must be a bpg accession like bpg0123456')
family_dir = '/clusterfs/ohana/bpg/pfacts/%s/%s/%s' % (
bpg_accession[0:4], bpg_accession[0:7], bpg_accession)
if not os.path.exists(family_dir):
opt_parser.error('Family %s not found on the filesystem.' %
bpg_accession)
family = Family.objects.get(id=family_id)
if family.status == 'bad':
opt_parser.error('Family %s is marked as bad in the database.' \
% bpg_accession)
alignment_file = os.path.join(family_dir, '%s.a2m' % bpg_accession)
f = open(alignment_file)
for alignment in AlignIO.parse(f, "fasta"):
break
alignment_seqs, aligned_column_indices \
= get_alignment_seqs_and_aligned_column_indices(alignment)
column_conserved_residue, column_score \
= get_conservation_info(alignment_seqs, aligned_column_indices)
outfname = os.path.join(family_dir,
bpg_accession + '.alignmentconservation.csv')
outf = open(outfname, 'w')
outf.write('ColumnIndex,ConservedResidue,Blosum62ConservationScore\n')
for j in aligned_column_indices:
outf.write('%d,%s,%f\n' %
(j, column_conserved_residue[j], column_score[j]))
outf.close()
root = family.canonical_root_node()
update_tree_node_alignment_conservation(root, aligned_column_indices,
column_conserved_residue,
column_score)
def pseudofam_convert_stockholm_to_fasta(input_file_name,
output_file_name=None):
from Bio import AlignIO
if output_file_name == None:
output_file_name = input_file_name.rstrip(".sto") + ".fasta"
input_handle = open(
input_file_name, "rU"
) #HJ: Apparently U has no affect, so this indicates it will only read (for "r").
output_handle = open(output_file_name, "w")
alignments = AlignIO.parse(input_handle, "stockholm")
AlignIO.write(alignments, output_handle, "fasta")
output_handle.close()
input_handle.close()
def get_fraction(position, msa_path, chars=True):
# print("get_fraction called with chars = " + str(chars)) # debug
sys.path.insert(0, '/groups/itay_mayrose/halabikeren/python_scripts/')
from utils.alterAlignments import get_format, get_alignment_sequences_amount
msa_format = get_format(msa_path)
seq_num = get_alignment_sequences_amount(msa_path)
chars_counter = 0
alignments = AlignIO.parse(open(msa_path), msa_format)
alignment = next(alignments)
for record in alignment:
sequence = str(record.seq)
if sequence[position - 1] != "-":
chars_counter += 1
chars_fraction = float(chars_counter / seq_num)
if not chars:
return float(1 - chars_fraction)
return chars_fraction
def main():
args = get_args()
# iterate through all the files to determine the longest alignment
files = get_files(args.input, args.input_format)
for count, f in enumerate(files):
new_records = []
for align in AlignIO.parse(f, args.input_format):
for oldseq in list(align):
seqstr = str(oldseq.seq)
#pdb.set_trace()
new_seq = re.sub("[acgtn]", "", seqstr)
new_seq = re.sub("-", "", new_seq)
new_seq_record = SeqRecord(Seq(new_seq, generic_dna), id=oldseq.id, name=oldseq.name, description=oldseq.description)
new_records.append(new_seq_record)
outf = os.path.join(args.output, os.path.split(f)[1])
SeqIO.write(new_records, open(outf, 'w'), 'fasta')
print count
def main():
options, args = interface()
# iterate through all the files to determine the longest alignment
files = get_files(options.input)
pos1, pos2 = [eval(i) for i in options.positions.strip().split(',')]
for count, f in enumerate(files):
align = AlignIO.parse(f, "nexus")
new_name = os.path.splitext(
os.path.split(f)[1])[0] + '.' + options.format
outf = os.path.join(options.output, new_name)
if options.shorten_name:
for item in rename(align, pos1, pos2, options.splitchar):
AlignIO.write(item, open(outf, 'w'), options.format)
else:
AlignIO.write(align, open(outf, 'w'), options.format)
print count