def fas2gbk(fas_file):
"""Convert a FastA file to Genbank format."""
record = load_fasta(fas_file)
gbk_file = fas_file[:fas_file.find('.fas')]+'.gbk'
# record.name = rec_name
# record.id = rec_name
record.seq.alphabet = generic_dna
write_genbank(gbk_file, record)
return gbk_file
def __init__(self, genome, seq_dir):
self.name = genome['name']
self.fas = None
self.gbk = None
self.offset = genome['offset']
self.nudge = genome['nudge']+1
self.invert = False
if genome['input'] == 'fas':
self.fas = seq_dir+genome['file']
self.gbk = fas2gbk(seq_dir+genome['file'])
elif genome['input'] == 'gbk':
self.gbk = seq_dir+genome['file']
self.fas = gbk2fas(seq_dir+genome['file'])
else:
print "ERROR in input format: FastA or Genbank required"
sys.exit()
self.len = len(load_fasta(self.fas).seq)
def annot_ctg(g_file, ctg_fas, annot_gbk, annot_aa, trn_file, prot_db,
blast_out, l_tag_base, blast_prefs):
"""Do functional annotation of contig from Fasta file, return record."""
# gene prediction
if not path.exists(trn_file):
train_prodigal(g_file, trn_file, "-q")
if not path.exists(annot_aa):
run_prodigal(ctg_fas, annot_gbk, annot_aa, trn_file, "-q")
# blast the amino acids against COG
if not path.exists(blast_out):
local_blastp_2file(annot_aa, prot_db, blast_out, blast_prefs)
# collect best hits
rec_cogs = collect_cogs(blast_out)
# consolidate annotated genbank file
record = load_fasta(ctg_fas)
record.features = []
aa_record = load_multifasta(annot_aa)
counter = 1
for aa_rec in aa_record:
this_prot = 'Query_'+str(counter)
annotation = rec_cogs[this_prot]
# get feature details from description line
# because prodigal output fails to load as valid genbank
defline = aa_rec.description
pattern = re.compile('.+#\s(\d+)\s#\s(\d+)\s#\s(\S*1)\s#\sID.+')
match = pattern.match(defline)
start_pos = int(match.group(1))
end_pos = int(match.group(2))
strand_pos = int(match.group(3))
feat_loc = FeatureLocation(start_pos, end_pos)
l_tag = l_tag_base+"_"+str(counter)
# consolidation feature annotations
quals = {'note': defline, 'locus_tag': l_tag,
'fct': annotation, 'translation': aa_rec.seq}
feature = SeqFeature(location=feat_loc,
strand=strand_pos,
id='cds_'+str(counter),
type='CDS',
qualifiers=quals)
record.features.append(feature)
counter +=1
return record
def __init__(self, genome, seq_dir):
self.name = genome['name']
self.fas = None
self.gbk = None
self.offset = genome['offset']
self.nudge = genome['nudge'] + 1
self.invert = False
self.dir = seq_dir + genome['cat'] + '/'
if genome['input'] == 'fas':
self.fas = self.dir + genome['file']
self.gbk = fas2gbk(self.dir + genome['file'])
elif genome['input'] == 'gbk':
self.gbk = self.dir + genome['file']
self.fas = gbk2fas(self.dir + genome['file'])
else:
print "ERROR in input format: FastA or Genbank required"
sys.exit()
self.len = len(load_fasta(self.fas).seq)
def basic_batch_blast(genomes, run_ref, blast_mode, r_root_dir, run_dirs,
fixed_dirs, blast_prefs, run_id, timestamp):
"""Send batch jobs to Blast. Muxes to multiple reference DBs."""
# load inputs
ref_n = run_ref.name
run_root = r_root_dir+run_id+"/"
in_root = run_root+run_dirs['ref_seg_dir']+ref_n+"/"
print " ", ref_n
# log
logstring = "".join(["\n\n# Blast segs to genomes @", timestamp, "\n\n"])
run_ref.log(logstring)
# do blast
for seg in run_ref.segs:
input_file = in_root+ref_n+"_"+seg['name']+".fas"
# translate if required
if blast_mode == 'tn':
record = load_fasta(input_file)
record.seq = record.seq.translate()
input_file = in_root+ref_n+"_"+seg['name']+"_aa.fas" # substitute
write_fasta(input_file, record)
out_dir = run_root+run_dirs['blast_out_dir']+ref_n+"/"+seg['name']+"/"
ensure_dir([out_dir])
print "\t", seg['name'],
for genome in genomes:
g_name = genome['name']
db_path = fixed_dirs['blast_db_dir']+g_name
outfile = out_dir+g_name+"_out.txt"
print ".",
if blast_mode == 'n':
local_blastn_2file(input_file, db_path, outfile, blast_prefs)
elif blast_mode == 'tx':
local_tblastx_2file(input_file, db_path, outfile, blast_prefs)
elif blast_mode == 'tn':
local_tblastn_2file(input_file, db_path, outfile, blast_prefs)
print ""
run_ref.log("All OK")
return "OK"
def glompX_blast_out(genomes, run_ref, blast_mode, r_root_dir, run_dirs,
run_id, fixed_dirs, blast_dtypes, references,
min_nt_match, min_nt_score, min_nt_idp, min_aa_match,
min_aa_score, min_aa_idp, capture_span, timestamp):
"""Collect Blast results and extract match contigs."""
# load inputs
ref_n = run_ref.name
run_root = r_root_dir+run_id+"/"
match_root = run_root+run_dirs['match_out_dir']+ref_n+"/"
capture_root = run_root+run_dirs['capture_dir']+ref_n+"/"
print " ", ref_n
# log
logstring = "".join(["\n\n# Collect Blast results @", timestamp, "\n\n"])
run_ref.log(logstring)
# collect results
ref_hits = {}
control_scores = []
run_ref.log("Segs/Gs\t")
run_ref.log("\t".join([genome['name'] for genome in genomes]))
for seg in run_ref.segs:
seg_n = seg['name']
print "\t", seg_n, "...",
run_ref.log("".join(["\n", seg_n]))
blast_dir = run_root+run_dirs['blast_out_dir']+ref_n+"/"+seg_n+"/"
capture_dir = capture_root+"/"+seg_n+"/"
ensure_dir([blast_dir, capture_dir])
ref_flag = True
for genome in genomes:
g_name = genome['name']
print "|",
# process
if g_name not in ref_hits.keys():
ref_hits[g_name] = {}
matches_dir = match_root+g_name+"/"
ensure_dir([matches_dir])
blast_infile = blast_dir+g_name+"_out.txt"
genome_ctg_dir = fixed_dirs['fas_contigs_dir']+g_name+"/"
rec_array = read_array(blast_infile, blast_dtypes)
if len(rec_array) > 0: # take qualified hits
p_cnt = 0
n_cnt = 0
if g_name in [ref['name'] for ref in references]:
copyfile(genome_ctg_dir+g_name+"_1.fas",
matches_dir+g_name+".fas")
if ref_flag:
# positive control TODO: better solution
control_scores.append(rec_array[0][11])
ref_flag = False
for line in rec_array:
idp = line[2]
q_start, q_stop = line[8], line[9]
score = line[11]
length = abs(q_stop-q_start)
# check the blast mode to use the right thresholds
if blast_mode == 'n' or blast_mode == 'tx':
min_match = min_nt_match
min_score = min_nt_score
min_idp = min_nt_idp
elif blast_mode == 'tn':
min_match = min_aa_match
min_score = min_aa_score
min_idp = min_aa_idp
else: # default to nucleotide mode
min_match = min_nt_match
min_score = min_nt_score
min_idp = min_nt_idp
if length>min_match and score>min_score and idp>min_idp:
print "+",
p_cnt +=1
contig_id = line[1]
if contig_id not in ref_hits[g_name].keys():
ref_hits[g_name][contig_id] = {seg_n: score}
else:
ref_hits[g_name][contig_id][seg_n] = score
pattern = re.compile(r'('+contig_id+')\.fas')
for item in listdir(genome_ctg_dir):
match = re.match(pattern, item)
if match:
fas_file = matches_dir+match.group(1)+".fas"
if not path.exists(fas_file):
copyfile(genome_ctg_dir+item, fas_file)
# context capture
capture_flag = False
while True:
try:
if int(seg_n) in run_ref.capture:
capture_flag = True
else:
break
except ValueError:
if seg_n in run_ref.capture:
capture_flag = True
else:
break
else:
break
if capture_flag:
# load the sequence
contig_file = matches_dir+contig_id+".fas"
contig_rec = load_fasta(contig_file)
# check orientation
if q_start < q_stop:
c_start = q_start-capture_span
c_stop = q_stop+capture_span
else:
c_start = q_stop-capture_span
c_stop = q_start+capture_span
print c_start, c_stop
# check limits
if c_start < 0:
c_start = 1
if c_stop > len(contig_rec.seq):
c_stop = len(contig_rec.seq)
# proceed
cxt_file = capture_dir+g_name+"_"+contig_id+".fas"
cxt_rec = SeqRecord(id=contig_id+"_"
+str(c_start)+"_"
+str(c_stop),
seq=contig_rec.seq
[c_start:c_stop])
write_fasta(cxt_file, cxt_rec)
else:
print "-",
n_cnt +=1
if n_cnt > 0:
logstring = "".join(["\t", str(p_cnt), " (",
str(n_cnt), ")"])
else:
logstring = "".join(["\t", str(p_cnt)])
run_ref.log(logstring)
else:
print "-",
run_ref.log("".join(["\t", "0"]))
print ""
return ref_hits, control_scores
def glompX_blast_out(genomes, run_ref, blast_mode, r_root_dir, run_dirs,
run_id, fixed_dirs, blast_dtypes, references,
min_nt_match, min_nt_score, min_nt_idp, min_aa_match,
min_aa_score, min_aa_idp, capture_span, timestamp):
"""Collect Blast results and extract match contigs."""
# load inputs
ref_n = run_ref.name
run_root = r_root_dir + run_id + "/"
match_root = run_root + run_dirs['match_out_dir'] + ref_n + "/"
capture_root = run_root + run_dirs['capture_dir'] + ref_n + "/"
print " ", ref_n
# log
logstring = "".join(["\n\n# Collect Blast results @", timestamp, "\n\n"])
run_ref.log(logstring)
# collect results
ref_hits = {}
control_scores = []
run_ref.log("Segs/Gs\t")
run_ref.log("\t".join([genome['name'] for genome in genomes]))
for seg in run_ref.segs:
seg_n = seg['name']
print "\t", seg_n, "...",
run_ref.log("".join(["\n", seg_n]))
blast_dir = run_root + run_dirs[
'blast_out_dir'] + ref_n + "/" + seg_n + "/"
capture_dir = capture_root + "/" + seg_n + "/"
ensure_dir([blast_dir, capture_dir])
ref_flag = True
for genome in genomes:
g_name = genome['name']
print "|",
# process
if g_name not in ref_hits.keys():
ref_hits[g_name] = {}
matches_dir = match_root + g_name + "/"
ensure_dir([matches_dir])
blast_infile = blast_dir + g_name + "_out.txt"
genome_ctg_dir = fixed_dirs['fas_contigs_dir'] + g_name + "/"
rec_array = read_array(blast_infile, blast_dtypes)
if len(rec_array) > 0: # take qualified hits
p_cnt = 0
n_cnt = 0
if g_name in [ref['name'] for ref in references]:
copyfile(genome_ctg_dir + g_name + "_1.fas",
matches_dir + g_name + ".fas")
if ref_flag:
# positive control TODO: better solution
control_scores.append(rec_array[0][11])
ref_flag = False
for line in rec_array:
idp = line[2]
q_start, q_stop = line[8], line[9]
score = line[11]
length = abs(q_stop - q_start)
# check the blast mode to use the right thresholds
if blast_mode == 'n' or blast_mode == 'tx':
min_match = min_nt_match
min_score = min_nt_score
min_idp = min_nt_idp
elif blast_mode == 'tn':
min_match = min_aa_match
min_score = min_aa_score
min_idp = min_aa_idp
else: # default to nucleotide mode
min_match = min_nt_match
min_score = min_nt_score
min_idp = min_nt_idp
if length > min_match and score > min_score and idp > min_idp:
print "+",
p_cnt += 1
contig_id = line[1]
if contig_id not in ref_hits[g_name].keys():
ref_hits[g_name][contig_id] = {seg_n: score}
else:
ref_hits[g_name][contig_id][seg_n] = score
pattern = re.compile(r'(' + contig_id + ')\.fas')
for item in listdir(genome_ctg_dir):
match = re.match(pattern, item)
if match:
fas_file = matches_dir + match.group(
1) + ".fas"
if not path.exists(fas_file):
copyfile(genome_ctg_dir + item, fas_file)
# context capture
capture_flag = False
while True:
try:
if int(seg_n) in run_ref.capture:
capture_flag = True
else:
break
except ValueError:
if seg_n in run_ref.capture:
capture_flag = True
else:
break
else:
break
if capture_flag:
# load the sequence
contig_file = matches_dir + contig_id + ".fas"
contig_rec = load_fasta(contig_file)
# check orientation
if q_start < q_stop:
c_start = q_start - capture_span
c_stop = q_stop + capture_span
else:
c_start = q_stop - capture_span
c_stop = q_start + capture_span
print c_start, c_stop
# check limits
if c_start < 0:
c_start = 1
if c_stop > len(contig_rec.seq):
c_stop = len(contig_rec.seq)
# proceed
cxt_file = capture_dir + g_name + "_" + contig_id + ".fas"
cxt_rec = SeqRecord(
id=contig_id + "_" + str(c_start) + "_" +
str(c_stop),
seq=contig_rec.seq[c_start:c_stop])
write_fasta(cxt_file, cxt_rec)
else:
print "-",
n_cnt += 1
if n_cnt > 0:
logstring = "".join(
["\t", str(p_cnt), " (",
str(n_cnt), ")"])
else:
logstring = "".join(["\t", str(p_cnt)])
run_ref.log(logstring)
else:
print "-",
run_ref.log("".join(["\t", "0"]))
print ""
return ref_hits, control_scores
def align_ctg2ref(run_ref, run_id, timestamp, r_root_dir, run_dirs, genomes,
mauve_exec, max_size, chop_mode, mtype):
"""Align contigs pairwise to the reference contig."""
# set inputs and outputs
ref_n = run_ref.name
run_root = r_root_dir + run_id + "/"
ref_ctg_file = run_ref.file
mauve_root = run_root + run_dirs['mauve_out_dir'] + ref_n + "/contigs/"
segments_root = run_root + run_dirs['aln_seg_dir'] + ref_n + "/contigs/"
q_ctgs_root = run_root + run_dirs['match_out_dir'] + ref_n + "/"
ensure_dir([segments_root])
print " ", ref_n
# log
logstring = "".join(["\n\n# Align contigs to ref @", timestamp, "\n"])
run_ref.log(logstring)
# cycle through genomes
for genome in genomes:
# set inputs and outputs
g_name = genome['name']
ctgs_fas_dir = q_ctgs_root + g_name + "/"
mauve_dir = mauve_root + g_name + "/"
aln_segs_root = segments_root + g_name + "/"
ensure_dir([mauve_dir])
print "\t", g_name, "...",
# log
logstring = "".join(["\n", g_name])
run_ref.log(logstring)
# list genbank files in matches directory
dir_contents = listdir(ctgs_fas_dir)
for item in dir_contents:
pattern = re.compile(r'.*_(\d*)\.fas$')
match = pattern.match(item)
if match:
ctg_num = match.group(1)
print ctg_num,
logstring = "".join(["\t", ctg_num])
run_ref.log(logstring)
# set inputs and outputs
q_contig = ctgs_fas_dir + item
file_list = (ref_ctg_file, q_contig)
mauve_outfile = mauve_dir + ctg_num + ".mauve"
aln_segs_dir = aln_segs_root + ctg_num + "/"
ensure_dir([aln_segs_dir])
segfile = aln_segs_dir + ctg_num + "_" + ref_n + "_segs.txt"
open(segfile, 'w').write('')
# do Mauve alignment
try:
open(ref_ctg_file, 'r')
open(q_contig, 'r')
except IOError:
msg = "\nERROR: File missing, cannot align\n\t\t\t"
run_ref.log(msg)
print msg
else:
align_mauve(file_list, mauve_outfile, mauve_exec)
try:
# parse Mauve output (without initial clumping)
coords = mauver_load2_k0(mauve_outfile + ".backbone",
0, mtype)
# chop segments that are too long
chop_array = chop_rows(coords, max_size, chop_mode,
mtype)
# make detailed pairwise alignments of the segments
ref_rec = load_genbank(ref_ctg_file)
query_rec = load_fasta(q_contig)
iter_align(chop_array, ref_rec, query_rec,
aln_segs_dir, segfile)
except IOError:
msg = "\nERROR: Mauve alignment failed\n\t\t\t"
run_ref.log(msg)
print msg
except Exception:
msg = "\nERROR: Iteration failed\n\t\t\t"
run_ref.log(msg)
print msg
print ""
def align_ctg2ref(run_ref, run_id, timestamp, r_root_dir, run_dirs,
genomes, mauve_exec, max_size, chop_mode, mtype):
"""Align contigs pairwise to the reference contig."""
# set inputs and outputs
ref_n = run_ref.name
run_root = r_root_dir+run_id+"/"
ref_ctg_file = run_ref.file
mauve_root = run_root+run_dirs['mauve_out_dir']+ref_n+"/contigs/"
segments_root = run_root+run_dirs['aln_seg_dir']+ref_n+"/contigs/"
q_ctgs_root = run_root+run_dirs['match_out_dir']+ref_n+"/"
ensure_dir([segments_root])
print " ", ref_n
# log
logstring = "".join(["\n\n# Align contigs to ref @", timestamp, "\n"])
run_ref.log(logstring)
# cycle through genomes
for genome in genomes:
# set inputs and outputs
g_name = genome['name']
ctgs_fas_dir = q_ctgs_root+g_name+"/"
mauve_dir = mauve_root+g_name+"/"
aln_segs_root = segments_root+g_name+"/"
ensure_dir([mauve_dir])
print "\t", g_name, "...",
# log
logstring = "".join(["\n", g_name])
run_ref.log(logstring)
# list genbank files in matches directory
dir_contents = listdir(ctgs_fas_dir)
for item in dir_contents:
pattern = re.compile(r'.*_(\d*)\.fas$')
match = pattern.match(item)
if match:
ctg_num = match.group(1)
print ctg_num,
logstring = "".join(["\t", ctg_num])
run_ref.log(logstring)
# set inputs and outputs
q_contig = ctgs_fas_dir+item
file_list = (ref_ctg_file, q_contig)
mauve_outfile = mauve_dir+ctg_num+".mauve"
aln_segs_dir = aln_segs_root+ctg_num+"/"
ensure_dir([aln_segs_dir])
segfile = aln_segs_dir+ctg_num+"_"+ref_n+"_segs.txt"
open(segfile, 'w').write('')
# do Mauve alignment
try:
open(ref_ctg_file, 'r')
open(q_contig, 'r')
except IOError:
msg = "\nERROR: File missing, cannot align\n\t\t\t"
run_ref.log(msg)
print msg
else:
align_mauve(file_list, mauve_outfile, mauve_exec)
try:
# parse Mauve output (without initial clumping)
coords = mauver_load2_k0(mauve_outfile+".backbone",
0, mtype)
# chop segments that are too long
chop_array = chop_rows(coords, max_size, chop_mode,
mtype)
# make detailed pairwise alignments of the segments
ref_rec = load_genbank(ref_ctg_file)
query_rec = load_fasta(q_contig)
iter_align(chop_array, ref_rec, query_rec,
aln_segs_dir, segfile)
except IOError:
msg = "\nERROR: Mauve alignment failed\n\t\t\t"
run_ref.log(msg)
print msg
except Exception:
msg = "\nERROR: Iteration failed\n\t\t\t"
run_ref.log(msg)
print msg
print ""
def filter_contigs(run_ref, run_id, genomes, norm_matches, seg_size, threshold, r_root_dir, run_dirs, fixed_dirs, timestamp):
"""Filter contigs."""
# set inputs and outputs
ref_n = run_ref.name
run_root = r_root_dir+run_id+"/"
fas_root = fixed_dirs['fas_contigs_dir']
report_root = run_root+run_dirs['reports']+ref_n+"/"
ensure_dir([report_root])
print " ", ref_n
# log
logstring = "".join(["\n\n# Filter contigs @", timestamp, "\n"])
run_ref.log(logstring)
# process
# evaluate segment specificity using negative controls
neg_controls = [genome['name'] for genome in genomes if ('ctrl' in genome.keys() and genome['ctrl'] == 'neg')]
neg_dat = [norm_matches[g_name]['ctg_scores'] for g_name in neg_controls]
neg_RA = np.vstack(neg_dat)
neg_mean = nanmean(neg_RA, axis=0)
# process the genomes we're testing
test_genomes = [genome['name'] for genome in genomes if not ('ctrl' in genome.keys())]
for g_name in test_genomes:
print "\t", g_name,
ctg_hits = norm_matches[g_name]['ctg_scores']
ctg_stats = {}
#process individual contigs
counter = 0
for ctg_RA in ctg_hits:
# identify this contig by name
ctg_name = norm_matches[g_name]['ctg_names'][counter]
counter += 1
# subtract background signal from match scores
recal_ctg_RA = np.subtract(ctg_RA, neg_mean)
recal_ctg_RA = recal_ctg_RA.clip(min=0)
# compute total similarity score
s_score = np.sum(recal_ctg_RA)
# compute clustering score (primitive)
streak = False
c_score = 0
for hit in recal_ctg_RA:
if hit == 0:
if streak == True:
c_score += -1
streak = False
else:
c_score += 0
elif hit > 0:
if streak == True:
c_score += 2
else:
c_score += 1
streak = True
# compute backbone vs. cargo burden
ctg_rec = load_fasta(fas_root+g_name+"/"+ctg_name+".fas")
bbone = np.sum(np.ma.make_mask(recal_ctg_RA))*seg_size
if bbone > len(ctg_rec):
bbone = len(ctg_rec) # workaround for last segment being always a little short
cargo = len(ctg_rec) - bbone
# make inverted array mask (used for redundancy detection)
ctg_mask = np.ma.getmaskarray(np.ma.masked_equal(recal_ctg_RA,0))
# consolidate contig information
ctg_stats[ctg_name] = {'s_score': s_score,
'c_score': c_score,
'vector': recal_ctg_RA,
'inv_mask':ctg_mask,
'bbone': bbone,
'cargo': cargo}
# detect redundant contigs
### use np.ma.mask_or(m1, m2)
### if any elements returns false there is a redundancy between two contigs
### if so evaluate which has better c_score and s_score
# compute overall stats for the genome
gs_score = sum([ctg_stats[contig]['s_score'] for contig in ctg_stats])
gc_score = sum([ctg_stats[contig]['c_score'] for contig in ctg_stats])
g_bbone = sum([ctg_stats[contig]['bbone'] for contig in ctg_stats])
g_cargo = sum([ctg_stats[contig]['cargo'] for contig in ctg_stats])
print gs_score, gc_score, g_bbone, g_cargo,
#
if gs_score > threshold:
## run plotters again
## pass the genome on to the next step (others will be dropped)
print "MATCH"
else:
print "(-)"
def batch_contig_annot(dataset):
"""Extract and annotate contigs."""
# identify dataset contig file
contigs_file = dirs['assembly_dir']+dataset['f_nick']+'/'+'contigs.fa'
# locate the COG database
cog_db = dirs['blast_db_dir']+'Cog_LE/Cog'
# make the training file
training_file = dirs['annot_dir']+dataset['f_nick']+'/'+'contigs.trn'
#train_prodigal(contigs_file, training_file)
# set output dirs
fas_out_dir = dirs['annot_dir']+dataset['f_nick']+'/fasta/'
gbk_out_dir = dirs['annot_dir']+dataset['f_nick']+'/predict/'
aa_out_dir = dirs['annot_dir']+dataset['f_nick']+'/aa/'
blast_out_dir = dirs['annot_dir']+dataset['f_nick']+'/rpsblast/'
solid_out_dir = dirs['annot_dir']+dataset['f_nick']+'/genbank/'
maps_out_dir = dirs['annot_dir']+dataset['f_nick']+'/maps/'
ensure_dir(fas_out_dir)
ensure_dir(gbk_out_dir)
ensure_dir(aa_out_dir)
ensure_dir(blast_out_dir)
ensure_dir(solid_out_dir)
# set phage hit collector
contig_hits = {}
sp_hit_list = dirs['annot_dir']+dataset['f_nick']+'/'\
+dataset['f_nick']+'_kw_hits.html'
all_hit_list = dirs['annot_dir']+dataset['f_nick']+'/'\
+dataset['f_nick']+'_all_hits.html'
sp_hit_list_handle = open(sp_hit_list, 'w')
all_hit_list_handle = open(all_hit_list, 'w')
sp_hit_list_handle.write("<ul>")
all_hit_list_handle.write("<ul>")
# load all contigs
contigs_list = load_multifasta(contigs_file)
# cycle through contigs
ctg_count = 0
gene_count = 0
for contig in contigs_list:
ctg_count +=1
# use regex to acquire relevant record ID info
pattern = re.compile(r'NODE_(\d*)_length_(\d*)_cov_(\d*)')
match = pattern.match(contig.id)
nick = match.group(1)+'_'+match.group(2)+'_'+match.group(3)
contig.id = nick
fasta_out = fas_out_dir+nick+'.fas'
# write record to file
write_fasta(fasta_out, contig)
# create contig entry in dict
contig_hits[nick] = []
# run the annotation
annot_gbk = gbk_out_dir+nick+'.gbk'
annot_aa = aa_out_dir+nick+'.fas'
#run_prodigal(fasta_out, annot_gbk, annot_aa, training_file)
# blast the amino acids against COG
print '\tblasting', dataset['f_nick'], nick
blast_out = blast_out_dir+nick+'.xml'
if path.isfile(blast_out):
print "\t\talready blasted"
else:
local_rpsblast_2file(annot_aa, cog_db, blast_out, blast_prefs)
# collect best hits
rec_cogs = collect_cogs(blast_out)
map_file = maps_out_dir+nick+'.pdf'
# consolidate annotated genbank file
record = load_fasta(fasta_out)
aa_defs = load_multifasta(annot_aa)
features = []
counter = 1
ctg_flag_1 = 0
ctg_flag_2 = 0
for protein in aa_defs:
gene_count +=1
# get feature details from description line
# necessary because the prodigal output is not parser-friendly
pattern = re.compile(r'\d+_\d+_\d+_\d+_\d+\s+\S+\s+(\d+)\s+\S+\s+(\d+)\s+\S+\s+(\S*\d)')
match = pattern.match(protein.description)
start_pos = int(match.group(1))
end_pos = int(match.group(2))
strand_pos = int(match.group(3))
feat_loc = FeatureLocation(start_pos, end_pos)
annotation = rec_cogs['Query_'+str(counter)]
if ctg_flag_1 is 0:
all_hit_list_handle.write("</ul><br><a href='"
+"../../../../"
+map_file
+"'>Contig "
+nick+"</a><ul>")
ctg_flag_1 = 1
all_hit_list_handle.write("<li>"+str(counter)
+'. '+annotation+"</li>")
# detect phage content in annotation
phi_pattern = re.compile(r".+(COG\d+).+"
"(phage|capsid|muramidase|tail|"
"replication|helicase|polymerase|"
"integrase|recombinase"
"suppressor|hydrolase|transposase).+",
re.IGNORECASE)
phi_match = phi_pattern.match(annotation)
if phi_match:
hit_flag = 'on'
hit_dict = {'CDS': counter,
'annot': annotation,
'COGs': phi_match.group}
contig_hits[nick].append(hit_dict)
# write out to summary file
if ctg_flag_2 is 0:
sp_hit_list_handle.write("</ul><br><a href='"
+"../../../../"
+map_file
+"'>Contig "
+nick+"</a><ul>")
ctg_flag_2 = 1
sp_hit_list_handle.write("<li>"+str(counter)
+'. '+annotation+"</li>")
else:
hit_flag = 'off'
# consolidation feature annotations
quals = {'note': protein.description,
'fct': annotation,
'flag': hit_flag}
feature = SeqFeature(location=feat_loc,
strand=strand_pos,
id=protein.id,
type='CDS',
qualifiers=quals)
features.append(feature)
counter +=1
record.features = features
record.description = dataset['f_nick']+'_contig_'+nick
record.name = nick
record.dbxrefs = ['Project:np1']
record.seq.alphabet = generic_dna
gbk_out = solid_out_dir+nick+'.gbk'
write_genbank(gbk_out, record)
# generate graphical map
ContigDraw(nick, gbk_out, map_file)
sp_hit_list_handle.write("</ul>")
all_hit_list_handle.write("</ul>")
sp_hit_list_handle.close()
all_hit_list_handle.close()
print "\t", gene_count, "predicted genes in", ctg_count, "contigs"
