def parse_blast_out6(out_file, blast_prefs):
"""Parse BLAST results formatted in Tabular format (outfmt=6)."""
from analysis.text_manipulation import adaptive_list_load
score_pref = blast_prefs['score']
len_pref = blast_prefs['length']
query_matches = []
# default blast outfmt yields
# 0=qseqid 1=sseqid 2=pident 3=length 4=mismatch 5=gapopen
# 6=qstart 7=qend 8=sstart 9=send 10=evalue 11=bitscore
results = adaptive_list_load(out_file, 0, (1, 2, 3, 6, 7, 8, 9, 10, 11))
for line in results:
contig_ID = line[0]
match_p100 = float(line[1])
length = int(line[2])
q_start = int(line[3])
q_end = int(line[4])
s_start = int(line[5])
s_end = int(line[6])
evalue = line[7]
bitscore = float(line[8])
if bitscore < score_pref:
pass # this is bad
elif length < len_pref:
pass # this is bad too
else:
if q_start > q_end: m_orient = '-'
else: m_orient = '+'
match_details = {'match_p100': match_p100,
'length': length, 'm_orient': m_orient,
'q_start': q_start, 'q_end': q_end,
's_start': s_start, 's_end': s_end,
'evalue': evalue, 'bitscore': bitscore}
match = {'contig_id': contig_ID, 'details': match_details}
query_matches.append(match)
return query_matches
def genome_sets_load(genomes_path, input_file, input_prefs, db_path):
"""Load genome datasets listed in an input file."""
import os, sys
from classes.analysis_obj import GenomeSet
from analysis.seqfile_ops import ensure_fasta
from analysis.text_manipulation import adaptive_list_load
from analysis.blasting import make_blastDB
header = input_prefs['header']
columns = input_prefs['columns']
genomes_list = adaptive_list_load(input_file, header, columns)
print "prepping BLAST databases"
genome_sets = []
for line in genomes_list:
genome_name = line[0]
seq_file = os.path.join(genomes_path, line[1])
try: db_infile = ensure_fasta(seq_file)
except: raise
else: print "genome FASTA sequence available in", db_infile
dbfile_path, DB_report = make_blastDB(db_path, genome_name,
seq_file, 'nucl')
if DB_report['status'] is 1:
print genome_name, ":", DB_report['message']['error']
sys.exit()
elif DB_report['status'] is 0:
print genome_name, ":", DB_report['message']
new_genome_set = GenomeSet(db_infile, genome_name)
genome_sets.append(new_genome_set)
print " ", len(genome_sets),"databases ready to search"
return genome_sets
def seq_subset_load(infile, subset_mode, subset_args):
"""Load a subset of sequence segments from a sequence file."""
from analysis.sequence_ops import feat_collect, feature_coords, \
coord_chop, get_seq_subset_by_coords
from analysis.seqfile_ops import load_multifasta, surefmt_load, \
write_fasta
from analysis.text_manipulation import adaptive_list_load
if subset_mode is 'flatfile':
# in this case the sequence file MUST be multifasta
try: subset = load_multifasta(infile)
except: raise
else:
print "set of", len(subset), "sequence segments"
subset_file = infile
else:
# load the query single sequence file (convert format if necessary)
try: seq_record = surefmt_load(infile, 'fasta', 'generic_dna')
except: raise
else: print "query sequence loaded from", infile
# load or generate coordinate pairs for target segments
if subset_mode is 'coordinates':
try:
coords_file = subset_args['file']
header = subset_args['header']
columns = subset_args['columns']
coords_list = adaptive_list_load(coords_file, header, columns)
except: raise
else: print len(coords_list), "segments loaded from", infile
elif subset_mode is 'features':
try:
feat_mode = subset_args
features = feat_collect(infile, feat_mode)
coords_list = feature_coords(features)
print coords_list
except: raise
else: print len(coords_list),"features loaded from", infile
elif subset_mode is 'size':
try:
size = subset_args['size']
chop_mode = subset_args['chop_mode']
coords_list = coord_chop(len(seq_record.seq), size, chop_mode)
except: raise
else: print len(coords_list), "segments generated to fit", size
else:
print "ERROR: A mode MUST be specified."
coords_list = None
# collect subset of sequence segments using resulting coords_list
try: subset = get_seq_subset_by_coords(seq_record, coords_list)
except: raise
else: print "subset of", len(subset), "sequence segments"
# save subset to multifasta file for later use or reference
subset_file = seq_record.id+'_subset.fas'
try: write_fasta(subset_file, subset)
except: raise
else: print "subset written to fasta file", subset_file
return subset, subset_file
def test_adaptive_list_load(self):
trimlines = text_manipulation.adaptive_list_load(self.filename, 0,
(1,3))
self.assertEqual(len(trimlines), 4)
self.assertEqual(trimlines[1][1], self.line_1_contents[3])