Minor changes

docs/tutorial.md

@@ -14,14 +14,14 @@ Install python dependencies as needed:
 [read more...] (install.md)
 
 Download & unpack reference database:  
-[http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.1.tar.gz](http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.1.tar.gz)  
-`tar -zxvf midas_db_v1.1.tar.gz`  
+[http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.2.tar.gz](http://lighthouse.ucsf.edu/MIDAS/midas_db_v1.2.tar.gz)  
+`tar -zxvf midas_db_v1.2.tar.gz`  
 [read more...] (ref_db.md)
 
 Update your environment:  
 `export PYTHONPATH=$PYTHONPATH:MIDAS`  
 `export PATH=$PATH:MIDAS/scripts`   
-`export MIDAS_DB=midas_db_v1.1`  
+`export MIDAS_DB=midas_db_v1.2`  
 
 Optionally, download & unpack example dataset:  
 [http://lighthouse.ucsf.edu/MIDAS/example.tar.gz](http://lighthouse.ucsf.edu/MIDAS/example.tar.gz)  

midas/analyze/track_strains.py

@@ -90,6 +90,8 @@ def call_markers(species, samples, args):
 	# open marker list
 	markers = utility.parse_file(species.paths['markers'])
 	marker = fetch_marker(markers) # dictionary for 1st marker allele
+	if marker is None:
+		sys.exit("\nError: no marker alleles found in file: %s\n" % species.paths['markers'])
 
 	# init markers per sample
 	for sample in samples.values():

midas/run/genes.py

@@ -170,9 +170,11 @@ def count_mapped_bp(args, species, genes):
 			continue
 		else:
 			gene_id = aln_file.getrname(aln.reference_id)
+			aln_len = len(aln.query_alignment_sequence)
+			gene_len = genes[gene_id].length
 			genes[gene_id].reads += 1
-			genes[gene_id].bases += len(aln.query_alignment_sequence)
-			genes[gene_id].depth += genes[gene_id].bases/float(genes[gene_id].length)
+			genes[gene_id].bases += aln_len
+			genes[gene_id].depth += aln_len/float(gene_len)
 			j += 1
 	print("  total aligned reads: %s" % i)
 	print("  total mapped reads: %s" % j)
@@ -193,7 +195,6 @@ def normalize(args, species, genes):
 	# compute marker depth
 	for gene in genes.values():
 		if gene.marker_id is not None:
-			gene.depth = gene.depth
 			species[gene.species_id].markers[gene.marker_id] += gene.depth
 	# compute median marker depth
 	for sp in species.values():

midas/run/snps.py

@@ -19,9 +19,9 @@ def build_genome_db(args, species):
 		db_stats['species'] += 1
 		infile = utility.iopen(sp.paths['fna'])
 		for r in Bio.SeqIO.parse(infile, 'fasta'):
-				outfile.write('>%s\n%s\n' % (r.id, str(r.seq).upper()))
-				db_stats['total_length'] += len(r.seq)
-				db_stats['total_seqs'] += 1
+			outfile.write('>%s\n%s\n' % (r.id, str(r.seq).upper()))
+			db_stats['total_length'] += len(r.seq)
+			db_stats['total_seqs'] += 1
 		infile.close()
 	outfile.close()
 	# print out database stats

scripts/call_consensus.py

@@ -146,7 +146,7 @@ def sequence_description(sample):
 	desc = {}
 	desc['length'] = len(sample.seq)
 	desc['percent_missing'] = percent_missing(sample.seq)
-	desc['mean_depth'] = round(sample.sample_depth, 2)
+	desc['mean_depth'] = round(sample.mean_depth, 2)
 	return desc
 
 def write_consensus(args, samples):