def _blast_feature(self, f, c1, c2):
trans = Translator(self._abort_event)
cds = trans.translate(f.extract(c1), 11)
sixframes = trans.translate_six_frames_single(c2, 11)
if not sixframes: return [(None, None, None)]
results = []
for frame in sixframes:
res = BlastCLI.s2s_blast(cds, frame, self.evalue, command='blastp', task='blastp')
if res: results.extend(res)
hsps = BlastCLI.all_hsps(results)
if not hsps: return [(None, None, None)]
f1 = []
f2 = []
col = []
fname = self._feature_name(f, default='CDS')
cds_len = len(cds)
min_len = len(cds) * self.min_length
for hsp in hsps:
if hsp.align_length < min_len: continue
if hsp.identities / float(hsp.align_length) < self.min_identity: continue
color_t = (float(hsp.identities) / hsp.align_length)
print '%s %s: %5.1f%% (%5.1f%%)' % (c1.description, fname, color_t * 100, float(hsp.identities) / cds_len * 100)
col.append(colors.linearlyInterpolatedColor(colors.Color(0, 0, 1, 0.2), colors.Color(0, 1, 0, 0.2),
0.2, 1, color_t))
qstart = (hsp.query_start - 1) * 3
qend = qstart + hsp.align_length * 3
sstart = (hsp.sbjct_start - 1) * 3
send = sstart + hsp.align_length * 3
f1.append(
SeqFeature(FeatureLocation(f.location.start + qstart, f.location.start + qend, strand=hsp.strand[0])))
f2.append(SeqFeature(FeatureLocation(sstart, send, strand=hsp.strand[1])))
return zip(f1, f2, col)
def _blast_feature(self, f, c1, c2, features1, features2, evalue, max_rlen):
results = BlastCLI.s2s_blast(f.extract(c1), c2, evalue, command='blastn', task='blastn')
hsps = BlastCLI.all_hsps(results, max_rlen)
if not hsps: return [(None, None, None)]
f1 = []
f2 = []
col = []
for hsp in hsps:
col.append(colors.linearlyInterpolatedColor(colors.Color(1,1,1,0.2), colors.Color(0,0,0,0.2),
0, 1, float(hsp.identities)/hsp.align_length))
f1.append(SeqFeature(FeatureLocation(f.location.start+hsp.query_start,
f.location.start+hsp.query_start+hsp.align_length, strand=0)))
f2.append(SeqFeature(FeatureLocation(hsp.sbjct_start, hsp.sbjct_start+hsp.align_length, strand=0)))
return zip(f1, f2, col)
def _blast_feature(self, f, c1, c2, features1, features2, evalue,
max_rlen):
trans = Translator(self._abort_event)
cds = trans.translate(f.extract(c1), 11)
sixframes = trans.translate_six_frames_single(c2, 11)
if not sixframes: return [(None, None, None)]
results = []
for frame in sixframes:
res = BlastCLI.s2s_blast(cds,
frame,
evalue,
command='blastp',
task='blastp')
if res: results.extend(res)
hsps = BlastCLI.all_hsps(results, max_rlen)
if not hsps: return [(None, None, None)]
f1 = []
f2 = []
col = []
c1_name = pretty_rec_name(c1)
if 'locus_tag' in f.qualifiers:
fname = f.qualifiers['locus_tag'][0]
else:
fname = 'CDS'
cds_len = len(cds)
for hsp in hsps:
color_t = (float(hsp.identities) / hsp.align_length)
print '%s %s: %5.1f%% (%5.1f%%)' % (c1_name, fname, color_t * 100,
float(hsp.identities) /
cds_len * 100)
col.append(
colors.linearlyInterpolatedColor(colors.Color(0, 0, 1, 0.2),
colors.Color(0, 1, 0, 0.2),
0.2, 1, color_t))
qstart = (hsp.query_start - 1) * 3
qend = qstart + hsp.align_length * 3
sstart = (hsp.sbjct_start - 1) * 3
send = sstart + hsp.align_length * 3
f1.append(
SeqFeature(
FeatureLocation(f.location.start + qstart,
f.location.start + qend,
strand=hsp.strand[0])))
f2.append(
SeqFeature(FeatureLocation(sstart, send,
strand=hsp.strand[1])))
return zip(f1, f2, col)
def blast_genes(self, db, evalue=10, **kwargs):
gresults = [None] * len(self)
for g in self.genes:
s = g.extract(self.contig)
results = BlastCLI.blast_seq(s, db, evalue, **kwargs)
print
print 'Results: %s' % str(results)
if not results:
print 'No results'
continue
print g
for rec in results:
print 'Record: %s, %d alignments' % (str(rec),
len(rec.alignments))
for alignment in rec.alignments:
print 'Alignment: %s' % alignment
for hsp in alignment.hsps:
print 'HSP: %s' % hsp
if __name__ == '__main__':
from multiprocessing import Event
from BioUtils.Tools.Output import user_message
from BioUtils.SeqUtils import load_files
_pid = os.getpid()
#setup signal handler
signal.signal(signal.SIGINT, sig_handler)
signal.signal(signal.SIGTERM, sig_handler)
signal.signal(signal.SIGQUIT, sig_handler)
if True:
# from DegenPrimer import MultiprocessingBase
# MultiprocessingBase.cpu_count = 1
abort_event = Event()
lb = BlastCLI(abort_event)
with user_message('Loading genomes...', '\n'):
genomes_dir = u'/home/allis/Dropbox/Science/Микра/Thermococcus/sequence/GenBank/Thermococcus'
genome_names = [
'Thermococcus_barophilus_Ch5-complete.gb',
'Thermococcus_onnurineus_NA1-complete-genome.gb',
'Thermococcus_sp._ES1.gb', 'Thermococcus-DS1-preliminary.gb'
]
genomes = load_files(
abort_event,
[os.path.join(genomes_dir, f) for f in genome_names], 'gb')
ref = genomes[0]
subj = genomes[1:]
if __name__ == '__main__':
from multiprocessing import Event
from BioUtils.Tools.Output import user_message
from BioUtils.SeqUtils import load_files
_pid = os.getpid()
#setup signal handler
signal.signal(signal.SIGINT, sig_handler)
signal.signal(signal.SIGTERM, sig_handler)
signal.signal(signal.SIGQUIT, sig_handler)
if True:
# from DegenPrimer import MultiprocessingBase
# MultiprocessingBase.cpu_count = 1
abort_event = Event()
lb = BlastCLI(abort_event)
with user_message('Loading genomes...', '\n'):
genomes_dir = u'/home/allis/Dropbox/Science/Микра/Thermococcus/sequence/GenBank/Thermococcus'
genome_names = ['Thermococcus_barophilus_Ch5-complete.gb',
'Thermococcus_onnurineus_NA1-complete-genome.gb',
'Thermococcus_sp._ES1.gb',
'Thermococcus-DS1-preliminary.gb']
genomes = load_files(abort_event, [os.path.join(genomes_dir, f) for f in genome_names], 'gb')
ref = genomes[0]
subj = genomes[1:]
@shelf_result
def g2g2shelf():
return lb.g2g_blastp(ref, subj, 11, features_of_interest=[{'ugene_name': 'FC-full'}, {'ugene_name': 'COC-full'}])
def _main(self):
query = simple_rec(
'AAACTGGGGCTAATACCCGATGGGTGAGGAGGCCTGGAATGGTTCTTCACCGAAAAGACGTTGAGACCATGCTTTTCAACGTTGCCTAAGGATGGGGCCGCGTCCGATCAGGTTGTTGGTGGGGTAACGGCTCACCAAGCCTATAACCGGTACGGGCCGTGGGAGCGGAAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCAGCAGTCGCGAAAACTCCGCAATGCGCGAAAGCGTGACGGGGCTACCCCGAGTGCCGTCCGCTGAGGATGGCTTTTCCCCGGTGTAATGAGCCTGGGGAATAAGGAGAGGGCAAGCCTGGTGTCAGCCGCCGCGGTAATACCAGCTCTCCGAGTGGTAGGGATGATTATTGGGCTTAAAGCGTCCGTAGCCAGCCCGGCAAGTCTCCCGTTAAATCCAGCGACCTAATCGTTGGGCTGCGGAAGATACTGTTGGGCTAGGGGGCGGGAGAGGCCGACGGTATTCCCGGGGTAGGGGTGAAATCCTATAATCCTGGGAGGACCACCAGTGGCGAAGGCTGTCGGCTAGAACGCGCTCGACGGTGAGGGACGAAAGCTGGGGGAGCGAACTGGATTAGATACCCGGGTAGTCCCAGCTGTAAACGATGCGGGCTAGGTGTTGGGGTGGCTACGAGCCACCTCAGTGCCGCAGGGAAGCCATTAAGCCCGCCGCCTGGGAAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGCGTGAAGCTTGCGGTTTAATTGGAGTCAACGCCGGGAACCTTACCGGGGGCGACAGCAGGATGAGGGCCAGATTGAAGGTCTTGCTTGACAAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCTGTTAAGTCAGGCAACGATCGAGACCCGCACCCTTAGTTGCAACCCCTGCGGAACCCGCAGGGGGCACACTACGGGAACTGCCGCCGATAAGGCGGAGGAAGGAGCGGGCCACGGCAGGTCAGTATGCCCCGAATCCCCCGGGCCACACGCGAGCTGCAATGGCAGAGACAATGGGTTCCAACCTTGAAAGAGGGAGGTAATCCCTAAACCCTGCCTCAGTTGGGATCGAGGGCTGCAACCCGCCCTCGTGAACATGGAATGCCTAGTAATCGCGTGTCATCATCGCGCGGTGAATACGTCCCCGCTCCTTGCACACACCGCCCGTCGCTCCATCCGAGTGGGGTTTGGGTGAGGCGTGGTCTGTTGGCCGCGTCGAATCTAGGCTTCGCGAGGAGGGAGAAGTCGTAACAAGGTGGCCGTAGGGGAACCTGCGGCCGGATCACCTCCT',
'BA2-16S')
suns_db = '/home/allis/Documents/INMI/SunS-metagenome/BlastDB-big/sunspring_meta'
silva_db = '/home/allis/Documents/INMI/SILVA-DB/SILVA_123_SSURef_Nr99_tax_silva'
additions = [
simple_rec(
'AAACTGGGGCTAATCCCCCATAGGCCTGGGGTACTGGAAGGTCCCCAGGCCGAAAGGG------GACCGTA-----AGGTCCCGCCCGAGGATGGGCCGGCGGCCGATTAGGTAGTTGGTGGGGTAACGGCCCACCAAG--CCGAAGATCGGTACGGGCC-GTGAGAGCGGGAGCCCGGAGATGGACA---CTGAGACACGGGTCCAGGCCCTACGGGGCGCAGCAGGCGCGAAACC-TCCGCAATGCGGGAAACCGCGACGGGGGGACCCCCAGTGCCGTGCCTCTGGC-----ACGGCTTTTCCGGAGTG-TAAAAAGCTCCGGGAATAAGGGCTGGGCAAGGCCGGTGGC-AGCCGCCGCGGTAATACCGGCGGCCCGAGTGGTGGCCACTATTATTGGGCCTAAAGCGGCCGTAGCCGGGCCCGTAAGTCCCTGGCG-AAATCCCACGGCTCAACCGTGGGGCTCGCTGGGGATACTGCGG-GCCTTGGGACCGGGAGAGGCCGGGGGTACC-CCCGGGGTAGGGGTGAAATCCTATAATCCCGGGGGGACCGCCAGT-GGCGAAGGCGCCC--GGCTGGAACGGGTCCGACGGTGAGGGCCGAAGGCC-AGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCTGGCTGTAAAGGATGCGGGCTAGGTGTCGGGCGAG-CTTCGAGCTCGC-CCGGTGCCGTAGGGAAGCCGTTAAGCCCGCCGCC-TGGGGAGTACGGCCGCAAGGCT-GAAACTTAAAGGAATT-GGCGGGGGAGC-ACTACAAGGGGTGGAGCGTGCGGTTTAATTGGATTCAACGCCGGGAACCTCACCGGGGGCGACGGCAGGATGAA-GGCCAGGCTGAAGGTCTTGCCGGACGCGCCGAGAGGAG-----------------------------------GTGCATGGCCGCCGTCAGCTCGTACCGTGAGGCGTCCA-CTTAAGTGTGGTAACGAGCGAGACCCGC--GCCCCCAGTTGCCAGTCCCTCCCGCTGGGA---GGGAGGC-ACTCTGGGGGG-ACTGCCGGCGAT-AAGCCGGAGGAAGGGGCGGGCGACGGTAGGTCAGTATG-CCCCGAAACCC-CCGGGCT-ACACGCGCGCTACAATGGGCGGGACAATGGGA-CCCGACCCCGAAAGGGGAAGGGAATCCCCTAAACCCGCCCTCAGTTCGGATCGCGGGCTG-CAACTCGCCCGCGTGAAGC-TGGAAT-CCCTAGTACCCGCGCGTCATCATCGCGCGGCGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCACTCCACCCGAG-CGGGGCCC-GGGTGAGGCCCGATCTCCTTCGGGAGGTCGGGTCGAGCCTGGGCTC-CGTGAGGGGGG-AGAAGTCGTAACAAGGTAGCC------------------------------'
.replace('-', ''), 'Thermococcus_chitonophagus'),
simple_rec(
'AAACTGGGATTAATACCCACTAAATGATAATACCTGGAATGGCTTATCATTGAAAGAC-TCTGGAAACATGCTTC-CAGCGTCGCCCAAGG-------------------------------------------------------------------------------GGAGCCCGGAGATGGAAA---CTGAGACAAGGTTCCAGGCCCTACGGGGCGCAGCAGGCGCGAAACC-TCCACAATGCGCGAAAGCGTGATGGGGTTATCCCGAGTGCCGTCCGATGAGG-----ATGGCTTTTCCTCGGTG-TAAGGATCCGAGGGAATAAAGGGGGGGCAAGACTGGTGTC-AGCCGCCGCGGTAATACCAGCTCCCTGAGTGGTAAGGACGATTATTTGGCCTAAAGCGTCCGTAGCCGGCTTATCAAGTCTCTTGTT-AAACCCAGTGATTCAATCATTGACCT-GCAAGAGATACTGTTA-TGCTAGAGGACGGGAGAGGTCGACGG---------GGGTAGGGGTGAAATCCTATAATCCTTGGAGGACCACCAGT-GGCGAAGGCGGTC--GACTAGAACGTGCCTGACGGTGAGGGACGAAAGCT-GGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCAGCTGTAAACGATGCGGGCTAGGTGTTGGGGTAG-CTACGAGCTACT-CCAGTGCCGCAGAGAAGTTGTTAAGCCCGCCGCC-TGGGGAGTACGGCCGCAAGGCT-GAAACTTAAAGGAATT-GGCGGGGGAGC-ACCACAAGGGGTGAAGGCTGCGGTTTAATTGGAGTCAACGCCGGGAACCTTACCGGGGCTGACAGCAGAGTGAA-GGCCAGACTGAAGATCTTGCCAGACAAGCTGAGAGGAGGTGCATGAAGATCTTGCCAGACAAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCT-GTTAAGTCAGGCAACGAACGAGACCCCC--ACTGTTAGTTGCCAGCGAATTCCAACGGAAT--GTCGGGC-ACACTAACAGG-ACTGCCACCGAT-AAGGTGGAGGAAGGAGGGGGCAACGGCAGGTCAGTATG-CCCC--------------------------------------------------------------------------------------------------------------GAACTCGCCCTCATGAACA-TGGAAT-CCCTAGTAACCGCGTGTCATCATCGCGCGGTGAATACGTCCCCGCTCCTTGCACACACCGCCCGTCGCTCCATCCAAG-TCGGGTCT-AGATGAGGCGCAGTCTTCT-----TGGCTACGTCGAATCTGGGTTC-GGTGAGGGGGG-AGAAGTCGTAACAAGGTGGCCGTAGGGGAACCTGCGGCCGGATCACCTCCT'
.replace('-', ''), 'SMTZ1-55'),
simple_rec(
'ACTCCGGTTGATCCTGCCGGACCCCACTGCTATCGGGGTAGGACTTAACCATGCGAGTTGTGCGTCCCCAAGCCATGGTGGGGGCGCGGCATACGGCTCAGTAACACGTGGCTAACCTAGCCTTTGGACGGGGACAACCCCGGGAAACTGGGGCTAATCCCCGATGGGTGGGAAGGCCTGGAATGGTTTCCCACCGAAAGGGCGTCTGAACCATGCTTCAGGCGTTGCCGAAGGATGGGGCCGCGGCCGATCAGGTTGTTGGTGAGGTAACGGCTCACCAAGCCTATAACCGGTACGGGCCGTGAGAGCGGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCAGCAGGTGCGAAAACTCCGCGATGCGCGAAAGCGTGACGGGGCTATCCCGAGTGCCGTCCGCTGAGGATGGCTTTTCCCCGGTGTAGGGAGCCGGGGGAATAAGGAGAGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCTCTCCGAGTGGTGGGGACAATTATTGGGCTTAAAGCGTCCGTAGCCGGCCCATCAAGTCTCTTGTTAAATCCAGCGATCCAATCGCTGGACTGCGGGAGATACTGCTGGGCTAGGGGGCGGGAGAAGCCGATGGTATTCTCGGGGTAGGGGTGAAATCCTATAATCCCGGGAGGACCACCAGTGGCGTAGGCGGTCGGCTAGAACGCGCCCGACGGTGAGGGACGAAAGCTGGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCAGCCGTAAACGATGCGGGCTAGGTGTTGGGGTGGCTACGAGCCACCCCAGTGCCGCATGGAAGCAATTAAGCCCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGGGTGAAGCTTGCGGTTTAATTGGAGTCAACGCCGGGAAAGGAACAGCGTTTTGTTGTTCCTCTGGATACCTTACCGGGGGCGACAGCAGGATGAAGGCCAGATTGAAGGTCTTGCTGGACGAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCTGTTAAGTCAGGTAACGATCGAGACCCACACCCCCAGTTGCTACCTCTTCGGAGGGCACTCTAGGGGTACTGCCGCCGATAAGGCGGAGGAAGGAGTGGGCCACGGCAGGTCAGTATGCCCCGAATCCCCCGGGCCACACGCGAGCTGCAATGGCAAGGACAATGGGTTCTGACCCCGAGAGGGGAAGGTAATCCCGAAACCCTGCCTCAGTTGGGATCGAGGGCTGAAACCCGCCCTCGTGAACATGGAATCCCTAGTAATCGCGGGTCACCAGCCCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCGCTCCATCCGAGTGGGGTTTAGGTGAGGCGTGGTCCTTGTGGCTGTGTCGAATCTAGGCTTCGCGAGGAGGGAGAAGTCGTAACAAGGTGGCCGTAGGGGAACCTGCGGCCGGATCACCTC',
'BA1-16S'),
simple_rec(
'CTGGTGGAAATATAGAAGAGGCCAAATCCGGGGTTCAGGCCGCCCGGGGTAATTACCCGTTGTCGGAGTGGGGGGGGGACGCTATTGGGGCTTAAGCCATCGTTAGCCCGTTTGACCAGGTCTCTTGTTAAATCAGGCGGATTTATTGGTCGATTGCAGGAGATTATGTTCGTCTTAGGGGCCGGAGGAGTCAACAGTATTCCCGGGGTAGGAGTGAATGCCTATATTCCCGGAGGTACCACCAGTGGGGACGCCGTTGGTATAGAACGCGCCGGCCGGTGATGGAATGAAAGTGAGGGAACCGACCCGAATTAGATACCGGGGTATTGCTACCGTTAACCGATGCAGCTTAGGTGTTCGGGTGGTTACTAGCCATTCGAGTGCGCCAGGGAAGCTGTCAGGCTTACCGCTTGGGAAGTGCGGCTGCAGGGCCAAAACTTAAGGAAATCGCCGGGGAAGCACCCCAGGGGGTGAAGCTTGCGCTTTAATGGAATTCACCGCGGTAATTCTCACCGGGGGAGCCACCAGGAGGAAAGCCAGATTAAAGTTCTTGTTGGCGGAGTGGAGAGGAGGTGCATGCCGTTCGCCAGTTCTTCCCGGGAGGTTCTTGTTAGTTCAGCCACCGATGAGGACCGCCATCCCCTGTTGTTATTGGCCTTGCGCCAGGCACACTGGGGAGACCGCCGCCGATAAGGCGGAGGAAGGAGCGGGCCACGGCAGGTCAGTATGCCCCGAATCCCCCGTCCACACGCGAGGGGCAATG',
'155a'),
simple_rec(
'CAAGTCCTATAACCGGTACGGGCCGTGGGAGCGGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCAGCAGTCGCGAAACCTCCGCAATACGCGAAAGCGTGACGGGGTCATCCCGAGTGCCGTCCGCTGAGGATGGCTTTTCCCCAGTGTAGACAGCTGGGGGAATAAGGAGAGGGCAAGTCGGGTGTCAGCCGCCGCGGTAATACCCGCTCTCCGAGTGGTGGGGACGCTTATTGGGCCTAAAGCATCCGTAGCCGGCTGGACAAGTCCCCTGTTAAATCCAGCGATTTAATCGTTGGACTGCGGGGGATACTGTCCGGCTAGGGGGCGGGAGAGGCCGACGGTATTTCCGGGGTAGGGGTGAAATCCTATAATCCCGGGAGGACCACCAGTGGCGAAGGCTGTCGGCTAGAACGCGCCCGACGGTGAGGGATGAAAGCTGGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCAGCCGTAAACGATGCAGGCTAGGTGTTCGGGTGGCTACGTGCCACTCGAGTGCCGCAGGGAAGCTGTTAAGCCTGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGGGTGAAGCTTGCGGTTTAATTGGAGTCAACGCCGGAAATCTCACCGGGGGAGACAGCAGGATGAAAGCCAGATTAAAGGTCTTGCTAGACGAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCTGTTAAGTCAAGGCAACGATCGAGACTCGCATCCTCTGTTGCTACTACCCTTGCGCCAAGGCACACTGGGGGAGACCGCCGCTCGATAAGGCGGAAGGAAGGAGCGGCCCACGGCAGTCAGTATGCCCCGAATTCCCTCGGCCACACGCAAGCTGCAATG',
'156a'),
simple_rec(
'GGGGATCGGGGCATACTGACCTGCCGTGGCCCGCTCCTTCCTCCGCCTTATCGGCGGCGGTCTCCCCAGTGTGCCTGGCGCAAGGGCAGTAACAACAGGGGATGGGGGTCTCGATCGGTGGCTGGCTTAACAGGAAACCTCACGGGACGAACTGGCGAACGGCATGGACCTTCTCTCAACTTGGCTAAGAAGAACTTTAATCTGGCTTTCATTCTGGTGGCTTCCCCGGTGAGAATTCCGGCGGTGACTCCCAATAAAACGCAAGCTTCACCCCTTGGGGTGGTTCCCCGGCCATTTCTTTAAGGTTCAAGCTTTGCGGCGGTATTCCCAAGCGGCAAGGTTAACAGCTTCCCTGCCGCACTCGAGTGGCACGTAACCACCCGAACAACTAACCTGCATCCGTTACCGGTTGGACTAACCCGGTATCTAATCCGGGTCGCTCCCCCAGCCTTCATTCCTTCACCGTCCGGCGCGGTTCTAAGCGACCGGCTTTCGCACTTGTGGTTCCTCCCGGGGATTATAAGAATTCACCCCTACCCCGGAAATTACGGTCCGGCTCCTCCGGCCCCTAACCCGACACGTAATCCCCCGCCAGTTCAACCGATTAAATCCGCTTGAATTTAACAAGGGGGACCTTGTCCAGCCGGCCTACGGATGCTTTAAGGCCCAATAAGCCGTCCCCACCACTCCGAGAGCGGGTAATAACCGCGGCCGGCCTGACAACCGACCTGGCCTCTCCTAAATCCCCCAGCTGTTCACACTTGGGAAAGGGCATTCCTCAGCGAACGGCACTTCGGGATGAACCCGTCACGCTTTCGCGTAATTGCGGGAAGGTTTCGCGAACTGCTGCGCCCCGTAAAGGCCTGGGTCCTTGTGTCTCAAATTGCCCCATCTCCGGGCTATACGCTCTCCACGGGCCCGTACC',
'157a')
]
#prepare filter
filt = BlastFilter(lambda a, r: a.hsps[0].align_length > 1100)
filt.AND = BlastFilter(
lambda a, r: all(hsp.score > 500 for hsp in a.hsps))
filt.AND.AND = BlastFilter(lambda a, r: all(
hsp.identities / float(hsp.align_length) > 0.8 for hsp in a.hsps))
#make ring-blast
blast = BlastCLI(self.abort_event)
orig_seqs = blast.ring_blast(query, suns_db, 100, filt, 3)
if not orig_seqs:
print 'No blast results.'
return 1
nseqs = len(orig_seqs)
print 'RingBlast to:\n%s\nreturned %d sequences.\n' % (suns_db, nseqs)
#save an initial alignment
self.fix_ids(orig_seqs)
alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.fasta'
with user_message('Aligning retrieved sequences...', '\n'):
if not AlignmentUtils.align(orig_seqs + [query] + additions,
outfile=alifile):
return 3
#search for additional homologs
add_seqs = blast.ring_blast(orig_seqs, silva_db, 100, filt, 0)
if add_seqs:
self.fix_ids(add_seqs)
print 'RingBlast to:\n%s\nreturned %d additional sequences.\n' % (
silva_db, len(add_seqs))
#build an alignment
seqs = orig_seqs + add_seqs + [query] + additions
alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.big.aln.fasta'
with user_message('Aligning retrieved sequences...', '\n'):
if not AlignmentUtils.align(seqs, outfile=alifile): return 3
#build a tree
treefile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.big.aln.tre'
if not PhyloUtils.build_fast_tree(alifile, treefile): return 4
#annotate the tree
if False:
with open(
'/home/allis/Documents/INMI/16S/SSBaF4-SSBaR4-1_243072232-iPCR-report.txt'
) as inp:
# SSBaF4-SSBaR4_65397396-iPCR-report.txt
sids = set()
len_re = re.compile(r'(\s|^)(\d+)(\sbp|\\s*:)?', re.MULTILINE)
entry = False
cur_sid = None
cur_len = -1
for l in inp:
if l == '========= histograms and electrophorograms of PCR products of each hit =========':
break
if l.startswith('---'):
entry = False
if cur_sid and cur_len > 0 and abs(cur_len - 920) < 60:
sids.add(cur_sid)
cur_sid = None
cur_len = -1
continue
if entry or '#' in l:
entry = True
plen = len_re.search(l)
if plen: cur_len = int(plen.group(2))
sid = BlastID.extract(l)[0]
if sid: cur_sid = sid
organisms = Organisms.from_records(seqs)
if PhyloUtils.annotate_tree(
treefile,
organisms,
reroot_at='Thermococcus_chitonophagus',
# beautify_leafs=True,
# collapse_taxa=['miscellaneous crenarchaeotic group', 'thaumarchaeota'],
# collapse_last=True,
# collapse_hard=True,
# mark_leafs=sids,
mark_leafs=[r.id for r in orig_seqs + [query] + additions],
lineage_colors={
'miscellaneous crenarchaeotic group': (0, 0, 255),
'thaumarchaeta': (255, 0, 0)
},
top_lineage=Lineage('archaea')):
return 0
return 2
def _main(self):
query = simple_rec('AAACTGGGGCTAATACCCGATGGGTGAGGAGGCCTGGAATGGTTCTTCACCGAAAAGACGTTGAGACCATGCTTTTCAACGTTGCCTAAGGATGGGGCCGCGTCCGATCAGGTTGTTGGTGGGGTAACGGCTCACCAAGCCTATAACCGGTACGGGCCGTGGGAGCGGAAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCAGCAGTCGCGAAAACTCCGCAATGCGCGAAAGCGTGACGGGGCTACCCCGAGTGCCGTCCGCTGAGGATGGCTTTTCCCCGGTGTAATGAGCCTGGGGAATAAGGAGAGGGCAAGCCTGGTGTCAGCCGCCGCGGTAATACCAGCTCTCCGAGTGGTAGGGATGATTATTGGGCTTAAAGCGTCCGTAGCCAGCCCGGCAAGTCTCCCGTTAAATCCAGCGACCTAATCGTTGGGCTGCGGAAGATACTGTTGGGCTAGGGGGCGGGAGAGGCCGACGGTATTCCCGGGGTAGGGGTGAAATCCTATAATCCTGGGAGGACCACCAGTGGCGAAGGCTGTCGGCTAGAACGCGCTCGACGGTGAGGGACGAAAGCTGGGGGAGCGAACTGGATTAGATACCCGGGTAGTCCCAGCTGTAAACGATGCGGGCTAGGTGTTGGGGTGGCTACGAGCCACCTCAGTGCCGCAGGGAAGCCATTAAGCCCGCCGCCTGGGAAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGCGTGAAGCTTGCGGTTTAATTGGAGTCAACGCCGGGAACCTTACCGGGGGCGACAGCAGGATGAGGGCCAGATTGAAGGTCTTGCTTGACAAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCTGTTAAGTCAGGCAACGATCGAGACCCGCACCCTTAGTTGCAACCCCTGCGGAACCCGCAGGGGGCACACTACGGGAACTGCCGCCGATAAGGCGGAGGAAGGAGCGGGCCACGGCAGGTCAGTATGCCCCGAATCCCCCGGGCCACACGCGAGCTGCAATGGCAGAGACAATGGGTTCCAACCTTGAAAGAGGGAGGTAATCCCTAAACCCTGCCTCAGTTGGGATCGAGGGCTGCAACCCGCCCTCGTGAACATGGAATGCCTAGTAATCGCGTGTCATCATCGCGCGGTGAATACGTCCCCGCTCCTTGCACACACCGCCCGTCGCTCCATCCGAGTGGGGTTTGGGTGAGGCGTGGTCTGTTGGCCGCGTCGAATCTAGGCTTCGCGAGGAGGGAGAAGTCGTAACAAGGTGGCCGTAGGGGAACCTGCGGCCGGATCACCTCCT',
'BA2-16S')
suns_db = '/home/allis/Documents/INMI/SunS-metagenome/BlastDB-big/sunspring_meta'
silva_db = '/home/allis/Documents/INMI/SILVA-DB/SILVA_123_SSURef_Nr99_tax_silva'
additions = [simple_rec('AAACTGGGGCTAATCCCCCATAGGCCTGGGGTACTGGAAGGTCCCCAGGCCGAAAGGG------GACCGTA-----AGGTCCCGCCCGAGGATGGGCCGGCGGCCGATTAGGTAGTTGGTGGGGTAACGGCCCACCAAG--CCGAAGATCGGTACGGGCC-GTGAGAGCGGGAGCCCGGAGATGGACA---CTGAGACACGGGTCCAGGCCCTACGGGGCGCAGCAGGCGCGAAACC-TCCGCAATGCGGGAAACCGCGACGGGGGGACCCCCAGTGCCGTGCCTCTGGC-----ACGGCTTTTCCGGAGTG-TAAAAAGCTCCGGGAATAAGGGCTGGGCAAGGCCGGTGGC-AGCCGCCGCGGTAATACCGGCGGCCCGAGTGGTGGCCACTATTATTGGGCCTAAAGCGGCCGTAGCCGGGCCCGTAAGTCCCTGGCG-AAATCCCACGGCTCAACCGTGGGGCTCGCTGGGGATACTGCGG-GCCTTGGGACCGGGAGAGGCCGGGGGTACC-CCCGGGGTAGGGGTGAAATCCTATAATCCCGGGGGGACCGCCAGT-GGCGAAGGCGCCC--GGCTGGAACGGGTCCGACGGTGAGGGCCGAAGGCC-AGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCTGGCTGTAAAGGATGCGGGCTAGGTGTCGGGCGAG-CTTCGAGCTCGC-CCGGTGCCGTAGGGAAGCCGTTAAGCCCGCCGCC-TGGGGAGTACGGCCGCAAGGCT-GAAACTTAAAGGAATT-GGCGGGGGAGC-ACTACAAGGGGTGGAGCGTGCGGTTTAATTGGATTCAACGCCGGGAACCTCACCGGGGGCGACGGCAGGATGAA-GGCCAGGCTGAAGGTCTTGCCGGACGCGCCGAGAGGAG-----------------------------------GTGCATGGCCGCCGTCAGCTCGTACCGTGAGGCGTCCA-CTTAAGTGTGGTAACGAGCGAGACCCGC--GCCCCCAGTTGCCAGTCCCTCCCGCTGGGA---GGGAGGC-ACTCTGGGGGG-ACTGCCGGCGAT-AAGCCGGAGGAAGGGGCGGGCGACGGTAGGTCAGTATG-CCCCGAAACCC-CCGGGCT-ACACGCGCGCTACAATGGGCGGGACAATGGGA-CCCGACCCCGAAAGGGGAAGGGAATCCCCTAAACCCGCCCTCAGTTCGGATCGCGGGCTG-CAACTCGCCCGCGTGAAGC-TGGAAT-CCCTAGTACCCGCGCGTCATCATCGCGCGGCGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCACTCCACCCGAG-CGGGGCCC-GGGTGAGGCCCGATCTCCTTCGGGAGGTCGGGTCGAGCCTGGGCTC-CGTGAGGGGGG-AGAAGTCGTAACAAGGTAGCC------------------------------'.replace('-', ''),
'Thermococcus_chitonophagus'),
simple_rec('AAACTGGGATTAATACCCACTAAATGATAATACCTGGAATGGCTTATCATTGAAAGAC-TCTGGAAACATGCTTC-CAGCGTCGCCCAAGG-------------------------------------------------------------------------------GGAGCCCGGAGATGGAAA---CTGAGACAAGGTTCCAGGCCCTACGGGGCGCAGCAGGCGCGAAACC-TCCACAATGCGCGAAAGCGTGATGGGGTTATCCCGAGTGCCGTCCGATGAGG-----ATGGCTTTTCCTCGGTG-TAAGGATCCGAGGGAATAAAGGGGGGGCAAGACTGGTGTC-AGCCGCCGCGGTAATACCAGCTCCCTGAGTGGTAAGGACGATTATTTGGCCTAAAGCGTCCGTAGCCGGCTTATCAAGTCTCTTGTT-AAACCCAGTGATTCAATCATTGACCT-GCAAGAGATACTGTTA-TGCTAGAGGACGGGAGAGGTCGACGG---------GGGTAGGGGTGAAATCCTATAATCCTTGGAGGACCACCAGT-GGCGAAGGCGGTC--GACTAGAACGTGCCTGACGGTGAGGGACGAAAGCT-GGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCAGCTGTAAACGATGCGGGCTAGGTGTTGGGGTAG-CTACGAGCTACT-CCAGTGCCGCAGAGAAGTTGTTAAGCCCGCCGCC-TGGGGAGTACGGCCGCAAGGCT-GAAACTTAAAGGAATT-GGCGGGGGAGC-ACCACAAGGGGTGAAGGCTGCGGTTTAATTGGAGTCAACGCCGGGAACCTTACCGGGGCTGACAGCAGAGTGAA-GGCCAGACTGAAGATCTTGCCAGACAAGCTGAGAGGAGGTGCATGAAGATCTTGCCAGACAAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCT-GTTAAGTCAGGCAACGAACGAGACCCCC--ACTGTTAGTTGCCAGCGAATTCCAACGGAAT--GTCGGGC-ACACTAACAGG-ACTGCCACCGAT-AAGGTGGAGGAAGGAGGGGGCAACGGCAGGTCAGTATG-CCCC--------------------------------------------------------------------------------------------------------------GAACTCGCCCTCATGAACA-TGGAAT-CCCTAGTAACCGCGTGTCATCATCGCGCGGTGAATACGTCCCCGCTCCTTGCACACACCGCCCGTCGCTCCATCCAAG-TCGGGTCT-AGATGAGGCGCAGTCTTCT-----TGGCTACGTCGAATCTGGGTTC-GGTGAGGGGGG-AGAAGTCGTAACAAGGTGGCCGTAGGGGAACCTGCGGCCGGATCACCTCCT'.replace('-', ''),
'SMTZ1-55'),
simple_rec('ACTCCGGTTGATCCTGCCGGACCCCACTGCTATCGGGGTAGGACTTAACCATGCGAGTTGTGCGTCCCCAAGCCATGGTGGGGGCGCGGCATACGGCTCAGTAACACGTGGCTAACCTAGCCTTTGGACGGGGACAACCCCGGGAAACTGGGGCTAATCCCCGATGGGTGGGAAGGCCTGGAATGGTTTCCCACCGAAAGGGCGTCTGAACCATGCTTCAGGCGTTGCCGAAGGATGGGGCCGCGGCCGATCAGGTTGTTGGTGAGGTAACGGCTCACCAAGCCTATAACCGGTACGGGCCGTGAGAGCGGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCAGCAGGTGCGAAAACTCCGCGATGCGCGAAAGCGTGACGGGGCTATCCCGAGTGCCGTCCGCTGAGGATGGCTTTTCCCCGGTGTAGGGAGCCGGGGGAATAAGGAGAGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCTCTCCGAGTGGTGGGGACAATTATTGGGCTTAAAGCGTCCGTAGCCGGCCCATCAAGTCTCTTGTTAAATCCAGCGATCCAATCGCTGGACTGCGGGAGATACTGCTGGGCTAGGGGGCGGGAGAAGCCGATGGTATTCTCGGGGTAGGGGTGAAATCCTATAATCCCGGGAGGACCACCAGTGGCGTAGGCGGTCGGCTAGAACGCGCCCGACGGTGAGGGACGAAAGCTGGGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCAGCCGTAAACGATGCGGGCTAGGTGTTGGGGTGGCTACGAGCCACCCCAGTGCCGCATGGAAGCAATTAAGCCCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGGGTGAAGCTTGCGGTTTAATTGGAGTCAACGCCGGGAAAGGAACAGCGTTTTGTTGTTCCTCTGGATACCTTACCGGGGGCGACAGCAGGATGAAGGCCAGATTGAAGGTCTTGCTGGACGAGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTGCCGTGAGGTGTCCTGTTAAGTCAGGTAACGATCGAGACCCACACCCCCAGTTGCTACCTCTTCGGAGGGCACTCTAGGGGTACTGCCGCCGATAAGGCGGAGGAAGGAGTGGGCCACGGCAGGTCAGTATGCCCCGAATCCCCCGGGCCACACGCGAGCTGCAATGGCAAGGACAATGGGTTCTGACCCCGAGAGGGGAAGGTAATCCCGAAACCCTGCCTCAGTTGGGATCGAGGGCTGAAACCCGCCCTCGTGAACATGGAATCCCTAGTAATCGCGGGTCACCAGCCCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCGCTCCATCCGAGTGGGGTTTAGGTGAGGCGTGGTCCTTGTGGCTGTGTCGAATCTAGGCTTCGCGAGGAGGGAGAAGTCGTAACAAGGTGGCCGTAGGGGAACCTGCGGCCGGATCACCTC',
'BA1-16S')
]
#prepare filter
filt = BlastFilter(lambda a: a.hsps[0].align_length > 1100)
filt.AND = BlastFilter(lambda a: all(hsp.score > 500 for hsp in a.hsps))
filt.AND.AND = BlastFilter(lambda a: all(hsp.identities/float(hsp.align_length) > 0.8 for hsp in a.hsps))
#make ring-blast
blast = BlastCLI(self.abort_event)
orig_seqs = blast.ring_blast(query, suns_db, 100, filt, 3)
if not orig_seqs:
print 'No blast results.'
return 1
nseqs = len(orig_seqs)
print 'RingBlast to:\n%s\nreturned %d sequences.\n' % (suns_db, nseqs)
#save an initial alignment
self.fix_ids(orig_seqs)
alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.fasta'
with user_message('Aligning retrieved sequences...', '\n'):
if not AlignmentUtils.align(orig_seqs+[query]+additions, outfile=alifile): return 3
#search for additional homologs
add_seqs = blast.ring_blast(orig_seqs, silva_db, 100, filt, 0)
if add_seqs:
self.fix_ids(add_seqs)
print 'RingBlast to:\n%s\nreturned %d additional sequences.\n' % (silva_db, len(add_seqs))
#build an alignment
seqs = orig_seqs+add_seqs+[query]+additions
alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.big.aln.fasta'
with user_message('Aligning retrieved sequences...', '\n'):
if not AlignmentUtils.align(seqs, outfile=alifile): return 3
#build a tree
treefile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.big.aln.tre'
if not PhyloUtils.build_fast_tree(alifile, treefile): return 4
#annotate the tree
with open('/home/allis/Documents/INMI/16S/SSBaF4-SSBaR4-1_243072232-iPCR-report.txt') as inp:
# SSBaF4-SSBaR4_65397396-iPCR-report.txt
sids = set()
len_re = re.compile(r'(\s|^)(\d+)(\sbp|\\s*:)?', re.MULTILINE)
entry = False
cur_sid = None
cur_len = -1
for l in inp:
if l == '========= histograms and electrophorograms of PCR products of each hit =========': break
if l.startswith('---'):
entry = False
if cur_sid and cur_len > 0 and abs(cur_len-920) < 60:
sids.add(cur_sid)
cur_sid = None
cur_len = -1
continue
if entry or '#' in l:
entry = True
plen = len_re.search(l)
if plen: cur_len = int(plen.group(2))
sid = BlastID.extract(l)[0]
if sid: cur_sid = sid
organisms = Organisms.from_records(seqs)
if PhyloUtils.annotate_tree(treefile, organisms,
reroot_at='Thermococcus_chitonophagus',
# beautify_leafs=True,
# collapse_taxa=['miscellaneous crenarchaeotic group', 'thaumarchaeota'],
# collapse_last=True,
# collapse_hard=True,
mark_leafs=sids,
# [r.id for r in orig_seqs+[query]+additions],
lineage_colors={'miscellaneous crenarchaeotic group':(0, 0, 255),
'thaumarchaeta':(255,0,0)},
top_lineage=Lineage('archaea')): return 0
return 2
def _main(self):
email = '*****@*****.**'
genome_dir = '/home/allis/Dropbox/Science/Микра/Thermococcus/sequence/GenBank/Thermococcales/Thermococcus/'
genome = 'Thermococcus_barophilus_Ch5.gb'
gene = 'TBCH5v1_1369' #cooS
database = 'nr'
segment = [3200, 12000]
seq = SeqLoader.load_file(os.path.join(genome_dir, genome))
if not seq: raise RuntimeError('No genome loaded')
seq = seq[0]
index = get_indexes_of_genes(seq, gene)
if not index: raise RuntimeError('No gene found')
feature = seq.features[index[0]]
query = feature.extract(seq)
segments_file = 'CO-clusters.gb'
#get cluster variants if needed
if not os.path.isfile(segments_file):
blast_file = 'blast.results.xml'
if os.path.isfile(blast_file):
blast = list(parse(open(blast_file)))
else:
blast = BlastCLI.blast_seq(query,
database,
100,
remote=True,
task='blastn',
parse_results=True,
save_results_to='blast.results.xml')
if not blast: raise RuntimeError('Blast returned no results')
flt = BlastFilter(lambda hsp, r: hsp.align_length > 700,
filter_hsps=True)
flt(blast)
queries = []
for ali in BlastCLI.iter_alignments(blast):
q = BlastCLI.Query(ali,
'hsp',
start_offset=segment[0],
end_offset=segment[1])
if q: queries.append(q)
print(queries[-1])
segments = BlastWWW.fetch_queries(email, queries)
safe_write(segments, segments_file)
for r in segments:
print('[%s] %s: %dbp' % (r.id, pretty_rec_name(r), len(r)))
return 0
#find primers in alignments of the selected features
local_files = [
os.path.join(genome_dir, f)
for f in ('Thermococcus_barophilus_DT4-complete-genome.gb',
'Thermococcus_ST-423.gb', 'Thermococcus_CH1-complete.gb')
]
loader = SeqLoader(self.abort_event)
segments = loader.load_files([segments_file] + local_files)
fprimers, transF_ali = find_primers(
segments, 'transF',
dict(plen=(20, 30),
max_mismatches=5,
min_first_matches=3,
AT_first=True))
rprimers, cooS_ali = find_primers(segments,
'cooS',
dict(plen=(20, 30),
max_mismatches=4,
min_first_matches=3,
AT_first=True),
reverse=True)
if not fprimers:
print('\nNo forward primers found')
return 1
if not rprimers:
print('\nNo reverse primers found')
return 1
print('\nForward primers:')
for p in fprimers:
print('%s: %s' % (p.id, p))
print('\nReverse primers:')
for p in rprimers:
print('%s: %s' % (p.id, p))
print()
#add primers to alignments and save them
transF_ali = PrimerFinder.add_primers_to_alignment(
fprimers, transF_ali)
cooS_ali = PrimerFinder.add_primers_to_alignment(rprimers,
cooS_ali,
reverse=True)
AlignmentUtils.save(transF_ali, 'transF.aln')
AlignmentUtils.save(cooS_ali, 'cooS.aln')
