def read_embl(path_to_embls: list, num_of_entries: int, exclude_csv: str, queue):
""" Reads entries from a list of existing embl files """
if exclude_csv is None:
# If no exclude csv is provided, we execute the reading without an if checking! (performance)
for input_f in path_to_embls:
# For each entry: try to read it and
# add it to the queue
try:
entries = SwissProt.parse(input_f)
for entry in entries:
queue.put(entry)
except Exception as e:
print("File '{}' could not be parsed and was excluded. Reason: {}".format(input_f, e))
else:
# If a exclude csv is provided, then a simple if check is added (reduced performance)
with open(exclude_csv) as in_f:
# Read the contents of the csv
csv_reader = csv.reader(in_f)
exclude_set = set(x[0] for x in list(csv_reader))
for input_f in path_to_embls:
# For each entry: try to read it and
# add it to the queue
try:
entries = SwissProt.parse(input_f)
for entry in entries:
if entry.accessions[0] in exclude_set:
# This effectively skips an entry at the cost to check whether to skip in EACH entry!
continue
queue.put(entry)
except Exception as e:
print("File '{}' could not be parsed and was excluded. Reason: {}".format(input_f, e))
def sync_query_list_with_response(response_fn, query_list):
db_data = {}
with open(response_fn, 'r') as fh:
for record in SwissProt.parse(fh):
acc = record.accessions[0]
# Select only EMBL and RefSeq crossrefs
refseq_refs, embl_refs = [], []
for db_ref in record.cross_references:
if db_ref[0] == 'RefSeq':
refseq_refs.append(db_ref[1:])
elif db_ref[0] == 'EMBL':
embl_refs.append(db_ref[1:])
db_data[acc] = {'RefSeq': refseq_refs,
'EMBL': embl_refs}
# This is to handle isoforms
# E.g. P03692 and P03692-1 can both be included in the query list
# P03705-2 can be in the query list but not P03705
for prot in query_list: # For each of the original queries
if (prot not in db_data) and ('-' in prot): # If the query is not returned
base_name = prot.split('-')[0] # Search for the fist part
if base_name in db_data: # If it is present in the db_data
if base_name not in query_list: # If it's not in the original query list
db_data[prot] = db_data[base_name] # Fill in the information for the corresponding protein
db_data.pop(base_name) # AND remove the original part
elif base_name in query_list: # If the first part is in the original query
db_data[prot] = db_data[base_name] # Fill in the information WITHOUT removing the original part
elif prot not in db_data:
print("I don't know what to do with this id: {}".format(prot))
pass
return db_data
def write_swissprot_annotations(outf, indentation_level, uniprot, uniprot_f):
uniprot_dat_indices = UniProtDatIndex.objects.filter(uniprot=uniprot)
for uniprot_dat_index in uniprot_dat_indices:
if uniprot_dat_index.uniprot_accession == uniprot.accession:
break
uniprot_f.seek(uniprot_dat_index.file_char)
record = SwissProt.parse(uniprot_f).next()
indented_write(outf, indentation_level + 1,
"Length: %d\n" % record.sequence_length)
if len(record.gene_name) > 0:
for name_spec in record.gene_name.replace('\n', ' ').split('; '):
name_type, names = name_spec.split('=')
indented_write(outf, indentation_level + 1,
"%s: %s\n" % (name_type, names))
for keyword in record.keywords:
indented_write(outf, indentation_level + 1, 'Keyword: %s\n' % keyword)
for comment in record.comments:
if comment[0:5] == '-----':
continue
components = comment.replace(':\n', ': ').split(': ')
comment_type = components[0]
comment_lines = ': '.join(components[1:]).split('\n')
indented_write(outf, indentation_level + 1, "%s:\n" % comment_type)
for line in comment_lines:
indented_write(outf, indentation_level + 2, "%s\n" % line)
for cross_reference in record.cross_references:
indented_write(
outf, indentation_level + 1,
"%s: %s\n" % (cross_reference[0], '; '.join(cross_reference[1:])))
def go_in_papers(sp_path):
# Returns: papers: key: pubmed_id; value: list of go_rec records
# go_rec record is a dictionary. Keys (values): 'sp_id' (swissprot id);
# 'go_id': (GO ID); 'go_ec': (GO Evidence Code).
# To be used with SP data, not GOA
papers = {}
go_ids = {}
sp_recs = {}
papers_prots = {}
sph = open(sp_path)
for sp_rec in SP.parse(sph):
cur_go_recs = get_go_evidence_codes(sp_rec)
# print cur_go_recs
if not cur_go_recs:
continue
cur_papers = get_papers(sp_rec)
for paper in cur_papers:
if paper not in papers_prots:
papers_prots[paper] = {sp_rec.entry_name: 1}
else:
papers_prots[paper][sp_rec.entry_name] = \
papers_prots[paper].get(sp_rec.entry_name,0)+1
for cur_go_rec in cur_go_recs:
d1 = dict(sp_id=sp_rec.entry_name,
go_id=cur_go_rec[0],
go_ec=cur_go_rec[1])
papers.setdefault(paper,[]).append(d1)
return papers, papers_prots
def pull_uniprot(repull=False):
xmlname = os.path.join(os.path.dirname(__file__),
'uniprot_sprot_human.dat')
if repull:
xmldata = pull_and_decompress(
'ftp.uniprot.org',
'/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/',
'uniprot_sprot_human.dat.gz')
with open(xmlname, 'w') as xmlfile:
xmlfile.write(xmldata)
seq_to_idlist = defaultdict(set)
#I only want the PRO sequences. One day, I could get the -1 -2 sequences as well if
# there were a reason.
with open(xmlname, 'r') as unif:
for record in SwissProt.parse(unif):
uniprotid = f'UniProtKB:{record.accessions[0]}'
#xrefs = [ f"{x[0]}:{x[1]}" for x in record.cross_references if x[0].lower() in ['mint','string','nextprot']]
#xrefs.append( f'PR:{record.accessions[0]}' )
#xrefs.append( uniprotid )
feats = [
f for f in record.features if f[4].startswith('PRO_')
and isinstance(f[1], int) and isinstance(f[2], int)
]
fseq = [(record.sequence[f[1] - 1:f[2]], f[4]) for f in feats]
#seq_to_idlist[record.sequence].update(xrefs)
for fs, fn in fseq:
seq_to_idlist[fs].add(f'{uniprotid}#{fn}')
return seq_to_idlist
def file_parse():
file = gzip.open("uniprot.gz")
#Declaration of arrays which check for repitions
non_rep_id = []
non_rep_org = []
non_rep_tax = []
swiss_records = SwissProt.parse(file)
for swiss_record in swiss_records:
#NCBI ID
id = swiss_record.taxonomy_id
if id not in non_rep_id:
non_rep_id.append(id)
#ORGANISM NAME
organism = (swiss_record.organism.strip('.'))
if organism not in non_rep_org:
non_rep_org.append(organism)
#TAXONOMY
taxonomy= (swiss_record.organism_classification)
if taxonomy not in non_rep_tax:
non_rep_tax.append(taxonomy)
#ZIP arrays to column/tab seperated output
for i in zip(non_rep_id, non_rep_org, non_rep_tax):
print ("".join(map((str), list(format(i)))))
def parse_uniprot(input_file):
dic_pfam = {}
dic_dom = {}
dic_king = {}
# probably faster/easier to use the XML parser directly
#print (input_file)
handle = open(input_file)
for record in SwissProt.parse(handle):
#print (record)
#print (record.entry_name)
#print (record.cross_references)
entry = record.entry_name
id = entry
dic_pfam[id] = ''
dic_dom[id] = 0
dic_king[id] = 'Unique'
for db in record.cross_references:
if (db[0] == "Pfam"):
dic_pfam[id] = dic_pfam[id] + db[1] + ";"
dic_dom[id] += 1
if (db[1] in shared_domains.keys()):
dic_king[id] = "Shared"
if (dic_dom[id] == 0):
dic_king[id] = 'None'
return dic_pfam, dic_dom, dic_king
def test_compute_features_return_empty_list_if_features_are_empty(self):
for record in SwissProt.parse(self.records):
protein = parse_record_into_protein(record)
break
protein.go_mf = None
protein.go_bp = None
protein.go_cc = None
protein.interpro = None
protein.pfam = None
protein.keywords = None
protein.save(self.session, commit=True)
protein = Protein.query.get(protein.id) # Refresh
features = compute_interaction_features(protein, protein)
expected = dict(go_mf=[],
go_bp=[],
go_cc=[],
ulca_go_mf=[],
ulca_go_bp=[],
ulca_go_cc=[],
interpro=[],
pfam=[],
keywords=[])
self.assertEqual(expected, features)
def test_can_parse_record_into_protein_objects(self):
for record in SwissProt.parse(self.records):
obj = parse_record_into_protein(record)
break
self.assertEqual(obj.uniprot_id, "P31946")
self.assertEqual(obj.gene_id, "YWHAB")
self.assertEqual(obj.reviewed, True)
def features(files): ft=['ZN_FING', 'REGION','METAL','SITE','SIGNAL','REPEAT', 'NP_REGION', 'BINDING','MOTIF','MOD_RES', 'LIPID','DOMAIN','DNA_BIND','DISULFID','CROSSLNK', 'CARBOHYD','CA_BIND', 'ACT_SITE'] for record in SwissProt.parse(open(files)): for l in record.features: if l[0] in ft: print l[0]+','+str(l[1])+'-'+str(l[2])+','+l[3]
def _parse_features( self ):
print( 'uniprot flat files, to get features...' )
with open( path + files[16], 'wt' ) as outf:
for j in [11,12,13,14]:
print( files[j] + '...' )
with open(path + files[j], 'rt') as handle:
for record in SwissProt.parse(handle):
if record.taxonomy_id[0] in ['9606', '10090', '10116']:
accs = record.accessions
acc = accs.pop(0)
feats = record.features
for f in feats:
f = list(f)
f.insert(3, '')
if re.search(r'^[^\.]+\.\s*$', f[4]):
m = re.match(r'^(.+)\.\s*$', f[4])
if m:
f[3] = m.group(1)
f[4] = ''
elif re.search(r'.+\.\s+\{', f[4]):
m = re.match(r'^(.+)\.\s*\{(.+)\}\.$', f[4])
if m:
f[3] = m.group(1)
f[4] = m.group(2)
elif re.search(r'.+\.\s+\/', f[4]):
m = re.match(r'^(.+)\.\s*\/(.+)\.$', f[4])
if m:
f[3] = m.group(1)
f[4] = m.group(2)
else :
f[4] = re.sub(r'[\{\}\.\/]', '', f[4])
#print(f)
outf.write( acc + "\t" + '\t'.join(map(str, f)) + '\n')
def test_compute_features_returns_None_if_target_is_None(self):
for record in SwissProt.parse(self.records):
protein = parse_record_into_protein(record)
break
protein.save(self.session, commit=True)
protein = Protein.query.get(protein.id) # Refresh
self.assertIsNone(compute_interaction_features(protein, None))
def get_genes (self,gene_name=""):
if gene_name != "":
print "Finding \"{}\" gene in Uniprot database...".format(gene_name)
upper_name = gene_name.upper() # Rho --> RHO
output_handle = open(self.fasta_file, "w")
for record in SwissProt.parse (self.fd):
match = record.gene_name[5:5+len(upper_name)+1].upper()
# Name=Rhodop; --> RHOD (Length of the queried name (rho)+1)
# For matching the two possibilities
# 1) Name=Rho;
# 2) Name=rho {ECO.....}
# So, it fill compare the queried gene name and match one e.g.
# in 1st case "RHO " == "RHO;" or "RHO;" == "RHO;"
# in 2nd case "RHO " == "RHO " or "RHO;" == "RHO "
# We do not consider gene names differ to "Name=...;" in swisprot file
if (upper_name+" ") == match or (upper_name+";") == match:
print "Add protein to fasta file: " + record.entry_name + ", ...." + record.gene_name
output = ">"+record.entry_name+"\n"+record.sequence.format("fasta")+"\n"
#print output
output_handle.write(output)
output_handle.write("")
output_handle.close()
def go_in_papers(sp_path):
# Returns: papers: key: pubmed_id; value: list of go_rec records
# go_rec record is a dictionary. Keys (values): 'sp_id' (swissprot id);
# 'go_id': (GO ID); 'go_ec': (GO Evidence Code).
# To be used with SP data, not GOA
papers = {}
go_ids = {}
sp_recs = {}
papers_prots = {}
sph = open(sp_path)
for sp_rec in SP.parse(sph):
cur_go_recs = get_go_evidence_codes(sp_rec)
# print cur_go_recs
if not cur_go_recs:
continue
cur_papers = get_papers(sp_rec)
for paper in cur_papers:
if paper not in papers_prots:
papers_prots[paper] = {sp_rec.entry_name: 1}
else:
papers_prots[paper][sp_rec.entry_name] = \
papers_prots[paper].get(sp_rec.entry_name,0)+1
for cur_go_rec in cur_go_recs:
d1 = dict(sp_id=sp_rec.entry_name,
go_id=cur_go_rec[0],
go_ec=cur_go_rec[1])
papers.setdefault(paper, []).append(d1)
return papers, papers_prots
def load_uniprot(self):
self.uniprot = None
if not self.exists('uniprot.txt'):
return
with self.open('uniprot.txt') as fp:
self.uniprot = []
for record in SwissProt.parse(fp):
self.uniprot.append(record)
def test_parses_function_as_None_for_entry_with_no_comment(self):
for record in SwissProt.parse(self.records):
r = record
break
r.comments = [x for x in r.comments if "FUNCTION: " not in x]
result = function(r)
expected = None
self.assertEqual(result, expected)
def generate_uniprot_record(self):
for file_handle, file_number in self._uniprot_file_handle():
data_source = self._file_number_to_source(file_number)
for record in SwissProt.parse(file_handle):
if self._check_id_to_use(record.accessions[0]):
current_record_dict = self._parse_record(
record, data_source)
yield current_record_dict
def get_ancestors_list():
i = 0
handle = open("uniprot_sprot.dat")
for record in SwissProt.parse(handle):
descriptions.append(record.sequence)
print(descriptions)
i += 1
if i == 1:
break
def _parse_flat_files( self ):
print( 'uniprot flat files...' )
with open( path + files[15], 'wt' ) as outf:
for j in [11,12,13,14]:
print( files[j] + '...' )
with open(path + files[j], 'rt') as handle:
for record in SwissProt.parse(handle):
if record.taxonomy_id[0] in ['9606', '10090', '10116']:
accs = record.accessions
acc = accs.pop(0)
rev = record.data_class
gname = re.sub(r'.*Name=([^;{]+)[{;].*', r'\1', record.gene_name).strip()
uid = record.entry_name
taxid = record.taxonomy_id[0]
seq = record.sequence
sinfo = str(record.seqinfo[0])
srcdb = 'sp'
if re.search(r'trembl', files[j]):
srcdb = 'tr'
rname = ''
fname = ''
sname = ''
flags = ''
if 'RecName' in record.description:
rname = re.sub(r'.*RecName: *Full=([^;{]+)[{;].*', r'\1', record.description, re.IGNORECASE).strip()
elif 'SubName' in record.description:
rname = re.sub(r'.*SubName: *Full=([^;{]+) *[;{].*', r'\1', record.description, re.IGNORECASE).strip()
if 'AltName' in record.description:
if re.search(r'AltName:[^:]*Full=', record.description, re.IGNORECASE):
fname = re.sub(r'.*AltName:[^:]*Full=([^;{]+)[{;].*', r'\1', record.description, re.IGNORECASE).strip()
if re.search(r'AltName:[^:]*Short=', record.description, re.IGNORECASE):
sname = re.sub(r'.*AltName:[^:]*Short=([^;{]+)[{;].*', r'\1', record.description, re.IGNORECASE).strip()
if 'Flags:' in record.description:
flags = re.sub(r'.*Flags: *([^;]+);.*', r'\1', record.description, re.IGNORECASE).strip()
refs = list()
eids = list()
mgis = list()
hgnc = list()
dids = list()
dnms = list()
ddbs = list()
for i in range(0, len(record.cross_references)):
if record.cross_references[i][0] == 'GeneID':
eids.append(record.cross_references[i][1])
if record.cross_references[i][0] == 'RefSeq':
refs.append(re.sub(r'\.\d+$', r'', record.cross_references[i][1]))
if record.cross_references[i][0] == 'MGI':
mgis.append(record.cross_references[i][1])
if record.cross_references[i][0] == 'HGNC':
hgnc.append(record.cross_references[i][1])
if record.cross_references[i][0] in xdoms:
dids.append(record.cross_references[i][1])
ddbs.append(record.cross_references[i][0])
dnms.append(record.cross_references[i][2])
outf.write( '\t'.join([ acc, uid, srcdb, taxid, rev, gname, rname, fname, sname, flags, '|'.join(accs), '|'.join(eids), '|'.join(refs), '|'.join(hgnc), '|'.join(mgis), '|'.join(ddbs), '|'.join(dids), '|'.join(dnms), sinfo, seq ]) + '\n' )
def test_parses_interpro_correctly(self):
for record in SwissProt.parse(self.records):
result = interpro_terms(record)
break
expected = [
'IPR000308',
'IPR023409',
'IPR036815',
'IPR023410',
]
self.assertEqual(result, expected)
def give_me_the_record(primary_id, swissprot_file):
"""
Return a single record given with the primary id
:param primary_id: A primary id
:param swissprot_file: A swissprot file
:return: A record with accession == primary id
"""
with open(swissprot_file, 'r') as fh:
for record in SwissProt.parse(fh):
if primary_id in record.accessions:
return record
def obtain_taxons(self, protein_dict, fh_sprot):
found = False
for rec in sp.parse(fh_sprot):
for ac in range(len(rec.accessions)):
if rec.accessions[ac] in protein_dict.keys():
# assign rec.taxonomy_id list to the protein
protein_dict[rec.accessions[ac]] = rec.taxonomy_id
found = True
break
#if found:
# break
return protein_dict
def __init__(self, sprot_cache='', trembl_cache='', organism='h**o sapien'):
self.records = {}
self.organism = organism.strip().lower()
if sprot_cache:
# Load the swissprot records if file can be found
try:
with open(sprot_cache) as fp:
for record in SwissProt.parse(fp):
for accession in record.accessions:
self.records[accession] = record
except IOError, e:
print(e); print("SwissProt cache not loaded")
def test_parses_keywords_correctly(self):
for record in SwissProt.parse(self.records):
result = keywords(record)
break
expected = [
'3D-structure', 'Acetylation', 'Alternative initiation',
'Complete proteome', 'Cytoplasm', 'Direct protein sequencing',
'Host-virus interaction', 'Isopeptide bond', 'Nitration',
'Phosphoprotein', 'Polymorphism', 'Reference proteome',
'Ubl conjugation'
]
self.assertEqual(result, expected)
def obtain_taxons(self, protein_dict, fh_sprot):
found = False
for rec in sp.parse(fh_sprot):
for ac in range(len(rec.accessions)):
if rec.accessions[ac] in protein_dict.keys():
# assign rec.taxonomy_id list to the protein
protein_dict[rec.accessions[ac]] = rec.taxonomy_id
found = True
break
#if found:
# break
return protein_dict
def species_filter(sp_handle, taxon_id):
target_id = int(taxon_id+"0000001")
outhandle = open("sp_species.%s.tfa" % taxon_id,"w")
for inrec in sp.parse(sp_handle):
if taxon_id in inrec.taxonomy_id:
outseq = SeqRecord(Seq(inrec.sequence),
id="T"+str(target_id),
description = "%s" %
(inrec.entry_name))
outseq_list = [outseq]
SeqIO.write(outseq_list,outhandle,"fasta")
target_id += 1
outhandle.close()
def make_sp_sql_table(sp_handle, out_handle, taxa_ids=[]):
"""
Make a table from swissprot that includes the following fields:
SP_ID, GO, Ontology, evidence code
"""
for sp_rec in sp.parse(sp_handle):
go_list = parse_go(sp_rec)
if not go_list:
continue
if taxa_ids and (not (sp_rec.taxonomy_id[0] in taxa_ids)):
continue
for go_entry in go_list:
out_handle.write("%s\t%s\t%s\t%s\n" %
(sp_rec.entry_name, go_entry['go_id'],
go_entry['ontology'], go_entry['evidence']))
def n_go_ec(sp_handle, taxon_id, allowed_ec=exp_ec):
# For each GO namespace, number of proteins annotated with allowed
# terms. Uses experimental evidence code, by default.
#
ncount = {}
ncount['BPO'] = 0
ncount['MFO'] = 0
ncount['CCO'] = 0
for inrec in sp.parse(sp_handle):
if taxon_id in inrec.taxonomy_id:
in_allowed = go_ec_filter(inrec, allowed_ec=exp_ec)
for onto in in_allowed:
if in_allowed[onto]:
ncount[onto] += 1
return ncount
def test_compute_features_maps_to_alts_to_stable_ontology_terms(self):
for record in SwissProt.parse(self.records):
protein = parse_record_into_protein(record)
break
protein.go_mf = 'GO:0000975'
protein.go_bp = None
protein.go_cc = None
protein.interpro = None
protein.pfam = None
protein.keywords = None
features = compute_interaction_features(protein, protein)
self.assertEqual(features['go_mf'], ['GO:0044212', 'GO:0044212'])
self.assertTrue('GO:0000975' not in features['ulca_go_mf'])
def __build_NEXP_accession_singleSpecies(fh_sprot, taxon_id, ontType, EXP_default=set([])):
'''
This method builds a list of accessions of the proteins whose annotations
have non-EXP evidence but no EXP evidence codes in a specific
UniProtKB/SwissProt file (file pointer fh_sprot) for some ontology
type (ontType). The method returns the list.
'''
# nexp_accessions: Initialize a list to store the accessions of the
# proteins that meet the criteria: (1) the protein whose annotation
# is supported some Non-EXP evidence code in the specific ontology
# ontType, but (2) the annotation is NOT supported by any EXP
# evidence code.
nexp_accessions = []
print(' Building the accession list with the proteins ' + \
'that have only non-EXP evidence codes at time t1 ...')
for rec in sp.parse(fh_sprot):
# Selects records that are related to a specific
# taxonomy id taxon_id:
if taxon_id in rec.taxonomy_id:
# ont_specific_code_exist: this varilable is initialized to False
# at the beginning of each iteration. If an evidence code (either
# EXP or Non-EXP) for the current record is found, this varilable
# will be set to True
ont_specific_code_exist = False
# exp_code: this variable is initialized to False at the beginning
# of each iteration. If an EXP evidence for the current record is
# found, this variable will be set to True.
exp_code = False
# Going over the list of DB reference entries:
for crossRef in rec.cross_references:
# Consider the cross_reference entries
# that relate to GO DB:
if crossRef[0] == 'GO':
goList = [crossRef[1],
(crossRef[3].split(':'))[0],
crossRef[2][0]]
if not ont_specific_code_exist and goList[2] == ontType:
ont_specific_code_exist = True
if goList[2] == ontType and \
(crossRef[3].split(':'))[0] in EXP_default:
exp_code = True
break
# If the protein's annotation is supported by some Non-EXP evidence
# code but is not supported by any EXP evidence code, append the
# protein's accessions list to the nexp_accessions list:
if ont_specific_code_exist and not exp_code:
nexp_accessions.append(rec.accessions)
return nexp_accessions
def obtain_goterms(self, goterm_dict, fh_sprot):
found = False
for rec in sp.parse(fh_sprot):
for ac in range(len(rec.accessions)):
goList = []
if rec.accessions[ac] in goterm_dict.keys():
for crossRef in rec.cross_references:
if crossRef[0] == 'GO':
goDef = (crossRef[1], (crossRef[3].split(':'))[0], \
crossRef[2][0])
goterm_dict[rec.accessions[ac]].add(goDef)
found = True
break
#if found:
#break
return goterm_dict
def UNIPROT_GENE_PLUS(UNIPROT): #LIST-The difference between this and UNIPROT_GENE is that UNIPROT_GENE_PLUS returns synonim genes as well if
#any and the gene name in the first entry
import urllib, urllib2
from Bio import SwissProt
url=urllib2.urlopen("http://www.uniprot.org/uniprot/%s.txt"%UNIPROT)
GENES=[]
for record in SwissProt.parse(url):
if len(record.gene_name.split(";"))>2:
GENES.append(record.gene_name.split(";")[0].split("=")[1])
SYN=record.gene_name.split(";")[1].split("=")[1].split(",")
for syno in SYN:
GENES.append("".join(syno.split()))
else:
GENES.append(record.gene_name.split(";")[0].split("=")[1])
return GENES
def obtain_goterms(self, goterm_dict, fh_sprot):
found = False
for rec in sp.parse(fh_sprot):
for ac in range(len(rec.accessions)):
goList = []
if rec.accessions[ac] in goterm_dict.keys():
for crossRef in rec.cross_references:
if crossRef[0] == 'GO':
goDef = (crossRef[1], (crossRef[3].split(':'))[0], \
crossRef[2][0])
goterm_dict[rec.accessions[ac]].add(goDef)
found = True
break
#if found:
#break
return goterm_dict
def count_GOterms_with_EXP(fh_sprot, taxon_id, EXP_default=set([])):
'''
This method extract the distinct GO terms for each gene that
have validation with any of the experimental evidence codes.
A set is created for these GO terms for each gene and then
are placed in a dictionary of each ontological categories.
At the end, these THREE dictionaries are returned.
'''
mfo_terms = OrderedDict()
bpo_terms = OrderedDict()
cco_terms = OrderedDict()
count = 0
for rec in sp.parse(fh_sprot):
# SELECT records that are related to a specific
# taxon_id such as 559292 for yeast:
if taxon_id in rec.taxonomy_id:
protName = rec.accessions[0]
# Initialize lists for adding GO terms:
terms_mfo = set()
terms_bpo = set()
terms_cco = set()
# Go over the list of DB cross references:
for crossRef in rec.cross_references:
# Consider the cross_reference entries that
# relate to GO DB:
if crossRef[0] == 'GO':
goList = [crossRef[1],
(crossRef[3].split(':'))[0],
crossRef[2][0]]
if (crossRef[3].split(':'))[0] in EXP_default:
# print goList
if goList[-1].upper() == 'F':
terms_mfo.add(goList[0])
elif goList[-1].upper() == 'P':
terms_bpo.add(goList[0])
elif goList[-1].upper() == 'C':
terms_cco.add(goList[0])
# Increase gene counts in BPO, CCO, and MFO categories
# depending on the corresponding flag values:
mfo_terms[protName] = terms_mfo
bpo_terms[protName] = terms_bpo
cco_terms[protName] = terms_cco
count += 1
if count > 20:
break
#break
return (mfo_terms, bpo_terms, cco_terms)
def count_genes_with_EXP_old(fh_sprot, taxon_id, EXP_default=set([])):
# The exp_bpo_ct variable counts total number of genes in
# the sprot file related to the taxonomy id taxon_id whose
# annotations have EXP evidence and in BPO ontological category:
exp_bpo_ct = 0
# The exp_cco_ct variable counts total number of genes in
# the sprot file related to the taxonomy id taxon_id whose
# annotations have EXP evidence and in CCO ontological category:
exp_cco_ct = 0
# The exp_mfo_ct variable counts total number of genes in
# the sprot file related to the taxonomy id taxon_id whose
# annotations have EXP evidence and in MFO ontological category:
exp_mfo_ct = 0
for rec in sp.parse(fh_sprot):
# SELECT records that are related to a specific
# taxon_id such as 559292 for yeast:
if taxon_id in rec.taxonomy_id:
bpo_exp_flag = cco_exp_flag = mfo_exp_flag = False
# Go over the list of GO information:
for crossRef in rec.cross_references:
# Consider the cross_reference entries that
# relate to GO DB:
if crossRef[0] == 'GO':
goList = [crossRef[1],
(crossRef[3].split(':'))[0],
crossRef[2][0]]
if (crossRef[3].split(':'))[0] in EXP_default:
if goList[-1].upper() == 'P':
bpo_exp_flag = True
elif goList[-1].upper() == 'C':
cco_exp_flag = True
elif goList[-1].upper() == 'F':
mfo_exp_flag = True
if (bpo_exp_flag and cco_exp_flag and mfo_exp_flag):
break
# Increase gene counts in BPO, CCO, and MFO categories
# depending on the corresponding flag values:
if bpo_exp_flag:
exp_bpo_ct += 1
if cco_exp_flag:
exp_cco_ct += 1
if mfo_exp_flag:
exp_mfo_ct += 1
return (exp_bpo_ct, exp_cco_ct, exp_mfo_ct)
def main():
"""Make a jazz noise here"""
args = get_args()
in_fh = args.FILE
keywords = args.keyword
skips = args.skip
out_fh = args.output
if not os.path.isfile(in_fh):
die('"{}" is not a file'.format(in_fh))
#print(keywords)
keylist = [keywords]
#print(keylist)
outfile = open(out_fh, "w")
fandle = open(in_fh)
print('Processing "{}"'.format(in_fh))
records = SwissProt.parse(fandle)
records = SeqIO.parse(fandle, 'swiss')
print(records)
#print(records)
i = 0
j = 0
for record in records:
print(record)
docset = record.keywords
docsetlower = [i.lower() for i in docset]
docsetlower = set(docsetlower)
userset = set(keylist)
i += 1
organismset = record.organism_classification
organismsetlower = [i.lower() for i in organismset]
organismsetlower = set(organismsetlower)
skipsetlower = [i.lower() for i in skips]
skipsetlower = set(skipsetlower)
if docsetlower.intersection(userset) and len(
organismsetlower.intersection(skipsetlower)) == 0:
j += 1
SeqIO.write(record, outfile, 'fasta')
print('Done, skipped {} and took {}. See output in "{}".'.format(
(i - j), j, out_fh))
def check_sprot_format(fh_sprot):
"""
This method checks whether the format of the file
(with file handle fh_sprot) is in UniProtKB/Swissprot format.
If the file is in UniProtKB/Swissprot format format,
it returns True
Otherwise,
it returns False.
"""
iter_handle = sp.parse(fh_sprot) # sp.parse method returns a generator
try:
for rec in iter_handle:
break
except:
return False
else:
return True
def check_sprot_format(fh_sprot):
"""
This method checks whether the format of the file
(with file handle fh_sprot) is in UniProtKB/Swissprot format.
If the file is in UniProtKB/Swissprot format format,
it returns True
Otherwise,
it returns False.
"""
iter_handle = sp.parse(fh_sprot) # sp.parse method returns a generator
try:
for rec in iter_handle:
break
except:
return False
else:
return True
def test_parses_gomf_correctly(self):
for record in SwissProt.parse(self.records):
result = go_terms(record, ont="mf")
break
expected = [
'GO:0045296',
'GO:0019899',
'GO:0042826',
'GO:0042802',
'GO:0051219',
'GO:0050815',
'GO:0008022',
'GO:0032403',
'GO:0019904',
'GO:0003714',
]
self.assertEqual(result, expected)
def count_genes_with_EXP(fh_sprot, taxon_id, EXP_default=set([])):
gene_count = {}
gene_count['MFO'] = 0
gene_count['BPO'] = 0
gene_count['CCO'] = 0
for rec in sp.parse(fh_sprot):
# SELECT records that are related to a specific
# taxon_id such as 559292 for yeast:
if taxon_id in rec.taxonomy_id:
# Three flags to check whether an Exp evidence is found
# in any of BPO, CCO, and MFO ontological categories:
exp_flag = {}
exp_flag['MFO'] = False
exp_flag['BPO'] = False
exp_flag['CCO'] = False
# Go over the list of DB cross references:
for crossRef in rec.cross_references:
# Consider the cross_reference entries that
# relate to GO DB:
if crossRef[0] == 'GO':
goList = [crossRef[1],
(crossRef[3].split(':'))[0],
crossRef[2][0]]
if (crossRef[3].split(':'))[0] in EXP_default:
if goList[-1].upper() == 'F':
exp_flag['MFO'] = True
elif goList[-1].upper() == 'P':
exp_flag['BPO'] = True
elif goList[-1].upper() == 'C':
exp_flag['CCO'] = True
# Whenever an exp evidence for all three ontological
# categories are found, break out the loop:
if (exp_flag['MFO'] and exp_flag['BPO'] and exp_flag['CCO']):
break
# Increase gene counts in BPO, CCO, and MFO categories
# depending on the corresponding flag values:
if exp_flag['MFO']:
gene_count['MFO'] += 1
if exp_flag['BPO']:
gene_count['BPO'] += 1
if exp_flag['CCO']:
gene_count['CCO'] += 1
return gene_count
def read_sprot_dat(sprot_dat_file, seq_dict):
num_record = 0
for record in SwissProt.parse(open(sprot_dat_file)): # Use Bio.SwissProt to parse the uniprot_sprot.dat file
for seqID in record.accessions:
if seqID in seq_dict:
num_record += 1
if num_record % 10000 == 0:
sys.stderr.write("{} records read so far\n".format(num_record))
go_terms = [i[1][3:] for i in record.cross_references if i[0] == 'GO'] # GO terms ['GO:0031012', 'GO:0005576', 'GO:0004222', 'GO:0008270']
organism = record.organism # organism name
lineage = record.organism_classification # taxonomic classification ['Viruses', 'dsDNA viruses, no RNA stage', 'Iridoviridae', 'Chloriridovirus']
tax_id = record.taxonomy_id[0] # taxonomy id '345201'
gene_name, OLN, ORF = parse_GN(record.gene_name) # GN line,include gene names, ordered locus names, and ORF names
full_name, EC = parse_DE(record.description) # DE line with descriptive information. RecName, AltName (Full=, short=, EC=, ...)
seq_dict[seqID] = {'organism' : organism, 'EC' : EC, 'gene_name' : gene_name,'OLN' : OLN, 'ORF' : ORF, 'GO': go_terms, 'KW': record.keywords, 'full_name': full_name, 'tax_id': tax_id, 'lineage': lineage} # map primary ID to annotation dictionary
else:
continue
sys.stderr.write("\nnumber of sequences is {}\n".format(len(seq_dict)))
return seq_dict
def process(files): #the file is a text file of a swissprot protein
parsed = sp.parse(files)
record = next(parsed)
sequence = record.sequence
length = len(sequence)
a = record.features
finished = False
output = []
for item in a:
if finished:
break
else:
if (
not (item[0] == "CHAIN") and not (item[0] == "DOMAIN")
): #this requires more refinement to allow for a range of domains
output.append([item[0], item[1], item[2]])
if item[2] == length:
finished = True
return output
def test_parses_gocc_correctly(self):
for record in SwissProt.parse(self.records):
result = go_terms(record, ont="cc")
break
expected = [
'GO:0005737',
'GO:0030659',
'GO:0005829',
'GO:0070062',
'GO:0005925',
'GO:0042470',
'GO:0016020',
'GO:0005739',
'GO:0005634',
'GO:0048471',
'GO:0043234',
'GO:0017053',
]
self.assertEqual(result, expected)
def setUp(self):
self.records = open(
os.path.normpath(
"{}/test_data/test_sprot_records.dat".format(base_path)), 'rt')
self.session, self.engine = create_session(db_path)
delete_database(self.session)
self.proteins = []
for record in SwissProt.parse(self.records):
protein = parse_record_into_protein(record)
protein.save(self.session, commit=True)
self.proteins.append(protein)
self.labels = ['Activation', 'Inhibition', 'Acetylation']
self.interactions = []
for protein_a, protein_b in product(self.proteins, self.proteins):
class_kwargs = compute_interaction_features(protein_a, protein_b)
label = '{},{}'.format(self.labels[protein_a.id - 1],
self.labels[protein_b.id - 1])
try:
interaction = create_interaction(protein_a,
protein_b,
labels=label,
session=self.session,
verbose=False,
save=True,
commit=True,
**class_kwargs)
self.interactions.append(interaction)
except ObjectAlreadyExists:
continue
self.X, self.y, _ = load_dataset(self.interactions,
self.labels,
selection=DEFAULT_SELECTION)
base = Pipeline(
steps=[('vectorizer',
CountVectorizer(lowercase=False, stop_words=[':', 'GO'])
), ('estimator', LogisticRegression(random_state=0))])
self.clf = MixedBinaryRelevanceClassifier(
[clone(base) for _ in range(len(self.labels))])
self.clf.fit(self.X, self.y)
def from_file(cls, path):
db_records = []
with open(path) as f:
db = SwissProt.parse(f)
for record in db:
db_records.append(
cls(
primary_accession=record.accessions[0],
primary_tax_id=int(record.taxonomy_id[0]),
gene_name=record.gene_name,
organism=record.organism,
description=record.description,
sequence=record.sequence,
comments=record.comments,
cross_references=record.cross_references,
accessions=record.accessions,
annotation_update=record.annotation_update,
created=record.created,
data_class=record.data_class,
entry_name=record.entry_name,
features=record.features,
host_organism=record.host_organism,
host_taxonomy_id=record.host_taxonomy_id,
keywords=record.keywords,
molecule_type=record.molecule_type,
organelle=record.organelle,
organism_classification=record.organism_classification,
protein_existence=record.protein_existence,
references=[x.__dict__ for x in record.references],
seqinfo=record.seqinfo,
sequence_length=record.sequence_length,
sequence_update=record.sequence_update,
taxonomy_id=record.taxonomy_id,
))
with database:
database.create_tables([cls])
with database.atomic():
cls.bulk_create(db_records, batch_size=250)
def UNIPROT_CHAIN_LIMITS(UNIPROT_ID): #Given a uniprot, it returns the limits of the mature protein numbering
import urllib2
from Bio import SwissProt
PAGE=urllib2.urlopen("http://www.uniprot.org/uniprot/%s.txt"%UNIPROT_ID)
PARSED_PAGE=SwissProt.parse(PAGE)
for record in PARSED_PAGE:
CHAIN_VALUES=[]
for feature in record.features:
if feature[0]=="CHAIN":
CHAIN_VALUES=CHAIN_VALUES+[str(feature[1]), str(feature[2])]
if any(X.isdigit()==False for X in CHAIN_VALUES) or not CHAIN_VALUES:
CHAIN_START=1
CHAIN_END=record.sequence_length
else:
CHAIN_START=min(int(X) for X in CHAIN_VALUES)
CHAIN_END=max(int(X) for X in CHAIN_VALUES)
return[CHAIN_START, CHAIN_END]
def SwissIterator(handle):
"""Break up a Swiss-Prot/UniProt file into SeqRecord objects.
Every section from the ID line to the terminating // becomes
a single SeqRecord with associated annotation and features.
This parser is for the flat file "swiss" format as used by:
- Swiss-Prot aka SwissProt
- TrEMBL
- UniProtKB aka UniProt Knowledgebase
For consistency with BioPerl and EMBOSS we call this the "swiss"
format. See also the SeqIO support for "uniprot-xml" format.
Rather than calling it directly, you are expected to use this
parser via Bio.SeqIO.parse(..., format="swiss") instead.
"""
swiss_records = SwissProt.parse(handle)
for swiss_record in swiss_records:
# Convert the SwissProt record to a SeqRecord
seq = Seq.Seq(swiss_record.sequence, Alphabet.generic_protein)
record = SeqRecord.SeqRecord(seq,
id=swiss_record.accessions[0],
name=swiss_record.entry_name,
description=swiss_record.description,
features=[_make_seqfeature(*f) for f
in swiss_record.features],
)
record.description = swiss_record.description
for cross_reference in swiss_record.cross_references:
if len(cross_reference) < 2:
continue
database, accession = cross_reference[:2]
dbxref = "%s:%s" % (database, accession)
if dbxref not in record.dbxrefs:
record.dbxrefs.append(dbxref)
annotations = record.annotations
annotations['accessions'] = swiss_record.accessions
if swiss_record.protein_existence:
annotations['protein_existence'] = swiss_record.protein_existence
if swiss_record.created:
annotations['date'] = swiss_record.created[0]
annotations['sequence_version'] = swiss_record.created[1]
if swiss_record.sequence_update:
annotations[
'date_last_sequence_update'] = swiss_record.sequence_update[0]
annotations['sequence_version'] = swiss_record.sequence_update[1]
if swiss_record.annotation_update:
annotations['date_last_annotation_update'] = swiss_record.annotation_update[0]
annotations['entry_version'] = swiss_record.annotation_update[1]
if swiss_record.gene_name:
annotations['gene_name'] = swiss_record.gene_name
annotations['organism'] = swiss_record.organism.rstrip(".")
annotations['taxonomy'] = swiss_record.organism_classification
annotations['ncbi_taxid'] = swiss_record.taxonomy_id
if swiss_record.host_organism:
annotations['organism_host'] = swiss_record.host_organism
if swiss_record.host_taxonomy_id:
annotations['host_ncbi_taxid'] = swiss_record.host_taxonomy_id
if swiss_record.comments:
annotations['comment'] = "\n".join(swiss_record.comments)
if swiss_record.references:
annotations['references'] = []
for reference in swiss_record.references:
feature = SeqFeature.Reference()
feature.comment = " ".join("%s=%s;" % k_v for k_v in reference.comments)
for key, value in reference.references:
if key == 'PubMed':
feature.pubmed_id = value
elif key == 'MEDLINE':
feature.medline_id = value
elif key == 'DOI':
pass
elif key == 'AGRICOLA':
pass
else:
raise ValueError(
"Unknown key %s found in references" % key)
feature.authors = reference.authors
feature.title = reference.title
feature.journal = reference.location
annotations['references'].append(feature)
if swiss_record.keywords:
record.annotations['keywords'] = swiss_record.keywords
yield record
from Bio import SwissProt
with open('../../samples/spfile.txt') as fh:
records = SwissProt.parse(fh)
for record in records:
print('Entry name: %s' % record.entry_name)
print('Accession(s): %s' % ','.join(record.accessions))
print('Keywords: %s' % ','.join(record.keywords))
print('Sequence: %s' % record.sequence)
#Input="HumanReview.txt" # Globle File Input #Testing #Input = "GLP.txt" """ AATarget1 = "TargetSequencePosition1.txt" AATarget2 = "TargetSequencePosition2.txt" """ # Zero Variables TargetSeq = [] GlobalStat = 0 from Bio import SwissProt handle = open (Input,"r") records = list(SwissProt.parse(handle)) print "Done Big List Parsing" """ HumanOut="HumanAccessions.txt" # Human Protein Accession File # (This need to be fasta format for later Analysis) HumanMAPInput=HumanOut HumanMAPOut="HumanMAPList.txt" AlignInput="HumanMAPList.txt" # This is a File Name (used in SeqIO.parse) MAPUpdateOutPut="HumanMAPFiltered.txt" CytoMitoInput=MAPUpdateOutPut CytoOutput="CytoList.txt"
# SwissProt / Uniprot flat file parsing
from Bio import SwissProt
for record in SwissProt.parse(open('/path/to/your/uniprot_sprot.dat')):
pid=record.accessions[0]
seq=record.sequence
for feature in record.features:
print feature
from Bio import SwissProt
import pickle
HANDLE=open("DATABASES/uniprot_sprot.dat")
DICT={}
for record in SwissProt.parse(HANDLE):
CHAIN_VALUES=[]
AC=[]
for ac in record.accessions:
AC.append(ac)
for feature in record.features:
if feature[0]=="CHAIN":
CHAIN_VALUES=CHAIN_VALUES+[str(feature[1]), str(feature[2])]
print CHAIN_VALUES
if any(X.isdigit()==False for X in CHAIN_VALUES) or not CHAIN_VALUES:
CHAIN_START=1
CHAIN_END=record.sequence_length
else:
CHAIN_START=min(int(X) for X in CHAIN_VALUES)
CHAIN_END=max(int(X) for X in CHAIN_VALUES)
print AC[0]
print CHAIN_START, CHAIN_END
DICT[AC[0]]=[int(CHAIN_START), int(CHAIN_END)]
PICKLE_OUT=open("DATABASES/OBJECTS/DICT_UNIPROT_CHAIN_LIMITS.pi", "w")
pickle.dump(DICT,PICKLE_OUT)
def uniprot2metaphors(outdir, hash2protid, accessions, verbose=True):
"""Parser for dat formatted dump of uniprot database.
It's quick, much faster than xml parsing!
But from time to time may encounter wrongly formatted DAT file.
"""
# create working dir
if not os.path.isdir(outdir):
os.makedirs(outdir)
#parse dump in dat format
files = {} # will store opened files
taxid2stats = {} # { taxid: [matches,total] }
for r in SwissProt.parse(sys.stdin):
#skip entry if taxid not of interest
taxid = int(r.taxonomy_id[0])
if taxid not in hash2protid:
continue
#update stats
if not taxid in taxid2stats:
taxid2stats[taxid] = [0, 0]
taxid2stats[taxid][1] += 1
#check if md5 match
md5 = hashlib.md5(r.sequence).hexdigest()
if md5 not in hash2protid[taxid]:
#skip if no match
continue
#save uniprot accession
for protid in hash2protid[taxid][md5]:
files = save_entry(outdir, files, protid, "accessions", r.accessions[0])
#provide only accessions if requested so
if accessions:
continue
#add xreference information for each external db
for ex_db_data in r.cross_references:
extdb, extid = ex_db_data[:2]
files = save_entry(outdir, files, protid, extdb, extid)
#save gene name
if r.gene_name.startswith('Name='):
extid = r.gene_name[5:].split(';')[0]
files = save_entry(outdir, files, protid, "GeneName", extid)
#save description
if r.description:
files = save_entry(outdir, files, protid, "Description", r.description)
#update stats
taxid2stats[taxid][0] += 1
#close opened files
for f in files:
files[f].close()
#print stats
print "#taxid\tmapped\ttotal\t%"
for taxid in sorted(taxid2stats.keys()):
mapped,total = taxid2stats[taxid]
print "%s\t%s\t%s\t%.2f" % (taxid, mapped, total, mapped*100.0/total)
print "%s\tDone." % datetime.now()
from Bio import SwissProt
with open('../../samples/spfile.txt') as fh:
record = next(SwissProt.parse(fh))
for att in dir(record):
if not att.startswith('__'):
print(att, getattr(record, att))
def appendSprot2goa(fh_sprot, goa_file_name, taxon_id, fh_merged_go):
"""
This method reads each reacord from the UniProtKB/SwissProt file
and checks wither it's for taxon_id. If it is, this method
then checks whether the GO term exists in the UniProt-GOA file
passed as the file name goa_file_name. If it is a new GO term,
this method invokes swissProt2GOA method for each such GO term
to construct a UniProt-GOA record which it appends at the end of
the merged UniProt-GOA file passed as file handle fh_merged_go.
"""
# Creates an iterator object for t1 file:
iter_handle, GAFFIELDS = create_iterator(goa_file_name)
# Construct a dictionary goa_dict with the proteins and
# the corresponding GO terms in t1 file:
goa_dict = {}
for ingen in iter_handle:
if ingen['DB_Object_ID'] in goa_dict.keys():
goa_dict[ingen['DB_Object_ID']].append([ingen['GO_ID'], \
ingen['Evidence'], ingen['Aspect']])
else:
goa_dict[ingen['DB_Object_ID']] = [[ingen['GO_ID'], \
ingen['Evidence'], ingen['Aspect']]]
# EXTRACTS the NEW GO terms in t2 file that are NOT found in t1 file:
goCount = 0
for rec in sp.parse(fh_sprot):
# SELECTS records that are related to a specific taxon_id
# such as 559292 for yeast:
if taxon_id in rec.taxonomy_id:
# Going over each of the entries of the accessions list:
for ac in range(len(rec.accessions)):
# knownProt is an indicator to detect whether the
# current sprot protein is already in GOA file:
knownProt = ""
if rec.accessions[ac] in goa_dict.keys():
# If the current sprot protein is already in the GOA
# file, the sprot protein is assigned to knownProt:
knownProt = rec.accessions[ac]
break
# Going over the list of GO information:
for crossRef in rec.cross_references:
# Consider the cross_reference entries that relate to GO DB:
if crossRef[0] == 'GO':
# goList is a list of GO ID, Aspect, and Evidence:
goList = [crossRef[1], (crossRef[3].split(':'))[0], \
crossRef[2][0]]
# Checking whether a new GO annotaion found:
if (not knownProt) or (knownProt and \
goList not in goa_dict[knownProt]):
# A new GO annotation is found in two situations:
# 1. if knownProt is empty (not knownProt) or
# 2. if knownProt is not empty but the GO annotation
# is not found in the GOA file
# Convert the sprot record to a GOA record:
goaRec = swissProt2GOA(rec, crossRef, GAFFIELDS)
# Write the converted GOA record to the output file:
GOAParser.writerec(goaRec, fh_merged_go, GAFFIELDS)
# if goCount in range(1, 20) or goCount in range(6400, 6420):
# print ('goCount: ' + str(goCount) + '\n')
# goaRec = swissProt2GOA(rec, crossRef, GAFFIELDS)
goCount += 1
return goCount
def parse_uniprot_data(data):
return dict((s.entry_name, s) for s in SwissProt.parse(data))
def SwissIterator(handle):
"""Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.
Every section from the ID line to the terminating // becomes
a single SeqRecord with associated annotation and features.
This parser is for the flat file "swiss" format as used by:
* Swiss-Prot aka SwissProt
* TrEMBL
* UniProtKB aka UniProt Knowledgebase
It does NOT read their new XML file format.
http://www.expasy.org/sprot/
For consistency with BioPerl and EMBOSS we call this the "swiss"
format.
"""
swiss_records = SwissProt.parse(handle)
for swiss_record in swiss_records:
# Convert the SwissProt record to a SeqRecord
seq = Seq.Seq(swiss_record.sequence, Alphabet.generic_protein)
record = SeqRecord.SeqRecord(seq,
id=swiss_record.accessions[0],
name=swiss_record.entry_name,
description=swiss_record.description,
)
record.description = swiss_record.description
for cross_reference in swiss_record.cross_references:
if len(cross_reference) < 2:
continue
database, accession = cross_reference[:2]
dbxref = "%s:%s" % (database, accession)
if not dbxref in record.dbxrefs:
record.dbxrefs.append(dbxref)
annotations = record.annotations
annotations['accessions'] = swiss_record.accessions
annotations['date'] = swiss_record.created[0]
annotations['date_last_sequence_update'] = swiss_record.sequence_update[0]
if swiss_record.annotation_update:
annotations['date_last_annotation_update'] = swiss_record.annotation_update[0]
if swiss_record.gene_name:
annotations['gene_name'] = swiss_record.gene_name
annotations['organism'] = swiss_record.organism.rstrip(".")
annotations['taxonomy'] = swiss_record.organism_classification
annotations['ncbi_taxid'] = swiss_record.taxonomy_id
if swiss_record.host_organism:
annotations['organism_host'] = [word.rstrip(".") \
for word \
in swiss_record.host_organism]
if swiss_record.comments:
annotations['comment'] = "\n".join(swiss_record.comments)
if swiss_record.references:
annotations['references'] = []
for reference in swiss_record.references:
feature = SeqFeature.Reference()
feature.comment = " ".join(["%s=%s;" % (key, value) \
for key, value \
in reference.comments])
for key, value in reference.references:
if key == 'PubMed':
feature.pubmed_id = value
elif key == 'MEDLINE':
feature.medline_id = value
elif key == 'DOI':
pass
elif key == 'AGRICOLA':
pass
else:
raise ValueError(\
"Unknown key %s found in references" % key)
feature.authors = reference.authors
feature.title = reference.title
feature.journal = reference.location
annotations['references'].append(feature)
if swiss_record.keywords:
record.annotations['keywords'] = swiss_record.keywords
yield record
table_def_2 = ', '.join(table_def_items) # definicion de la tabla
cur.execute("CREATE TABLE IF NOT EXISTS " + tabla_sequence + " (" + table_def_2 + ") ENGINE=InnoDB;")
con.commit()
# Variables del loop
i = 0
j = 0
ptm = ''
out = []
listap = []
listaq = []
listar = []
olista = []
interes = []
with open(uniprot_file) as uniprot: # esto me abre y cierra el archivo al final
for record in SwissProt.parse(uniprot): # parseando los records de uniprot
i += 1
if i % 1000 == 0:
print(i)
con.commit()
data = empty_data.copy() # en vez de vaciar el diccionario, le asigno el dafault sin enlazarlo al vacío
# Acá cargo los datos generales para las PTMs de una proteína/entrada de uniprot (instancias de entradas)
# tienen que cargarse en el orden de las columnas en la ptmdb y el del insert
# print(record.accessions[0])
data['AC'] = record.accessions[0] # solo el principal, el resto nose.
data['SQ'] = record.sequence
data['LENGTH'] = record.sequence_length # todo acá hay un problema? no entran las de mas de 999 residuos
data['ORG'] = record.organism # el bicho
data['OC'] = record.organism_classification[0] # el dominio del bicho
data['OX'] = record.taxonomy_id[0] # Id taxonomica del bicho
# guardar el CREATE en output
table_def_items = [] # lista para concatenaciones de key y valor
for cat, value in categories.items(): # concatenaciones key y valor
table_def_items.append(cat + ' ' + value) # guardadaes en la lista
table_def_2 = ', '.join(table_def_items) # definicion de la tabla
#cur.execute("CREATE TABLE IF NOT EXISTS sprot2 (" + table_def_2 + ") ENGINE=InnoDB")
#con.commit()
ptm = ''
out = []
listap = []
listaq = []
listar = []
with open(sprot_file) as sprot: # esto me abre y cierra el archivo al final
for record in SwissProt.parse(sprot):
i += 1
data = empty_data
contenido_aa = count_amino_acids_ext(record.sequence)
listaq = []
for q in contenido_aa.itervalues():
listaq.append(str(q)) # y los pongo en una lista
sql_insert_values_q = ', '.join(listaq)
cur.execute("INSERT INTO count_aa VALUES ('"
+ record.accessions[0] + "', '"
+ record.organism_classification[0] + "', "
+ str(record.sequence_length)
+ ", " + sql_insert_values_q + ")")
con.commit()
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
assert len(records) == 1
assert isinstance(records[0], SeqRecord)
#Check matches what we got earlier without the iterator:
assert records[0].seq.tostring() == seq_record.seq.tostring()
assert records[0].description == seq_record.description
assert records[0].name == seq_record.name
assert records[0].id == seq_record.id
# With the RecordParser
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
assert len(records) == 1
assert isinstance(records[0], SProt.Record)
#Check matches what we got earlier without the iterator:
assert records[0].sequence == record.sequence
assert records[0].description == record.description
assert records[0].entry_name == record.entry_name
assert records[0].accessions == record.accessions