def write_fastas(self):
mytcdb = []
myquery = []
tcdb = SeqIO.parse(self.tcdb, 'fasta')
self.tcdbHits = nr_dict(tcdb)
queries = SeqIO.parse(self.query, 'fasta')
self.queries = SeqIO.to_dict(queries)
##### gabo's addition
done = dict()
for query, hit, hsp, q_len, h_len, qcov, hcov in self.goodresults:
hit = hit[0]
query = ParseDefline(query).id
myquery.append(self.queries[str(query)])
subject = ParseDefline(hit.title, True).id
if subject not in done.keys():
done[subject] = 1
try:
mytcdb.append(self.tcdbHits[subject])
except:
(family, tcid, acc) = ParseTC(hit.title)
#print tcid,acc
print ParseDefline(hit.title, True).id
#print hit.title
quit()
query_file = open(self.indir + "/myqueries.faa", 'wb')
tcdb_file = open(self.indir + "/mytcdb.faa", 'wb')
SeqIO.write(myquery, query_file, 'fasta')
SeqIO.write(mytcdb, tcdb_file, 'fasta')
def plotHydro(self, genome, hit, acc, hsp):
#File Paths
queryPath = self.indir + '/img/' + genome + '_hydro.png'
hitPath = self.indir + '/img/' + acc + '-' + genome + '_hydro.png'
quod = ' -s -q -d {} --width 10 --height 3 --xticks 50'.format(
self.indir + "/img/")
#Query Hydropathy
if not os.path.exists(queryPath):
query = ParseDefline(genome).id
querySeq = self.queries[str(query)].seq
query = 'quod.py {} -o {} -c blue -w {}-{} -l {}'.format(
querySeq, genome + '_hydro', hsp.query_start, hsp.query_end,
genome) + quod
#os.system(query)
subprocess.call(query.split())
#Hit Hydropathy
if not os.path.exists(hitPath):
hitID = ParseDefline(hit.title, True).id
hitSeq = self.tcdbHits[str(hitID)].seq
hit = 'quod.py {} -o {} -c red -w {}-{} -l {}'.format(
hitSeq, acc + '-' + genome + '_hydro', hsp.sbjct_start,
hsp.sbjct_end, acc) + quod
#os.system(hit)
subprocess.call(hit.split())
def calculate_tms_scores(self):
for genome, tcdb, hsp, q_len, h_len, qcov, hcov in self.goodresults:
genome = ParseDefline(genome).id
tcdb = tcdb[0]
delta = hsp.sbjct_start - hsp.query_start
tcdbid = ParseDefline(tcdb.title, True).id
try:
genome_tms = self.tms['queries'][genome].values()
tcdb_tms = self.tms['tcdb'][tcdbid].values()
except KeyError:
# Genome or TCDB hit dont have a TMS.
# These must be manually revised later!
self.notmsresults.append(
(genome, tcdb, hsp, q_len, h_len, qcov, hcov, None))
continue
g_tms = [[i[0] + delta, i[1] + delta] for i in genome_tms]
overlap = self.find_overlap(g_tms, tcdb_tms)
row = (genome, tcdb, hsp, q_len, h_len, qcov, hcov, overlap)
self.bestresults.append(row)
if self.esort:
self.bestresults.sort(
key=lambda x: (x[1].e, x[7], self.tcsort(x[1].title)))
self.notmsresults.sort(
key=lambda x: (x[1].e, self.tcsort(x[1].title)))
else:
self.bestresults.sort(key=lambda x: (self.tcsort(x[1].title), x[1].
e, -1.0 * max(x[6], x[5])))
self.notmsresults.sort(key=lambda x: (self.tcsort(x[1].title), x[1]
.e, -1.0 * max(x[6], x[5])))
def relate(self, loc, subject):
res = open(loc + '/' + subject + '.xml')
results = NCBIXML.parse(res)
for result in results:
genhits = []
orthologs = []
title = result.query
title = ParseDefline(title)
query = title.id
if query in self.ignore_keys:
continue
self.ignore_keys.append(query)
orthologs.append(query)
for aln in result.alignments:
hsps = list(aln.hsps)
title = aln.title
title = ParseDefline(title, 'True')
hit = title.id
if hit in self.ignore_keys:
continue
hsps.sort(key=lambda x: self.hspsort(x), reverse=True)
if self.hspsort(hsps[0]) >= self.identity:
# Found an ortholog, check with genhits.
genome = self.genome_keys[hit]
if genome in genhits:
continue
genhits.append(genome)
orthologs.append(hit)
self.ignore_keys.append(hit)
if bool(len(orthologs)):
self.orthologs.append(orthologs)
def tcsort(self, title):
if self.ortho is not False:
return 1
title = ParseDefline(title, True).description
(family, tc, acc) = ParseTC(title)
tc = tc.split('.')
return (int(tc[0]), str(tc[1]), int(tc[2]), int(tc[3]), int(tc[4]))
def write_results(self):
bestresults = copy.deepcopy(self.bestresults)
bestresults.extend(self.notmsresults)
#create and open the necessary files for results (VI)
html_results = open(self.indir + '/results.html', 'wb')
content = open(self.indir + '/content.html', 'wb')
tsv_results = open(self.indir + '/results.tsv', 'wb')
'''
We are unsure of why the local number variable( the one that is supposed to count which result it is) is the last number in the rows. --Vasu Pranav Sai Iddamsetty
'''
#write to results.html and content.html (VI)
html = '''<html><table width="100%%" border="1"> <tr> <td>Query ID</td> <td>Hit ID</td>
<td>Hit TCID</td> <td>Hit Description</td> <td>Match Len</td> <td>e-Val</td> <td>% Identity</td> <td>Query Length</td> <td>Hit Length</td> <td>Query Coverage</td> <td>Hit Coverage</td> <td>Query TMS#</td>
<td>Hit TMS#</td> <td>TM-Overlap Score</td> <td>Family Abrv.</td><td>Predicted Substrate</td> <td> #</td> </tr><br>\n\n'''
html_results.write(html)
content.write("<html>")
#write the column descriptions to results.tsv (VI)
columnDescription = '''#Query_id\tHit_xid\tHit_tcid\tHit_desc\tMatch_length\te-value\t%_identity\tQuery_Length\tHit_Length\tQuery_Coverage\tHit_Coverage\tQuery_n_TMS\tHit_n_TMS\tTM_Overlap_Score\tFamily_Abrv\tPredicted_Substrate\trow_number\n'''
tsv_results.write(columnDescription)
self.myqueries = SeqIO.parse(self.indir + '/myqueries.faa', 'fasta')
self.mytcdb = SeqIO.parse(self.indir + '/mytcdb.faa', 'fasta')
self.myqueries = SeqIO.to_dict(self.myqueries)
self.mytcdb = SeqIO.to_dict(self.mytcdb)
if self.cdd_on:
self.cdd_extract()
self.queryhmg = hmmgap.annotate()
self.tcdbhmg = hmmgap.annotate()
self.queryhmg.hmmtop = self.tms['queries']
self.tcdbhmg.hmmtop = self.tms['tcdb']
for res in bestresults:
#retrieve relevant formaatted data and write it to the files (VI)
(row, data, txt) = self.build_view(res)
html_results.write(row)
content.write(data)
tsv_results.write(txt)
print "Generated Results for :: %s" % ParseDefline(res[0]).id
#end tags for the .html files
html_results.write("</table></html>")
content.write("</html>")
def parse_secondary(self):
records = NCBIXML.parse(open('secondary.xml'))
positives = []
for record in records:
title = ParseDefline(record.query)
for desc in record.descriptions:
if desc.e <= self.expect_diff:
positives.append(title.id)
print positives
hipster = SeqIO.parse(open(self.substract),'fasta')
hipster = SeqIO.to_dict(hipster)
unique = list(set(hipster.keys())-set(positives))
handle = open('unique.faa','wb')
for key in unique:
record = hipster[key]
SeqIO.write(record,handle,'fasta')
def parse_blast(self):
print 'Locating Orthologs...'
if os.path.exists('parsed'):
self.orthologs = pickle.load(open('parsed'))
return
results = NCBIXML.parse(open('primary.xml'))
for row in results:
group = {}
query = row.query
for desc in row.descriptions:
title = ParseDefline(desc.title,True)
e = desc.e
org = title.id.split('_')[0]
if org != self.genomes[0][0] and e <= self.expect:
group.setdefault(org,[]).append(title.id)
if len(group.keys()) == len(self.genomes)-1:
self.orthologs.append(group.values())
dump = open('parsed','wb')
pickle.dump(self.orthologs,dump)
def scan_file(self, fasta_file):
hmtool = 'hmmtop' if 'hmmtop' not in os.environ else os.environ[
'hmmtop']
cmd = "%s -if=%s -sf=FAS -is=pseudo -pi=spred" % (hmtool, fasta_file)
handle = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
results = handle.communicate()[0]
tms = re.compile("(IN|OUT)\s+([0-9]+)\s+([^\n]+)?")
ranges = re.compile("(\d+)\s+(\d+)")
name = re.compile("^>HP:\s+\d+?\s+(\S+)")
lines = [i for i in results.split('\n') if len(i) > 1]
(res, symbols) = [], []
for pos, i in enumerate(lines):
line = tms.search(i).groups()
if int(line[1]) is 0:
continue
keys = {}
for x in enumerate(ranges.finditer(line[2])):
keys.setdefault(x[0] + 1, []).append(int(x[1].groups()[0]))
keys.setdefault(x[0] + 1, []).append(int(x[1].groups()[1]))
#symbol used to be name.search(i).groups()[0].replace('>','')
symbols.append(ParseDefline(name.search(i).groups()[0]).id)
res.append(keys)
return res, symbols
def build_in(self):
for genome in self.genomes:
xmlfile = genome + '.xml'
results = NCBIXML.parse(open(xmlfile))
subjects = SeqIO.parse(open(genome), 'fasta')
subjects = SeqIO.to_dict(subjects)
inn = []
for result in results:
title = result.query
title = ParseDefline(title, False)
title = title.id
for aln in result.alignments:
hsps = list(aln.hsps)
hsps.sort(key=lambda x: self.hspsort(x), reverse=True)
i = self.hspsort(hsps[0])
if i >= self.identity:
inn.append(title)
out = list(set(subjects.keys()) - set(inn))
infile = open('in/' + genome, 'wb')
outfile = open('out/' + genome, 'wb')
for seq in inn:
SeqIO.write(subjects[seq], infile, 'fasta')
for seq in out:
SeqIO.write(subjects[seq], outfile, 'fasta')
def build_view(self, data):
(genome, tcdb, hsp, q_len, h_len, qcov, hcov, overlap) = data
try:
os.mkdir(self.indir + "/img")
except:
pass
genome = ParseDefline(genome).id
tid = ParseDefline(tcdb.title, True).id
if os.path.exists(self.indir + "/img/" + genome + ".png") is False:
try:
san = self.queryhmg(self.myqueries[genome], hsp.query)
tan = self.tcdbhmg(self.mytcdb[tid], hsp.sbjct)
self.what(hsp.query, hsp.sbjct,
self.indir + "/img/" + genome + ".png", [san, tan])
except:
print hsp.query
print hsp.sbjct
print genome
print 'error, quit'
quit()
(family, tcid,
acc) = ParseTC(ParseDefline(tcdb.title, True).description)
try:
query_tms = len(self.tms['queries'][genome])
except:
query_tms = 0
try:
hit_tms = len(self.tms['tcdb'][ParseDefline(tcdb.title, True).id])
except:
hit_tms = 0
self.globalcount += 1
if self.ortho is False:
family = self.names.get_family_abr('.'.join(tcid.split('.')[0:3]))
else:
family = 'family_place_holder'
'''
Edits made by Vasu Pranav Sai Iddamsetty (VI)
-Adding another file that is a tsv(tab seperated values) file so that the output of gblast
may be parsed by another program easily.
****************************************************
This is where the substrates are found.
They populate the 'mysubstrate' variable.
****************************************************
'''
ident = round((float(hsp.identities) / len(hsp.match)) * 100)
'''
substrate_info= self.substrates.get_tcid_substrates(tcid)
mysubstrate_html = ''
mysubstrate_tsv = ''
if substrate_info is not None:
category,gen_sub,spec_sub,chebi_id,status = substrate_info
chebi_info = chebi_id.replace('"','').replace(' ','').split(',')
chebi = ''
for i in chebi_info:
chebi += ' <a href="https://www.ebi.ac.uk/chebi/searchId.do;jsessionid=A9D16DCB24C6F74339FC28A4941EFBB6?chebiId=CHEBI:{}">{}</a>'.format(i,i)
mysubstrate_html = '{},{},{},{},{}'.format(category,gen_sub,spec_sub,chebi,status)
mysubstrate_tsv = ",".join(substrate_info)
else:
mysubstrate_html = 'None'
mysubstrate_tsv = 'None'
'''
substrate = ''
try:
substrate = self.substrates[tcid]
except:
substrate = 'None'
'''
html_results (VI)
'''
glink = '<a href="content.html#%s">%s</a>' % (genome, genome)
tclink = '<a href="http://tcdb.org/search/result.php?tc={}">{}</a>'.format(
tcid, tcid)
h_row = (glink,acc,tclink,tcdb.title,len(hsp.match),tcdb.e,ident,q_len,h_len,qcov,hcov,query_tms,\
hit_tms,overlap,family,substrate,self.globalcount)
h_row = ['<td>' + str(i) + '</td>' for i in h_row]
htmlrow = "<tr>\n%s\n</tr>" % ("\n\t".join(h_row))
'''
text results (VI)
'''
row = (genome, acc, tcid, tcdb.title, len(hsp.match), tcdb.e, ident,
q_len, h_len, qcov, hcov, query_tms, hit_tms, overlap, family,
substrate, self.globalcount)
row = [str(i) for i in row]
txtrow = "%s\n" % ("\t".join(row))
'''
content results (VI)
'''
self.plotHydro(genome, tcdb, acc, hsp)
#self.rows.append(htmlrow)
if self.cdd_on is True:
mycdd = 'Query & TC-Hit Conserved Domains:<br><img src=\'cdd/%s.1.png\'><br><img src=\'cdd/%s.2.png\'><br>' % (
genome, genome)
else:
mycdd = ''
ol = float(overlap) if overlap is not None else float(0)
content = '''<div class='result' id='%s'> <h3><a name='%s'>%s</a></h3> <p>Hit Accession: %s<br> Hit TCID: %s</p> <p>Hit Description: %s<br>
<br> Mach Len: %i<br> e:%f</p> <p>Query TMS Count : %i<br> Hit TMS Count: %i <br> TMS-Overlap Score: %f<br>
Predicted Substrates:%s <br><br> BLAST Alignment:<br> <pre> %s </pre> <br> <table><tr><th>Protein Hydropathy Plots:</th></tr>
<tr><td><img src='img/%s_hydro.png'></td> <td><img src='img/%s-%s_hydro.png'></td></tr><br>
<tr><th><br> Pairwise Alignment-Hydropathy Plot:<br></th></tr>
<tr><td colspan="2" style="text-align: center;"><img src='img/%s.png'></td></tr></table><br>%s </p> </div>\n''' %(genome,genome,genome,acc,tcid,tcdb.title,\
len(hsp.match),tcdb.e,query_tms,hit_tms,ol,substrate,str(hsp),genome,acc,genome,urlencode(genome),mycdd)
#self.data.append(content)
return htmlrow, content, txtrow
