def test_EMBL_CCDS_RefSeq(self):
exp = [
CodingSequence(
'CR456855', 'EMBL',
Seq(
'ATGGAGGGTCAACGCTGGCTGCCGCTGGAGGCCAATCCCGAGGTCACCAACCAGTTTCTTAAACAATTAGGTCTACATCCTAACTGGCAATTCGTTGATGTATATGGAATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCTTAA',
IUPACUnambiguousDNA()),
Seq(
'MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA',
ExtendedIUPACProtein())),
CodingSequence(
'DQ917642', 'EMBL',
Seq(
'ATGACGGGCAATGCCGGGGAGTGGTGCCTCATGGAAAGCGACCCCGGAGTCTTCACCGAGCTCATTAAAGGATTCGGTTGCCGAGGAGCCCAAGTAGAAGAAATATGGAGTTTAGAGCCTGAGAATTTTGAAAAATTAAAGCCAGTTCATGGGCTGATTTTTCTTTTCAAGTGGCAGCCCGGAGAAGAACCAGCAGGCTCTGTGGTTCAGGACTCCCGACTTGACACGATATTTTTTGCCAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTAAGTGTGTTATTGAACTGTACCCATCAGGATGTCCATTTAGGAGAGACATTGTCAGAGTTTAAGGAATTCTCACAAAGTTTTGATGCAGCTATGAAAGGTTTGGCCCTGAGTAATTCGGATGTGATTCGCCAAGTACACAACAGTTTCGCCAGACAGCAAATGTTTGAATTTGATGCAAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTTGTCAGTTACGTTCCTGTGAATGGAAGACTGTACGAATTAGATGGATTAAGAGAAGGACCGATCGATTTAGGTGCATGCAATCAAGATGACTGGATCAGCGCAGTGAGGCCAGTCATAGAAAAAAGGATACAAAAGTACAGTGAAGGTGAAATTCGATTTAACTTAATGGCCATTGTGTCTGACAGGAAAATGATATATGAACAGAAGATAGCAGAGTTACAAAGACAGCTTGCTGAGGAGGAACCCATGGATACAGATCAGGGTAGTAACATGTTAAGTGCTATTCAGTCAGAAGTTGCCAAAAATCAGATGCTTATTGAAGAAGAAGTACAGAAATTAAAAAGATATAAGATTGAAAACATCAGAAGGAAGCATAATTATCTGCCTTTCATTATGGAACTGTTAAAGACTTTAGCAGAACACCAGCAGTTAATACCTCTCGTAGAAAAGGCAAAAGAAAAACAGAATGCGAAGAAGGCACAGGAAACCAAATGA',
IUPACUnambiguousDNA()),
Seq(
'MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDAKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEEPMDTDQGSNMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK',
ExtendedIUPACProtein())),
CodingSequence(
'NM_001270952', 'RefSeq',
Seq(
'ATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAG',
IUPACUnambiguousDNA()),
Seq(
'MDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA',
ExtendedIUPACProtein())),
CodingSequence(
'CCDS73586.1', 'CCDS',
Seq('ATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAG'
),
Seq('MDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA'
)),
CodingSequence(
'CCDS86041.1', 'CCDS',
Seq('ATGACGGGCAATGCCGGGGAGTGGTGCCTCATGGAAAGCGACCCCGGGGTCTTCACCGAGCTCATTAAAGGATTCGGTTGCCGAGGAGCCCAAGTAGAAGAAATATGGAGTTTAGAGCCTGAGAATTTTGAAAAATTAAAGCCAGTTCATGGGTTAATTTTTCTTTTCAAGTGGCAGCCAGGAGAAGAACCAGCAGGCTCTGTGGTTCAGGACTCCCGACTTGACACGATATTTTTTGCTAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTGAGTGTGTTACTGAACTGTACCCACCAGGATGTCCATTTAGGCGAGACATTATCAGAGTTTAAAGAATTTTCACAAAGTTTTGATGCAGCTATGAAAGGCTTGGCACTGAGCAATTCAGATGTGATTCGACAAGTACACAACAGTTTCGCCAGACAGCAAATGTTTGAATTTGATACGAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTTGTCAGTTATGTTCCTGTTAATGGGAGACTGTATGAATTAGATGGATTAAGAGAAGGACCGATTGATTTAGGTGCATGCAATCAAGATGATTGGATCAGTGCAGTAAGGCCTGTCATAGAAAAAAGGATACAAAAAGACGGGTTTTCACCATGTTGCCCAGGCTGGTCTCAGACTCCTGAGCTCAAGCCATCCGCCTGCCTCGACCTCCCAAAGTGGTACAGTGAAGGTGAAATTCGATTTAATTTAATGGCCATTGTGTCTGACAGAAAAATGATATATGAGCAGAAGATAGCAGAGTTACAAAGACAACTTGCAGAGGAACCCATGGATACAGATCAAGGTAATAGTATGTTAAGTGCTATTCAGTCAGAAGTTGCCAAAAATCAGATGCTTATTGAAGAAGAAGTACAGAAATTAAAAAGATACAAGATTGAGAATATCAGAAGGAAGCATAATTATCTGCCTTTCATTATGGAATTGTTAAAGACTTTAGCAGAACACCAGCAGTTAATACCACTAGTAGAAAAGGCAAAAGAAAAACAGAACGCAAAGAAAGCTCAGGAAACCAAATGA'
),
Seq('MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKDGFSPCCPGWSQTPELKPSACLDLPKWYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK'
))
]
ids = {
'EMBL': ['CR456855.1', 'DQ917642.1'],
'RefSeq': ['NM_001270952.1'],
'CCDS': ['CCDS73586.1', 'CCDS86041.1']
}
formatter = dba.UrlFormatter()
queries = []
for database, id_list in ids.items():
queries += formatter.format(database, id_list)
loop = asyncio.get_event_loop()
fetcher = dba.Entry_fetcher()
entries = loop.run_until_complete(fetcher.fetch_all(queries))
splitter = dba.EntrySplitter()
entries = splitter.split(entries)
loop.close()
parser = dba.DnaParser()
res = parser.parse(entries)
for item in res:
self.assertTrue(item in exp)
self.assertEqual(len(exp), len(res))
def seqcategory(oneseq):
seqtype=''
seqDNA=Seq(oneseq,IUPACAmbiguousDNA()) #Produce a sequence using the string received and the DNA alphabet.
seqRNA=Seq(oneseq,IUPACAmbiguousRNA()) #Produce a sequence using the string received and the RNA alphabet.
seqProt=Seq(oneseq,ExtendedIUPACProtein()) #Produce a sequence using the string received and the protein alphabet.
if Alphabet._verify_alphabet(seqDNA): #Verify if is a DNA sequence.
seqtype='DNA'
elif Alphabet._verify_alphabet(seqRNA): #Verify if is a RNA sequence.
seqtype='RNA'
else:
if Alphabet._verify_alphabet(seqProt): #Verify if is a protein sequence.
seqtype='protein'
else:
seqtype='noseq' #If any, is not a valid sequence.
return seqtype
def parse(self, html_soup):
# title: Report for CCDS[id].[version] (current version)
#.[version] is optional.
#" (current version)" might not be present
titlematcher = re.compile(r'Report for CCDS[0-9]*(?:\.[0-9]*)(?:\ \(current version\))?')
id_ = html_soup.find_all(string=titlematcher)[0] #find() does not take kwargs
idmatcher = r'CCDS[0-9]*(?:.[0-9]*)?'
id_ = re.search(idmatcher, id_).group(0)
nucleotides = html_soup.find_all('span', {'id':re.compile('n[0-9]+')})
aminoacids = html_soup.find_all('span', {'id':re.compile('p[0-9]+')})
dna_seq = Seq(''.join([nt.text for nt in nucleotides]),
IUPACUnambiguousDNA())
aa_seq = Seq(''.join([aa.text for aa in aminoacids]), ExtendedIUPACProtein())
assert aa_seq == dna_seq.translate(cds=True)
return CodingSequence(id_, 'CCDS', dna_seq, aa_seq)
def __init__(self,
unknown1letter='X',
unknown3letter='UNK',
gapchar='',
separator='',
UPPER=1):
"""Optional parameters are: unknown letter and code (when unknown code or letter encountered, respecively),
gap code for single letter, separator between codes in returned three-letter sequence, plus UPPER flag whether
not to distinguish upper/lower case as an input - output is always uppercase.
"""
self.alphabet = ExtendedIUPACProtein()
self.unknown1 = unknown1letter
self.unknown3 = unknown3letter
self.gap_char = gapchar
self.separator = separator
self.upper = UPPER
self.blankseq3 = ['Xer', 'Xaa', 'Ter', 'Sel']
type=int,
default='60',
help='pairwise alignment output width')
args = parser.parse_args()
for file in (args.query_seq, args.target_seq):
if not path.isfile(file):
parser.error("File %s doesn't exist" % file)
# alphabet
if args.seq_type == 'dna':
args.seq_abc = IUPACAmbiguousDNA()
elif args.seq_type == 'rna':
args.seq_abc = IUPACAmbiguousRNA()
else:
args.seq_abc = ExtendedIUPACProtein()
# Aligners setup
aligners = {'global': PairwiseAligner(), 'local': None}
aligners['global'].mode = 'global'
if args.seq_type in ('dna', 'rna'):
aligners['global'].match = args.match_score
aligners['global'].mismatch = args.mismatch_score
if not args.open_gap_score:
args.open_gap_score = -5
if not args.extend_gap_score:
args.extend_gap_score = -2
else:
sub_matrix = getattr(import_module('Bio.SubsMat.MatrixInfo'),
args.sub_matrix)
aligners['global'].substitution_matrix = sub_matrix
class Polypeptide(seq.SequenceMolecule):
alphabet_dict = {'strict':IUPACProtein(),'permissive':ExtendedIUPACProtein()}
def realign(aln_file, path_contig_ma_prot):
"""
:param aln_file: aln file opened by open_aln function
:param path_contig_ma_prot: path to fasta file containing
the contigs multi-aligned in proteins
:type aln: list of lists
:type path_contig_ma_prot: String
:return: msa_prot
:rtype: list of BioPython sequences multi aligned in nt
.. note:: requires BioPython library
meant to be used in main function
to have an output, use realign_w_output
"""
#initialization
msa_prot = []
#opening fasta file
prot_bioseq, prot_id0 = open_fasta(path_contig_ma_prot,
ab=ExtendedIUPACProtein())
prot_id = []
for i in range(len(prot_id0)):
prot_id.append(prot_id0[i].split('_ORGANISM')[0])
"""
opening the aln file and creating dictionaries
"""
nb_seq_aln = aln_file[0]
contig_query = aln_file[1]
contig_frame = aln_file[2]
contig_beg, contig_end = aln_file[3:5]
contig_prot = aln_file[5]
subject_acc = aln_file[6]
subject_beg = aln_file[8]
subject_prot = aln_file[10]
#some contig queries are the same so we change the second name
used_queries = []
for i in range(len(contig_query)):
if contig_query[i] in used_queries:
n = used_queries.count(contig_query[i])
used_queries.append(contig_query[i])
#defining the frame
frame = True
if contig_frame[i] < 0:
frame = False
contig_query[i] = contig_query[i]+"__"+str(n+1)+"__coord_"+\
str(contig_beg[i])+"_"+str(contig_end[i])+"_"+str(frame)
else:
used_queries.append(contig_query[i])
"""
we build nested dictionaries, one dictionary per protein acc
each one contains one dictionary per subject_query having
start, contig_prot, contig_end as keys
aln name of the main dict
aln = {
acc1 = {
"entire",
query1 = {"start",
"contig",
"subject"},
query2:
...
},
acc2 = {
...
},
...
}
"""
aln = {}
#find all unique subject_acc
unique_acc = []
for acc in subject_acc:
if acc not in unique_acc:
unique_acc.append(acc)
#creating the dictionaries
for acc in unique_acc:
if acc in prot_id:
acc_in_fasta = prot_id.index(acc)
aln.update({acc: {"entire": prot_bioseq[acc_in_fasta].seq}})
indexes = [i for i in range(nb_seq_aln) if subject_acc[i] == acc]
for index in indexes:
aln[acc].update({
contig_query[index]: {
"start": subject_beg[index] - 1,
"contig": contig_prot[index],
"subject": subject_prot[index]
}
})
"""
counting the number of indels that need to be added in front of the partial
sequence
using indels_front function from realigning_functions module
"""
used_acc = []
for acc in aln:
used_queries = []
for query in aln[acc]:
if query != "entire":
aln[acc][query]["indels_front"] = indels_front(
aln[acc][query]["start"], aln[acc][query]["subject"],
aln[acc]["entire"])
#adding the indels of this query on both the entire and partial sequence
j = 0
no_indels_front = aln[acc][query]["indels_front"]
while j <= (len(aln[acc][query]["subject"])) - 1:
if aln[acc]["entire"][
no_indels_front +
j] == "-" and aln[acc][query]["subject"][j] != "-":
aln[acc][query]["subject"] = aln[acc][query][
"subject"][:j] + "-" + aln[acc][query]["subject"][
j:]
aln[acc][query]["contig"] = aln[acc][query][
"contig"][:j] + "-" + aln[acc][query]["contig"][j:]
if aln[acc][query]["subject"][j] == "-" and aln[acc][
"entire"][no_indels_front + j] != "-":
aln[acc]["entire"] = aln[acc]["entire"][:(no_indels_front + j)]\
+"-" \
+aln[acc]["entire"][(no_indels_front + j):]
#we add the same indel on the previous queries from this acc
for prev_query in used_queries:
aln[acc][prev_query]["subject"] = \
aln[acc][prev_query]["subject"][:(no_indels_front + j)] \
+ "-" \
+ aln[acc][prev_query]["subject"][(no_indels_front + j):]
aln[acc][prev_query]["contig"] = \
aln[acc][prev_query]["contig"][:(no_indels_front + j)] \
+ "-" \
+ aln[acc][prev_query]["contig"][(no_indels_front + j):]
#we add the same indel on the entires of acc not processed
for acc0 in aln:
if acc0 != acc and acc0 not in used_acc:
aln[acc0]["entire"] = aln[acc0]["entire"][:(no_indels_front + j)] \
+ "-" \
+ aln[acc0]["entire"][(no_indels_front + j):]
#we add the same indel everywhere on the sequences we already processed
for acc0 in aln:
if acc0 != acc and acc0 in used_acc:
for query0 in aln[acc0]:
if query0 == "entire":
aln[acc0][query0] = aln[acc0][query0][:(no_indels_front + j)] \
+ "-" \
+ aln[acc0][query0][(no_indels_front + j):]
else:
aln[acc0][query0]["subject"] = \
aln[acc0][query0]["subject"][:(no_indels_front + j)] \
+ "-" \
+ aln[acc0][query0]["subject"][(no_indels_front + j):]
aln[acc0][query0]["contig"] = \
aln[acc0][query0]["contig"][:(no_indels_front + j)] \
+ "-" \
+ aln[acc0][query0]["contig"][(no_indels_front + j):]
j += 1
#counting the indels at the back of subject
dico = aln[acc][query]
dico["indels_back"] = len(aln[acc]["entire"]) - \
(dico["indels_front"] + len(dico["subject"]))
aln[acc][query] = dico
#adding the indels on the subject
dico = aln[acc][query]
dico["subject"] = "-" * dico["indels_front"] + dico["subject"] \
+ "-" * dico["indels_back"]
dico["contig"] = "-" * dico["indels_front"] \
+ dico["contig"] \
+ "-" * dico["indels_back"]
used_queries.append(query)
aln[acc][query] = dico
used_acc.append(acc)
"""
converting to BioPython protein sequences
"""
for acc in aln:
aln[acc]["entire_bioseq"] = SeqRecord(Seq(str(aln[acc]["entire"]),
Alphabet),
id=acc,
name="No name",
description="subject")
msa_prot.append(aln[acc]["entire_bioseq"])
for query in aln[acc]:
if query != "entire" and query != "entire_bioseq" and "coord" not in query:
dico = aln[acc][query]
dico["contig_bioseq"] = SeqRecord(Seq(dico["contig"],
Alphabet),
id=query,
name="No name",
description="contig")
aln[acc][query] = dico
msa_prot.append(aln[acc][query]["contig_bioseq"])
elif query != "entire" and query != "entire_bioseq":
dico = aln[acc][query]
dico["contig_bioseq"] = SeqRecord(
Seq(dico["contig"], Alphabet),
id=(query.split("__coord")[0]),
name="No name",
description="_contig_" + query.split("__")[-1])
aln[acc][query] = dico
msa_prot.append(aln[acc][query]["contig_bioseq"])
return msa_prot