def splitFastaFile(infile, informat, outdir):
for record in SeqIO.parse(open(infile), informat):
iid = record.id
if not os.path.exists(outdir):
os.mkdir(outdir)
f_out = os.path.join(outdir,iid+'.fasta')
SeqIO.write([record],open(f_out,'w'),"fasta")
def test_generated(self):
"""Write and read back odd SeqRecord objects"""
record1 = SeqRecord(Seq("ACGT"*500, generic_dna), id="Test", description="Long "*500,
letter_annotations={"phred_quality":[40,30,20,10]*500})
record2 = SeqRecord(MutableSeq("NGGC"*1000), id="Mut", description="very "*1000+"long",
letter_annotations={"phred_quality":[0,5,5,10]*1000})
record3 = SeqRecord(UnknownSeq(2000,character="N"), id="Unk", description="l"+("o"*1000)+"ng",
letter_annotations={"phred_quality":[0,1]*1000})
record4 = SeqRecord(Seq("ACGT"*500), id="no_descr", description="", name="",
letter_annotations={"phred_quality":[40,50,60,62]*500})
record5 = SeqRecord(Seq("",generic_dna), id="empty_p", description="(could have been trimmed lots)",
letter_annotations={"phred_quality":[]})
record6 = SeqRecord(Seq(""), id="empty_s", description="(could have been trimmed lots)",
letter_annotations={"solexa_quality":[]})
record7 = SeqRecord(Seq("ACNN"*500), id="Test_Sol", description="Long "*500,
letter_annotations={"solexa_quality":[40,30,0,-5]*500})
record8 = SeqRecord(Seq("ACGT"), id="HighQual", description="With very large qualities that even Sanger FASTQ can't hold!",
letter_annotations={"solexa_quality":[0,10,100,1000]})
#TODO - Record with no identifier?
records = [record1, record2, record3, record4, record5, record6, record7, record8]
#TODO - Have a Biopython defined "DataLossWarning?"
warnings.simplefilter('ignore', BiopythonWarning)
#TODO - Include phd output?
for format in ["fasta", "fastq", "fastq-solexa", "fastq-illumina", "qual"]:
handle = StringIO()
SeqIO.write(records, handle, format)
handle.seek(0)
compare_records(records,
list(SeqIO.parse(handle, format)),
truncation_expected(format))
warnings.filters.pop()
def loop(self, filename, format):
original_records = list(SeqIO.parse(open(filename, "rU"), format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver = DBDRIVER,
user = DBUSER, passwd = DBPASSWD,
host = DBHOST, db = TESTDB)
db_name = "test_loop_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
#Now read them back...
biosql_records = [db.lookup(name=rec.name)
for rec in original_records]
#And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
#Now write to a handle...
handle = StringIO()
SeqIO.write(biosql_records, handle, "gb")
#Now read them back...
handle.seek(0)
new_records = list(SeqIO.parse(handle, "gb"))
#And check they still agree
self.assertEqual(len(new_records), len(original_records))
for old, new in zip(original_records, new_records):
#TODO - remove this hack because we don't yet write these (yet):
for key in ["comment", "references", "db_source"]:
if key in old.annotations and key not in new.annotations:
del old.annotations[key]
self.assertTrue(compare_record(old, new))
#Done
server.close()
def run_pal2nal(fname_aln, fname_nuc, fname_prot):
"""
Generate a codon alignment via PAL2NAL.
@param fname_aln:
MSA of protein sequences in CLUSTAL format (.aln)
@param fname_nuc:
Nucleotide sequences in FASTA format (.fasta)
@param fname_prot:
Protein sequences in FASTA format (.fasta)
@return:
Codon alignment in CLUSTAL format (.aln), suitable for codeml
1"""
sys.stderr.write("\nSTEP: run_pal2nal(%s, %s)\n" % (fname_aln, fname_nuc))
# Reorder fname_nuc according to the order of the proteins in fname_aln, which
# was reordered due to CLUSTALW2. Note that the first protein in each of
# these files remains the same as at the start, however; this first protein
# is our original query protein.
nuc_records = [record for record in SeqIO.parse(fname_nuc, "fasta")]
prot_records = [record for record in SeqIO.parse(fname_prot, "fasta")]
records_map = dict((pr.id, nr) for pr, nr in zip(prot_records, nuc_records))
fname_nuc2 = "homologs_ordered.dna.fasta"
with open(fname_nuc2, "w") as f:
for record in SeqIO.parse(fname_aln, "clustal"):
SeqIO.write(records_map[record.id], f, "fasta")
fname_codon = "homologs.codon.aln"
# TODO: use subprocess
os.system("%s/pal2nal.pl %s %s -output paml > %s" % (bin_dir(), fname_aln, fname_nuc2, fname_codon))
return fname_codon
def test_fastq_2000(self):
"""Read and write back simple example with upper case 2000bp read"""
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here", "ACGT"*500, "[email protected]~"*500)
handle = StringIO()
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
def setUp(self):
self.aln_file = [TEST_ALIGN_FILE1,
TEST_ALIGN_FILE2,
TEST_ALIGN_FILE3,
TEST_ALIGN_FILE4,
TEST_ALIGN_FILE5,
TEST_ALIGN_FILE6]
alns = []
for i in self.aln_file:
if i[1] == 'parse':
nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, alphabet=codonalign.default_codon_alphabet)
elif i[1] == 'index':
nucl = SeqIO.index(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, alphabet=codonalign.default_codon_alphabet, max_score=20)
elif i[1] == 'id':
nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with open(i[0][2]) as handle:
id = dict((i.split()[0], i.split()[1]) for i in handle)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, corr_dict=id, alphabet=codonalign.default_codon_alphabet)
alns.append(caln)
nucl.close() # Close the indexed FASTA file
self.alns = alns
def needle_score(seq1, seq2, verbose=False, keep=False):
"""
get needlman-wunsch score for aligning two sequences
"""
ntf = tempfile.NamedTemporaryFile
with ntf(prefix='seq1', delete = not keep) as fh1, \
ntf(prefix='seq2', delete = not keep) as fh2, \
ntf(prefix='align_out') as outfile, \
open(os.devnull) as dn:
SeqIO.write(seq1, fh1, 'fasta')
fh1.flush()
SeqIO.write(seq2, fh2, 'fasta')
fh2.flush()
cmd = ['needle', '-gapopen', '0',
'-gapextend', '0',
'-outfile', outfile.name,
fh1.name, fh2.name]
if verbose:
print(' '.join(cmd))
subprocess.check_call(cmd, stderr=dn)
result = outfile.read()
pattern = re.compile(r'# Score: (.*)')
score = pattern.search(result)
if score is not None:
return float(score.group(1))
return 0
def frameshift_writer(contigs, file):
sys.stderr.write("[predict] writing frameshifts...")
seqs = [SeqRecord(seq=c.seq, id=c.id, description=c.description) for c in contigs.values()
if c.annotation['majority_frameshift']]
SeqIO.write(seqs, file, "fasta")
file.close()
sys.stderr.write("\tdone.\n")
def no_relatives_writer(contigs, file):
sys.stderr.write("[predict] writing contigs with no relatives...")
seqs = [SeqRecord(seq=c.seq, id=c.id, description=c.description) for c in contigs.values() if
c.annotation['num_relatives'] == 0]
SeqIO.write(seqs, file, "fasta")
file.close()
sys.stderr.write("\tdone.\n")
def __format__(self, format_spec):
"""Returns the record as a string in the specified file format.
This method supports the python format() function added in
Python 2.6/3.0. The format_spec should be a lower case string
supported by Bio.SeqIO as an output file format. See also the
SeqRecord's format() method.
"""
if not format_spec:
#Follow python convention and default to using __str__
return str(self)
from Bio import SeqIO
if format_spec in SeqIO._BinaryFormats:
#Return bytes on Python 3
try:
#This is in Python 2.6+, but we need it on Python 3
from io import BytesIO
handle = BytesIO()
except ImportError:
#Must be on Python 2.5 or older
from StringIO import StringIO
handle = StringIO()
else:
from StringIO import StringIO
handle = StringIO()
SeqIO.write(self, handle, format_spec)
return handle.getvalue()
def main():
if len (sys.argv) != 4 :
print "Please provide file, the file format, and the desired file format "
sys.exit (1)
else:
f = sys.argv[1]
fout = "".join(f.split('.')[:-1])
formatin = sys.argv[2]
formatout = sys.argv[3]
if formatout == 'nexus':
AlignIO.convert(f,formatin,fout+'.'+formatout,formatout,alphabet= IUPAC.ambiguous_dna)
if formatout == 'mega':
handle = open(f, "rU")
record_dict = SeqIO.to_dict(SeqIO.parse(handle, "phylip-relaxed"))
handle.close()
outfile = open(fout+'.'+formatout,'w')
outfile.write('#mega'+"\n")
outfile.write('!Title Mytitle;'+"\n")
outfile.write('!Format DataType=DNA indel=-;'+"\n\n")
for n in record_dict:
outfile.write('#'+n+"\n")
newseq=wrap(str(record_dict[n].seq),60)
for s in newseq:
outfile.write(s+"\n")
outfile.close()
else:
AlignIO.convert(f,formatin,fout+'.'+formatout,formatout)
def filter_reads_by_length(fq1, fq2, quality_format, min_length=20):
"""
removes reads from a pair of fastq files that are shorter than
a minimum length. removes both ends of a read if one end falls
below the threshold while maintaining the order of the reads
"""
logger.info("Removing reads in %s and %s that "
"are less than %d bases." % (fq1, fq2, min_length))
fq1_out = utils.append_stem(fq1, ".fixed")
fq2_out = utils.append_stem(fq2, ".fixed")
fq1_single = utils.append_stem(fq1, ".singles")
fq2_single = utils.append_stem(fq2, ".singles")
if all(map(utils.file_exists, [fq1_out, fq2_out, fq2_single, fq2_single])):
return [fq1_out, fq2_out]
fq1_in = SeqIO.parse(fq1, quality_format)
fq2_in = SeqIO.parse(fq2, quality_format)
with open(fq1_out, 'w') as fq1_out_handle, open(fq2_out, 'w') as fq2_out_handle, open(fq1_single, 'w') as fq1_single_handle, open(fq2_single, 'w') as fq2_single_handle:
for fq1_record, fq2_record in izip(fq1_in, fq2_in):
if len(fq1_record.seq) >= min_length and len(fq2_record.seq) >= min_length:
fq1_out_handle.write(fq1_record.format(quality_format))
fq2_out_handle.write(fq2_record.format(quality_format))
else:
if len(fq1_record.seq) > min_length:
fq1_single_handle.write(fq1_record.format(quality_format))
if len(fq2_record.seq) > min_length:
fq2_single_handle.write(fq2_record.format(quality_format))
return [fq1_out, fq2_out]
def gather_est2genome_seqs(refseq_obj, est2genome_handle, log_line, velvet_file):
seq_dir = log_line.split("\t")[1]
tmp_refseq = seq_dir.split("/")[3].replace(".","%2E")#hardcoded in this position
gff_file = refseq_obj.id + ".velvet_contigs.maker.output/" + seq_dir + "/" + tmp_refseq + ".gff"
gff_handle = open(gff_file,'r')
for gff_line in gff_handle:
if(re.search("est2gneome",gff_line) and \
re.search("\texpressed_sequence_match\t",gff_line)):
curr_start = int(gff_line.split("\t")[3])
curr_stop = int(gff_line.split("\t")[4])
curr_strand = gff_line.split("\t")[6]
tmp_handle = open(velvet_file,'r')
tmp_fasta = SeqIO.to_dict(SeqIO.parse(tmp_handle,"fasta"))
tmp_handle.close()
if seq_dir.split("/")[3] in tmp_fasta:
curr_record = tmp_fasta[seq_dir.split("/")[3]]
else:
continue
new_seq = curr_record.seq[curr_start - 1:curr_stop]
if(curr_strand == "-"):
new_seq = curr_record.seq[curr_start - 1:curr_stop].reverse_complement()
new_record = SeqRecord(new_seq,id=seqname,name=seqname,description="")
SeqIO.write(est2genome_handle,"fasta")
def check_convert_fails(in_filename, in_format, out_format, alphabet=None):
qual_truncate = truncation_expected(out_format)
#We want the SAME error message from parse/write as convert!
err1 = None
try:
records = list(SeqIO.parse(in_filename,in_format, alphabet))
handle = StringIO()
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.write(records, handle, out_format)
if qual_truncate:
warnings.filters.pop()
handle.seek(0)
assert False, "Parse or write should have failed!"
except ValueError as err:
err1 = err
#Now do the conversion...
try:
handle2 = StringIO()
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.convert(in_filename, in_format, handle2, out_format, alphabet)
if qual_truncate:
warnings.filters.pop()
assert False, "Convert should have failed!"
except ValueError as err2:
assert str(err1) == str(err2), \
"Different failures, parse/write:\n%s\nconvert:\n%s" \
% (err1, err2)
def main_build_markov(promotor_filename = "promotor.fa", genome_filename = "genom.fa", symbol_length = 2, load_cached = False, save_cache = True):
''' Na podstawie plików z sekwencjami promotorowymi i genomem funkcja buduje model Markova'''
promotor_sequences = [ x for x in SeqIO.parse("promotor.fa", "fasta")]
genome = [ x for x in SeqIO.parse("genom.fa", "fasta")]
if not load_cached:
promotor_freqs = calc_symbol_freq(promotor_sequences)
genome_freqs = calc_symbol_freq(genome)
if save_cache:
dump_obj(promotor_freqs, Dumpfiles.promotor_freq)
dump_obj(genome_freqs, Dumpfiles.genome_freq)
else:
promotor_freqs = load_obj(Dumpfiles.promotor_freq)
genome_freqs = load_obj(Dumpfiles.genome_freq)
promotor_counts = calc_counts(promotor_sequences)
genome_counts = calc_counts(genome)
print promotor_counts
promotor_freqs = fold_and_normalize(promotor_freqs[symbol_length], symbol_length, promotor_counts[symbol_length])
genome_freqs = fold_and_normalize(genome_freqs[symbol_length], symbol_length, genome_counts[symbol_length])
for k in promotor_freqs:
assert(k in genome_freqs)
for k in genome_freqs:
assert(k in genome_freqs)
print promotor_freqs
(markov, states) = build_markov(genome_freqs, promotor_freqs)
return (markov, states)
def illumina2sangerFq(inputfile):
print help(SeqIO.convert)
filename = inputfile[:-3]+'.fastq'
SeqIO.convert(inputfile, "fastq-illumina", filename, "fastq")
def cluster_pid(folder):
result = []
f_name = folder.split("/")[-1]
try:
genes = pd.read_csv(folder + "/report/" + f_name + "_genes.csv")
genes = genes.loc[~(genes['cluster'].isin(['na', '0', 0])) & (genes['species'] == 'Homo sapiens')]
if genes.shape[0] > 0:
for cluster in set(genes['cluster']):
pids = []
accs = genes.loc[genes['cluster'] == cluster, 'prot_acc'].values
for seq1 in accs:
for seq2 in accs:
seq_1 = [x.seq for x in SeqIO.parse("../cgpf_ncbi/all_seqs.fa", 'fasta') if
x.name.split("|")[2] == seq1]
seq_2 = [x.seq for x in SeqIO.parse("../cgpf_ncbi/all_seqs.fa", 'fasta') if
x.name.split("|")[2] == seq2]
aln = pairwise2.align.globalxx(seq_1[0], seq_2[0])[0]
mean_len = (len(aln[0]) + len(aln[1])) / 2
pids.append(aln[2] / mean_len)
n_genes = len(pids)
mean_pid = np.mean(pids)
sd_id = np.std(pids)
result.append(cluster, n_genes, mean_pid, sd_id)
print(cluster)
return result
except OSError:
return None
def CutOutDomain(coords,filename, header=False, column_id=0, column_start=8, column_stop=9):
"""COMMENTS"""
from Bio import SeqIO
fh=open(coords)
seqfile=open(filename)
Towrite=[]
CoordIDDic={}
if header==True:
print 'header set to True, first line of %s will be ignored'%coords
skip_header=fh.readline()
else:
print 'header not set to True, first line of %s will be processed'%coords
for unformatedLine in fh:
l=unformatedLine.replace('\xa0', '').strip().split(',')
if l[column_id] not in CoordIDDic:
CoordIDDic[l[column_id]]=l[column_start], l[column_stop]
else:
for s in SeqIO.parse(seqfile, 'fasta'):
if s.id in CoordIDDic:
start=(int(CoordIDDic.get(s.id)[0])-1)
stop=int(CoordIDDic.get(s.id)[1])
s.id=s.id+'_%s_%s'%((start+1), stop)
Towrite.append(s[start:stop])
else:
Output=open('CutOutdomain_%s'%filename, 'w')
SeqIO.write(Towrite, Output, 'fasta')
def main(gbdir, outdir):
os.makedirs(gbdir, exist_ok=True)
os.makedirs(outdir, exist_ok=True)
tempq = 'tempquery.fasta'
tempdb = 'tempdb.fasta'
for org in tqdm(Organism.objects.all()):
# get genbank and convert to fasta
fpath = os.path.join(gbdir, '{}.gb'.format(org.accession))
if not os.path.isfile(fpath):
print('\nFetching {} with accession {}'.format(
org.name,
org.accession
))
fetch(fpath)
SeqIO.convert(fpath, 'genbank', tempdb, 'fasta')
# get spacers of organism and convert to fasta
spacers = Spacer.objects.filter(loci__organism=org)
fastatext = ''.join(['>{}\n{}\n'.format(spacer.id, spacer.sequence)
for spacer in spacers])
with open(tempq, 'w') as f:
f.write(fastatext)
# run blast and save output
outpath = os.path.join(outdir, '{}.json'.format(org.accession))
commandargs = ['blastn', '-query', tempq,
'-subject', tempdb, '-out', outpath, '-outfmt', '15']
subprocess.run(commandargs, stdout=subprocess.DEVNULL)
os.remove(tempq)
os.remove(tempdb)
def _get_seq_dict(self):
"""Internal reusable function to get the sequence dictionary.
"""
seq_handle = open(self._test_seq_file)
seq_dict = SeqIO.to_dict(SeqIO.parse(seq_handle, "fasta"))
seq_handle.close()
return seq_dict
def blastclust_to_fasta(infname, seqfname, outdir):
"""Converts input BLASTCLUST output list to a subdirectory of FASTA files.
Each individual FASTA file contains all sequences from a single cluster.
The sequences matching the IDs listed in the BLASTCLUST output .lst file
should all be found in the same file.
Returns the output directory and a list of the files, as a tuple.
"""
outdirname = os.path.join(outdir, "blastclust_OTUs")
if not os.path.exists(outdirname):
os.makedirs(outdirname)
seqdict = SeqIO.index(seqfname, 'fasta')
outfnames = []
with open(infname, 'r') as fh:
otu_id = 0
for line in fh:
otu_id += 1
outfname = os.path.join(outdirname,
"blastclust_OTU_%06d.fasta" % otu_id)
SeqIO.write((seqdict[key] for key in line.split()),
outfname, 'fasta')
outfnames.append(outfname)
return (outdirname, outfnames)
def not_t_full_celegans(self):
"""Test the full C elegans chromosome and GFF files.
This is used to test GFF on large files and is not run as a standard
test. You will need to download the files and adjust the paths
to run this.
"""
# read the sequence information
seq_file = os.path.join(self._full_dir, "c_elegans.WS199.dna.fa")
gff_file = os.path.join(self._full_dir, "c_elegans.WS199.gff3")
seq_handle = open(seq_file)
seq_dict = SeqIO.to_dict(SeqIO.parse(seq_handle, "fasta"))
seq_handle.close()
#with open(gff_file) as gff_handle:
# possible_limits = feature_adder.available_limits(gff_handle)
# pprint.pprint(possible_limits)
rnai_types = [('Orfeome', 'PCR_product'),
('GenePair_STS', 'PCR_product'),
('Promoterome', 'PCR_product')]
gene_types = [('Non_coding_transcript', 'gene'),
('Coding_transcript', 'gene'),
('Coding_transcript', 'mRNA'),
('Coding_transcript', 'CDS')]
limit_info = dict(gff_source_type = rnai_types + gene_types)
for rec in GFF.parse(gff_file, seq_dict, limit_info=limit_info):
pass
def test_fasta_out(self):
"""Check FASTQ to FASTA output"""
records = SeqIO.parse("Quality/example.fastq", "fastq")
h = StringIO()
SeqIO.write(records, h, "fasta")
with open("Quality/example.fasta") as expected:
self.assertEqual(h.getvalue(), expected.read())
def main(args):
server = BioSeqDatabase.open_database(driver=args.driver, db=args.database, user=args.user, host=args.host, passwd=args.password)
if args.database_name not in server.keys():
server.new_database(args.database_name)
db = server[args.database_name]
gen = []
if args.fasta is not None:
for rec in SeqIO.parse(args.fasta, 'fasta'):
gen.append(rec.name)
elif args.genbank is not None:
for rec in SeqIO.parse(args.genbank, 'genbank'):
gen.append(rec.name)
elif args.input is not None:
with open(args.input) as fp:
for line in fp:
gen.append(line.rstrip())
if args.remove:
taxon_id = None
else:
taxon_id = add_new_taxonomy(server, args.new_taxons, args.taxid)
for rec in gen:
server.adaptor.execute('update bioentry set taxon_id = %s where bioentry_id = %s',(taxon_id, db.adaptor.fetch_seqid_by_display_id(db.dbid, rec)))
server.commit()
def test_fastq_1000(self):
"""Read and write back simple example with mixed case 1000bp read"""
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here", "ACGTNncgta"*100, "abcd!!efgh"*100)
handle = StringIO()
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
def count_overlap(filename):
for seq_record in SeqIO.parse(filename, "fasta"):
for seq_record_1 in SeqIO.parse(filename, "fasta"):
s1 = seq_record.seq
s2 = seq_record_1.seq
if s1 != s2 and s1[-3:] == s2[0:3]:
print(seq_record.id + " " + seq_record_1.id)
def load_examples_from_fasta(signal, org, data_path):
"""
load examples from fasta file
signal
"""
fn_pos = "%s/%s_sig_%s_example.fa" % (data_path, signal, "pos")
fn_neg = "%s/%s_sig_%s_example.fa" % (data_path, signal, "neg")
print "loading: \n %s \n %s" % (fn_pos, fn_neg)
# parse file
xt_pos = [str(rec.seq) for rec in SeqIO.parse(fn_pos, "fasta")]
xt_neg = [str(rec.seq) for rec in SeqIO.parse(fn_neg, "fasta")]
labels = [+1] * len(xt_pos) + [-1] * len(xt_neg)
examples = xt_pos + xt_neg
print (
"organism: %s, signal %s,\t num_labels: %i,\t num_examples %i,\t num_positives: %i,\t num_negatives: %i"
% (org, signal, len(labels), len(examples), len(xt_pos), len(xt_neg))
)
examples_shuffled, labels_shuffled = helper.coshuffle(examples, labels)
ret = {"examples": numpy.array(examples_shuffled), "labels": numpy.array(labels_shuffled)}
return ret
def _validate_fasta(self, text):
try:
SeqIO.parse(text, 'fasta').next()
return text
except StopIteration:
raise argparse.ArgumentTypeError(
"{0} is not fasta file".format(text))
def standard_test_procedure(self, cline):
"""Standard testing procedure used by all tests."""
# Overwrite existing files.
cline.force = True
# Mark output files for later cleanup.
self.add_file_to_clean(cline.outfile)
if cline.guidetree_out:
self.add_file_to_clean(cline.guidetree_out)
input_records = SeqIO.to_dict(SeqIO.parse(cline.infile, "fasta"))
self.assertEqual(str(eval(repr(cline))), str(cline))
output, error = cline()
self.assertTrue(not output or output.strip().startswith("CLUSTAL"))
# Test if ClustalOmega executed successfully.
self.assertTrue(error.strip() == "" or
error.startswith("WARNING: Sequence type is DNA.") or
error.startswith("WARNING: DNA alignment is still experimental."))
# Check the output...
align = AlignIO.read(cline.outfile, "clustal")
output_records = SeqIO.to_dict(SeqIO.parse(cline.outfile, "clustal"))
self.assertEqual(len(set(input_records.keys())), len(set(output_records.keys())))
for record in align:
self.assertEqual(str(record.seq), str(output_records[record.id].seq))
# TODO - Try and parse this with Bio.Nexus?
if cline.guidetree_out:
self.assertTrue(os.path.isfile(cline.guidetree_out))
def test_acba_annot(self):
replicon_filename = 'acba.007.p01.13'
replicon_id = 'ACBA.007.P01_13'
command = "integron_finder --outdir {out_dir} --func-annot --path-func-annot {annot_bank} --promoter-attI " \
"--gbk --keep-tmp " \
"{replicon}".format(out_dir=self.out_dir,
annot_bank=self.resfams_dir,
replicon=self.find_data(os.path.join('Replicons', '{}.fst'.format(replicon_filename)))
)
with self.catch_io(out=True, err=False):
main(command.split()[1:], loglevel='WARNING')
result_dir = os.path.join(self.out_dir, 'Results_Integron_Finder_{}'.format(replicon_filename))
gbk = '{}.gbk'.format(replicon_id)
expected_gbk = self.find_data(os.path.join('Results_Integron_Finder_{}.annot'.format(replicon_filename), gbk))
gbk_test = os.path.join(result_dir, gbk)
expected_gbk = SeqIO.read(expected_gbk, 'gb')
gbk_test = SeqIO.read(gbk_test, 'gb')
self.assertSeqRecordEqual(expected_gbk, gbk_test)
output_filename = '{}.integrons'.format(replicon_filename)
expected_result_path = self.find_data(os.path.join('Results_Integron_Finder_{}.annot'.format(replicon_filename),
output_filename))
test_result_path = os.path.join(result_dir, output_filename)
self.assertIntegronResultEqual(expected_result_path, test_result_path)
output_filename = os.path.join('tmp_{}'.format(replicon_id), replicon_id + '_Resfams_fa_table.res')
expected_result_path = self.find_data(os.path.join('Results_Integron_Finder_{}.annot'.format(replicon_filename),
output_filename))
test_result_path = os.path.join(result_dir, output_filename)
self.assertHmmEqual(expected_result_path, test_result_path)
