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
