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Wrapped the options reference path getter calls with calls to os.path.join #6

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Jun 23, 2014
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Wrapped the options reference path getter calls with calls to os.path.join #6

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12 changes: 6 additions & 6 deletions sepp/metagenomics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def build_profile(input,output_directory):
binned_fragments=bin_to_markers(input,temp_dir)

#load up taxonomy for 30 marker genes
(taxon_map, level_map, key_map) = load_taxonomy(options().__getattribute__('reference').path + 'refpkg/rpsB.refpkg/all_taxon.taxonomy')
(taxon_map, level_map, key_map) = load_taxonomy(os.path.join(options().__getattribute__('reference').path, 'refpkg/rpsB.refpkg/all_taxon.taxonomy'))

#all classifications stored here
classifications = {}
Expand All @@ -63,15 +63,15 @@ def build_profile(input,output_directory):
for (gene,frags) in binned_fragments.items():
#Get size of each marker
total_taxa = 0
with open(options().__getattribute__('reference').path + 'refpkg/%s.refpkg/sate.size'%gene, 'r') as f:
with open(os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/sate.size'%gene), 'r') as f:
total_taxa = int(f.readline().strip())
decomp_size = options().alignment_size
if (decomp_size > total_taxa):
decomp_size = int(total_taxa/2)
cpus = options().cpu
if (len(frags.keys()) < cpus):
cpus = len(frags.keys())
os.system('run_tipp.py -c %s --cpu %s -m %s -f %s -t %s -adt %s -a %s -r %s -tx %s -txm %s -at %0.2f -pt %0.2f -A %d -P %d -p %s -o %s -d %s' % (options().config_file.name, cpus, options().molecule, temp_dir+"/%s.frags.fas.fixed" % gene,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/sate.taxonomy'%gene,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/sate.tree'%gene,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/sate.fasta'%gene,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/sate.taxonomy.RAxML_info'%gene,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/all_taxon.taxonomy'%gene,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/species.mapping'%gene,options().alignment_threshold,options().placement_threshold,decomp_size,total_taxa,temp_dir+"/temp_file","tipp_%s" % gene,output_directory+"/markers/"))
os.system('run_tipp.py -c %s --cpu %s -m %s -f %s -t %s -adt %s -a %s -r %s -tx %s -txm %s -at %0.2f -pt %0.2f -A %d -P %d -p %s -o %s -d %s' % (options().config_file.name, cpus, options().molecule, temp_dir+"/%s.frags.fas.fixed" % gene,os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/sate.taxonomy'%gene),os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/sate.tree'%gene),os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/sate.fasta'%gene),os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/sate.taxonomy.RAxML_info'%gene),os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/all_taxon.taxonomy'%gene),os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/species.mapping'%gene),options().alignment_threshold,options().placement_threshold,decomp_size,total_taxa,temp_dir+"/temp_file","tipp_%s" % gene,output_directory+"/markers/"))
if (not os.path.exists(output_directory+"/markers/tipp_%s_classification.txt" % gene)):
continue

Expand Down Expand Up @@ -217,7 +217,7 @@ def bin_to_markers(input,temp_dir):
_write_fasta(gene_frags,gene_file)

#Now run HMMER search
hmmer_search(gene_file,options().__getattribute__('reference').path + 'refpkg/%s.refpkg/sate.profile'%gene,temp_dir+"/%s.out" % gene)
hmmer_search(gene_file,os.path.join(options().__getattribute__('reference').path, 'refpkg/%s.refpkg/sate.profile'%gene),temp_dir+"/%s.out" % gene)
results=read_hmmsearch_results(temp_dir+"/%s.out" % gene)

#Now select best direction for each frag
Expand Down Expand Up @@ -269,7 +269,7 @@ def read_mapping(input, header=False, delimiter='\t'):

def bin_blast_results(input):
#Map the blast results to the markers
gene_mapping = read_mapping(options().__getattribute__('reference').path + 'blast/markers/seq2marker.tab')
gene_mapping = read_mapping(os.path.join(options().__getattribute__('reference').path, 'blast/markers/seq2marker.tab'))

genes = {}
with open(input) as f:
Expand All @@ -291,7 +291,7 @@ def hmmer_search(input, hmmer,output):
def blast_fragments(input, output):
'''Blast the fragments against all marker genes+16S sequences, return output
'''
os.system('%s -db %s -outfmt 6 -query %s -out %s -num_threads %d -max_target_seqs 1 ' % (options().__getattribute__('blast').path, options().__getattribute__('reference').path + "blast/markers/alignment.fasta.db", input, output,options().cpu))
os.system('%s -db %s -outfmt 6 -query %s -out %s -num_threads %d -max_target_seqs 1 ' % (options().__getattribute__('blast').path, os.path.join(options().__getattribute__('reference').path, "blast/markers/alignment.fasta.db"), input, output,options().cpu))

def reverse_sequence(sequence):
global character_map
Expand Down