def main():
'''
Script to extract reads without any alignments
'''
# Input arguments
argparser = ArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
# ------------------ #
print '1. Loading tax tree...'
start = time.time()
tax_tree = TaxTree()
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------ #
print '2. Loading alignment file...'
start = time.time()
read_container = ReadContainer()
read_container.load_alignment_data(args.alignment_file)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------ #
# Loop through reads and take those with no alignments
out_file = open(args.read_ids_out, 'w')
no_aln_count = 0
for read in read_container.fetch_all_reads(format=list):
if not read.has_alignments():
out_file.write("{0}\n".format(read.id))
no_aln_count += 1
out_file.close()
total_read_count = read_container.get_read_count()
print("total number of reads : {0}".format( total_read_count ))
print("reads without alignments: {0}".format(no_aln_count))
print
print("no aln percentage: {0:.2f}%".format(no_aln_count * 100 / float(total_read_count)))
def main():
'''
Script to run binner in one of the most common
usage scenarios.
* load alignment data
* load taxonomy data
* do basic alignment data filtering (remove host reads ecc)
'''
#----------------------------------#
#------ INPUT ARGUMENTS -----------#
argparser = TestRunArgParser()
args = argparser.parse_args()
#----------------------------------#
#------- STATIC DATA SOURCE -------#
# CDS - GI2TAXID -- NAMES -- NODES #
dataAccess = DataAccess(args)
#raw_input('Data access created')
#----------------------------------#
#-------- TAXONOMY TREE -----------#
print '1. Loading tax tree...'
tax_tree = TaxTree()
# tax_tree.load_taxonomy_data(dataAccess)
print 'done.'
#----------------------------------#
#------- ALIGNMENT DATA SOURCE ----#
print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.input)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
# Remember total number of reads
total_read_num = read_container.get_read_count()
print 'done'
#------- FILTER HOST READS -------#
print '3. Filtering host reads & alignments...'
new_reads = host_filter.filter_potential_host_reads(
read_container.fetch_all_reads(format=list),
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
#delete_host_alignments =
True,
#filter_unassigned =
True,
#unassigned_taxid=
-1,
host_filter.perc_of_host_alignments_larger_than)
dataAccess.clear_cache() # deletes gi2taxid cache
reads_with_no_host_alignments = host_filter.filter_potential_hosts_alignments(
new_reads,
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
True, # delete host alignments
True, # filter unassigned
-1) # unassigned taxid
host_read_count = len(read_container.fetch_all_reads(format=list)) - len(reads_with_no_host_alignments)
read_container.set_new_reads(reads_with_no_host_alignments)
print 'done'
#----------------------------------#
#------- LOAD ALL RECORDS -------#
print '4. Loading referenced records...'
record_container = RecordContainer()
record_container.set_db_access(dataAccess)
record_container.populate(read_container.fetch_all_reads_versions(), table='cds')
print 'done'
#----------------------------------#
#-- MAP ALIGNMENTS TO GENES -----#
print '5. Mapping alignments to genes...'
read_container.populate_cdss(record_container)
#----------------------------------#
#- RECORD ALL ALIGNEMENTS TO GENE -#
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container.fetch_all_reads(format=list))
print 'done'
print '6. Estimating organisms present in sample...'
target_organisms = [633, 632, 263, 543, 86661, 1392, 55080, 1386] # What is this part?
print 'done.'
print '7. Annotating reads...'
annotated_reads = rstate.annotate_reads(
read_container.fetch_all_reads(format=list),
cds_aln_container.read2cds,
tax_tree,
target_organisms)
read_container.set_new_reads(annotated_reads)
print 'done'
print '8. Binning reads...'
orgs = bin_reads(
read_container.fetch_all_reads(format=list),
cds_aln_container.cds_repository,
cds_aln_container.read2cds,
tax_tree,
target_organisms,
None,
None,
False)
'''
for org in orgs.values():
print org.name
print len(set(org.get_reads()))
print len(org.identified_coding_regions)
print 'done.'
'''
print ("total_read_num: " + str(total_read_num))
print '9. Generating XML...'
dataset = Dataset(args.xml_description_file)
xml_organisms = []
host = Organism (host_read_count, host_read_count/float(total_read_num), None, None, "Host",
None, None, [], [], [], is_host=True)
xml_organisms.append(host)
for org in orgs.values():
xml_organisms.append(org.to_xml_organism(tax_tree, total_read_num))
xml_organisms.sort(key=operator.attrgetter("amount_count"), reverse=True)
xml = XMLOutput(dataset, xml_organisms, args.output)
xml.xml_output();