def intersect_keys(keys, reffile, cache=False):
"""Extract SeqRecords from the index by matching keys."""
# Build/load the index of reference sequences
index = None
if cache:
refcache = reffile + '.sqlite'
if os.path.exists(refcache):
if os.stat(refcache).st_mtime < os.stat(reffile).st_mtime:
logging.warn("Outdated cache; rebuilding index")
else:
try:
index = SeqIO.index_db(refcache)
except Exception:
logging.warn("Skipping corrupted cache; rebuilding index")
index = None
else:
refcache = ':memory:'
if index is None:
# Rebuild the index, for whatever reason
index = SeqIO.index_db(refcache, [reffile], 'fasta')
# Extract records by key
for key in keys:
try:
record = index[key]
except LookupError:
# Missing keys are rare, so it's faster not to check every time
logging.info("No match: %s", repr(key))
continue
yield record
def key_check(self, filename, format, alphabet, comp):
"""Check indexing with a key function."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]
key_list = [add_prefix(id) for id in id_list]
with warnings.catch_warnings():
if "_alt_index_" in filename:
# BiopythonParserWarning: Could not parse the SFF index:
# Unknown magic number b'.diy' in SFF index header:
# b'.diy1.00'
warnings.simplefilter("ignore", BiopythonParserWarning)
rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
if not sqlite3:
return
# In memory,
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
# check error conditions
self.assertRaises(ValueError, SeqIO.index_db, ":memory:", format="dummy", key_function=add_prefix)
self.assertRaises(ValueError, SeqIO.index_db, ":memory:", filenames=["dummy"], key_function=add_prefix)
rec_dict.close()
del rec_dict
# Saving to file...
index_tmp = filename + ".key.idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
# Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
# Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet, key_function=add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
os.remove(index_tmp)
def key_check(self, filename, format, alphabet, comp):
"""Check indexing with a key function."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]
key_list = [add_prefix(id) for id in id_list]
rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
if not sqlite3:
return
#In memory,
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
#check error conditions
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", format="dummy",
key_function=add_prefix)
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", filenames=["dummy"],
key_function=add_prefix)
rec_dict.close()
del rec_dict
#Saving to file...
index_tmp = filename + ".key.idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet,
key_function=add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
os.remove(index_tmp)
def simple_check(self, filename, format, alphabet):
"""Check indexing (without a key function)."""
id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]
rec_dict = SeqIO.index(filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict._proxy._handle.close() #TODO - Better solution
del rec_dict
if not sqlite3:
return
#In memory,
#note here give filenames as list of strings
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
#check error conditions
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", format="dummy")
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", filenames=["dummy"])
#Saving to file...
index_tmp = filename + ".idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
#To disk,
#note here we give the filename as a single string
#to confirm that works too (convience feature).
rec_dict = SeqIO.index_db(index_tmp, filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
os.remove(index_tmp)
def makeSQLindex(infiles=None, data_inpath='', mode='grouped', outname=None):
''' Creates an SQL index out of either an uncompressed file or a compressed .bgzf file
if infiles is a string it is interpreted as a glob
if infiles is list, goes through all file names in list.
- mode - grouped: all files are indexed to a single index file, specified by outname
'''
starting_dir = os.getcwd()
if data_inpath:
os.chdir(data_inpath)
if outname is None:
outname = 'reads.idx'
if type(infiles) is str:
# Fetch files by file types using glob
import glob
infiles = glob.glob(infiles)
elif type(infiles) is not list and type(infiles) is not tuple:
raise Exception("Invalid input files specified.")
assert infiles, 'No files found, or no files passed.'
# Handle multiple types of input for infiles
if mode == 'grouped':
idx_filename = outname
tak = time.time()
print 'Writing {0} files to SQL index ...'.format(len(infiles))
SeqIO.index_db(idx_filename, infiles , 'fastq')
idx_t = time.time() - tak
print 'Finished Indexing to {0}\n after {1}\n'.format(idx_filename, time.strftime('%H:%M:%S', time.gmtime(idx_t)))
elif mode == 'separate':
for filename in infiles:
tak = time.time()
print 'Writing SQL index file for {0} ...'.format(filename)
idx_filename = filename.split('.')[0] + '.idx'
SeqIO.index_db(idx_filename, filename , 'fastq')
print '{0} written successfully'.format(idx_filename)
idx_t = time.time() - tak
print 'Finished Indexing after {1}\n'.format(time.strftime('%H:%M:%S', time.gmtime(idx_t)))
if os.getcwd() != starting_dir:
os.chdir(starting_dir)
def key_check(self, filename, format, alphabet):
"""Check indexing with a key function."""
if format in SeqIO._BinaryFormats:
mode = "rb"
else :
mode = "r"
id_list = [rec.id for rec in \
SeqIO.parse(open(filename, mode), format, alphabet)]
key_list = [add_prefix(id) for id in id_list]
rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
if not sqlite3:
return
#In memory,
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
#check error conditions
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", format="dummy",
key_function=add_prefix)
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", filenames=["dummy"],
key_function=add_prefix)
#Saving to file...
index_tmp = filename + ".key.idx"
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet,
key_function=add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
os.remove(index_tmp)
def load(self, files, dbname=None):
if isinstance(files, basestring): files = [files]
self.close()
valid = []
schemas = set()
for filename in files:
if not os.path.isfile(filename):
print 'No such file: %s' % filename
continue
schema = SeqLoader.guess_schema(filename)
if not schema:
print 'Unable to guess schema from filename: %s' % filename
continue
schemas.add(schema)
valid.append(filename)
if len(schemas) != 1:
raise ValueError('All files should be of the same type, but %d types found: %s' % (len(schemas), schemas))
if not valid:
print 'No valid files provided.'
return False
if not dbname:
self.dbname = mktmp_name('_SeqView.db')
safe_unlink(self.dbname)
self.tmp_db = True
else: self.dbname = dbname
self.db = SeqIO.index_db(self.dbname, valid, schemas.pop())
self._ids = tuple(sorted(self.db.keys()))
self.master = True
return bool(self)
def _unpickle_SeqView(dbname, ids, upper):
v = SeqView(upper)
v.dbname = dbname
v.db = SeqIO.index_db(dbname)
v.master = True
v._ids = ids
return v
def reload(self, dbname):
self.close()
self.dbname = dbname
self.db = SeqIO.index_db(self.dbname)
self._ids = sorted(self.db.keys())
self.tmp_db = False
self.master = True
def extract_estseq(self):
'''Function to extract and print the ESTSeq slice.'''
self.logger.debug("Extracting the slice from ESTSeq.")
estseqOut = os.path.join(
self.dataFolder, "{0}.{1}.fa".format(self.new_name,
self.estseq_alias))
if os.path.exists(estseqOut) and os.path.getsize(estseqOut)>0:
self.logger.warn("ESTSeq file for alias {0} already present. Exiting".format(
self.estseq_alias))
return
index=SeqIO.index_db(self.estseq)
if self.chrom not in index:
self.logger.critical("Chromosome {0} not in ESTSeq. Exiting.".format(self.chrom))
self.failed=True
return
start = max(self.start-self.flank-1, 0)
end = min(len(index[self.chrom])-1,
self.end-1+self.flank)
seq=index[self.chrom][start:end]
with open(estseqOut,'w') as out:
seq.id=self.new_name
seq.description=""
print(seq.format('fasta'), file=out)
self.logger.debug("Finished extracting the CONSeq sequence.")
return
def test_old_files_same_dir(self):
"""Load existing index with correct files (from same directory)."""
os.chdir("Roche")
d = SeqIO.index_db("triple_sff.idx",
["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"])
self.assertEqual(54, len(d))
self.assertEqual(395, len(d["alpha"]))
def filter_clusters2(cluster_filepath, idx_filepath, size_range, output_dirpath):
""" Writes a subset of cluster sizes to FastQ files
The representative sequence is the first sequence record written.
make the sequence record instead of passing it.
"""
starting_dir = os.getcwd()
idx_dir = os.path.split(idx_filepath)[0]
# Check and create directory
if not os.path.exists(output_dirpath):
os.makedirs(output_dirpath)
cluster_gen = parse(cluster_filepath, idx_filepath)
seqrec_lookup = SeqIO.index_db(idx_filepath)
size_counter = Counter()
for cluster in cluster_gen:
# Check if cluster size is within defined range
if cluster.size > size_range[0] and cluster.size < size_range[1]:
size_counter[cluster.size] += 1
# Get the sequence records for the cluster
if os.getcwd() != idx_dir:
os.chdir(idx_dir)
# Representative sequence first
seqrecord = seqrec_lookup[cluster.rep_seq_id]
if os.getcwd() != output_dirpath:
os.chdir(output_dirpath)
# Write cluster to a file
fname = "clustersize{0}-No{1}.fastq".format(str(cluster.size), str(size_counter[cluster.size]))
if os.path.isfile(fname):
output_handle = open(fname, "wb")
output_handle.close()
output_handle = open(fname, "a")
SeqIO.write(seqrecord, output_handle, "fastq")
for member in cluster.members_id :
if os.getcwd() != idx_dir:
os.chdir(idx_dir)
# Representative sequence first
seqrecord = seqrec_lookup[member]
if os.getcwd() != output_dirpath:
os.chdir(output_dirpath)
# Write sequence record to file
SeqIO.write(seqrecord, output_handle, "fastq")
if os.getcwd() != starting_dir:
os.chdir(starting_dir)
def test_order_index_db(self):
"""Check index_db preserves order in multiple indexed files."""
files = ["GenBank/NC_000932.faa", "GenBank/NC_005816.faa"]
ids = []
for f in files:
ids.extend(r.id for r in SeqIO.parse(f, "fasta"))
d = SeqIO.index_db(":memory:", files, "fasta")
self.assertEqual(ids, list(d))
def simple_check(self, filename, format, alphabet):
"""Check indexing (without a key function)."""
if format in SeqIO._BinaryFormats:
mode = "rb"
else :
mode = "r"
id_list = [rec.id for rec in \
SeqIO.parse(open(filename, mode), format, alphabet)]
rec_dict = SeqIO.index(filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
if not sqlite3:
return
#In memory,
#note here give filenames as list of strings
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
#check error conditions
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", format="dummy")
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", filenames=["dummy"])
#Saving to file...
index_tmp = filename + ".idx"
#To disk,
#note here we give the filename as a single string
#to confirm that works too (convience feature).
rec_dict = SeqIO.index_db(index_tmp, filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
os.remove(index_tmp)
def indexer(index_name):
'''Set up an index to search a large fasta file. We are going to try to use the SeqIO.index_db
because it creates (and subsequently loads) a SQLite database on disk instead of a giant
2GB thing in memory.'''
index=SeqIO.index_db(index_name, 'fasta')
return index
def intersect_keys(keys, reffile, cache=False, clean_accs=False):
"""Extract SeqRecords from the index by matching keys.
keys - an iterable of sequence identifiers/accessions to select
reffile - name of a FASTA file to extract the specified sequences from
cache - save an index of the reference FASTA sequence offsets to disk?
clean_accs - strip HMMer extensions from sequence accessions?
"""
# Build/load the index of reference sequences
index = None
if cache:
refcache = reffile + '.sqlite'
if os.path.exists(refcache):
if os.stat(refcache).st_mtime < os.stat(reffile).st_mtime:
logging.warn("Outdated cache; rebuilding index")
else:
try:
index = (SeqIO.index_db(refcache,
key_function=clean_accession)
if clean_accs
else SeqIO.index_db(refcache))
except Exception:
logging.warn("Skipping corrupted cache; rebuilding index")
index = None
else:
refcache = ':memory:'
if index is None:
# Rebuild the index, for whatever reason
index = (SeqIO.index_db(refcache, [reffile], 'fasta',
key_function=clean_accession)
if clean_accs
else SeqIO.index_db(refcache, [reffile], 'fasta'))
# Extract records by key
if clean_accs:
keys = (clean_accession(k) for k in keys)
for key in keys:
try:
record = index[key]
except LookupError:
# Missing keys are rare, so it's faster not to check every time
logging.info("No match: %s", repr(key))
continue
yield record
def check(self, index_file, sff_files):
if os.path.isfile(index_file):
os.remove(index_file)
# Build index...
d = SeqIO.index_db(index_file, sff_files, "sff")
self.assertEqual(395, len(d["alpha"]))
d._con.close() # hack for PyPy
d.close()
self.assertEqual([os.path.abspath(f) for f in sff_files],
[os.path.abspath(f) for f in d._filenames])
# Load index...
d = SeqIO.index_db(index_file, sff_files)
self.assertEqual(395, len(d["alpha"]))
d._con.close() # hack for PyPy
d.close()
self.assertEqual([os.path.abspath(f) for f in sff_files],
[os.path.abspath(f) for f in d._filenames])
os.remove(index_file)
def _init_storage(self, genome):
"""Load sequences from genome, their sizes and init links"""
# load fasta into index
self.sequences = SeqIO.index_db(genome+".db3", genome, 'fasta')
self.seq = self.sequences
# prepare storage
self.contigs = {c: len(self.seq[c]) for c in self.seq} # this is very ineffective as it loads the record!
self.links = {c: [{}, {}] for c in self.contigs}
self.ilinks = 0
def find_and_open(self, input_directory):
filename = self.get_filename(input_directory)
if not os.path.isfile(filename):
return False
else:
self.filename = filename
self.index_filename = filename.replace('.fasta', '.idx')
self.index = SeqIO.index_db(self.index_filename, self.filename, 'fasta', generic_protein)
self._open = True
return True
def main(args, loglevel):
logging.basicConfig(format="%(levelname)s: %(message)s", level=loglevel)
if args.seqfile[-3:] == '.gz':
fh = gzip.open(args.seqfile, 'rt')
else:
fh = open(args.seqfile, 'r')
for line in fh:
if line[0] == '>':
filetype = 'fasta'
break
elif line[0] == '@':
filetype = 'fastq'
break
else:
raise RuntimeError("Cannot guess file type for %s" % args.seqfile)
fh.close()
logging.info("Indexing {} file {}".format(filetype, args.seqfile))
record_dict = SeqIO.index_db(args.seqfile + '.idx', args.seqfile, filetype)
logging.info("Reading filter file {}".format(args.filterfile))
with open(args.filterfile, 'r') as fh:
id_count = sum(1 for line in fh)
fh.seek(0)
start_time = time.time()
try:
for i, line in enumerate(fh):
if i % 1000 == 0:
try:
rate = i / (time.time()-start_time)
time_remain = (id_count - i) / rate
except ZeroDivisionError:
rate = 0
time_remain = 0
logging.info("Processed {} of {} IDs ({:.2f} per second, est. complete at {})".
format(i, id_count, rate, time.asctime(time.localtime(time.time() + time_remain))))
try:
rec = record_dict[line.rstrip()]
print(rec.format(filetype))
except KeyError:
logging.debug('record id {} not found'.format(line.strip()))
pass
except IOError:
try:
sys.stdout.close()
except IOError:
pass
try:
sys.stderr.close()
except IOError:
pass
def __init__(self, guide_seq, all_seq_keys, length_threshold, evalue_threshold, gb_dir, num_cores):
"""
Input: name of FASTA file containing guide sequences, dictionary of all GenBank sequences,
a list of ingroup/outgroup sequences, the e-value threshold to cluster, and the
threshold of sequence length percent similarity to cluster taxa,
and the GenBank directory.
Generates a list of clusters (each cluster is itself a list of keys to sequences).
"""
ClusterBuilder.__init__(self, all_seq_keys)
lock = multiprocessing.Lock()
manager = multiprocessing.Manager()
already_compared = manager.list()
clusters = manager.list()
color = Color()
# check for fasta file of guide sequences
if not os.path.isfile(guide_seq):
print(color.red + "FASTA file of guide sequences not found. Please re-try." + color.done)
sys.exit(0)
else:
# initialize an empty list for each cluster
guide_sequences = SeqIO.parse(open(guide_seq, "rU"), "fasta")
for guide in guide_sequences:
clusters.append([])
# make blast database
gb = SeqIO.index_db(gb_dir + "/gb.idx")
output_handle = open('blast_db.fasta', 'w')
records = []
for key in all_seq_keys:
record = gb[key]
records.append(record)
SeqIO.write(records, output_handle, 'fasta')
output_handle.close()
# spawn processes
print(color.blue + "Spawning " + color.red + str(num_cores) + color.blue + " processes to make clusters." + color.done)
processes = []
for i in range(num_cores):
p = multiprocessing.Process(target=self.make_guided_clusters_worker, args=(guide_seq, all_seq_keys, \
length_threshold, evalue_threshold, clusters, already_compared, lock, i, gb_dir))
p.start()
processes.append(p)
for p in processes:
p.join()
sys.stdout.write("\n")
sys.stdout.flush()
self.clusters = clusters
if os.path.isfile("blast_db.fasta"):
os.remove("blast_db.fasta")
def sqlite(path):
"""
Sets up the SQLite db for the GenBank division.
Path is the absolute path of the GB files.
Returns a dictionary of SeqRecord objects.
"""
color = Color()
if os.path.exists(path + "/gb.idx"):
print(color.purple + "Genbank database already downloaded. Indexing sequences..." + color.done)
return SeqIO.index_db(path + "/gb.idx")
else:
files = os.listdir(path)
path_files = []
if len(files) == 0:
print(color.red + "GenBank files not found. Re-download with the -d option. See --help for more details." + color.done)
sys.exit(0)
for file in files:
path_files.append(path + "/" + file)
print(color.purple + "Genbank database already downloaded. Indexing sequences..." + color.done)
return SeqIO.index_db(path + "/gb.idx", path_files, "genbank")
def fasta2homozygous(out, fasta, identity, overlap, minLength, \
libraries, limit, \
threads=1, joinOverlap=200, endTrimming=0, verbose=0):
"""Parse alignments and report homozygous contigs"""
#create/load fasta index
if verbose:
sys.stderr.write("Indexing fasta...\n")
faidx = SeqIO.index_db(fasta.name+".db3", fasta.name, "fasta")
genomeSize = sum(len(faidx[c]) for c in faidx)
# depth-of-coverage info
c2cov, covTh = None, None
if libraries:
c2cov, covTh = get_coverage(faidx, fasta.name, libraries, limit, \
verbose)
# run blat for identity >= 0.85
similarity, name = blat, "BLAT"
# or run last for more diverged haplotypes
if identity < 0.85:
similarity, name = last_single, "LAST"
# multi-threading on python 2.7+ only, as 2.6 stalls
if threads > 1 and sys.version_info[0] == 2 \
and sys.version_info[1] > 6:
similarity, name = last_multi, "multithreaded LAST"
#run blat
psl = fasta.name + ".psl.gz"
if not os.path.isfile(psl):
if verbose:
sys.stderr.write("Running %s...\n"%name)
similarity(fasta.name, identity, threads, verbose)
if verbose:
sys.stderr.write("Parsing alignments...\n")
#filter alignments
hits, overlapping = psl2hits(psl, identity, overlap, joinOverlap, endTrimming)
#remove redundant
## maybe store info about removed also
contig2skip, identity = hits2skip(hits, faidx, verbose)
#print "\n".join("\t".join(map(str, x)) for x in overlapping[:100]); return
#report homozygous fasta
nsize, k, skipped, ssize, merged = merge_fasta(out, faidx, contig2skip, \
overlapping, minLength, verbose)
#summary
info = "%s\t%s\t%s\t%s\t%.2f\t%s\t%.2f\t%.3f\t%s\t%s\t%.2f\t%s\t%.2f\n"
sys.stderr.write(info%(fasta.name, genomeSize, len(faidx), ssize, 100.0*ssize/genomeSize, \
skipped, 100.0*skipped/len(faidx), identity, len(merged), \
nsize, 100.0*nsize/genomeSize, k, 100.0*k/len(faidx)))
return genomeSize, len(faidx), ssize, skipped, identity
def make_contigs_and_split_hints(input_filename, output_filenames, genome_filename):
prefix = input_filename.replace('.sorted.hints', '')
genome_filename = genome_filename.replace(prefix, '')
index_filename = re.sub(FASTA_RE,'.idx', genome_filename)
hints_file = open(input_filename)
contig_list_filename = output_filenames[0].replace(prefix, '')
contig_list_output_file = open(contig_list_filename,'w')
genome_dict = SeqIO.index_db(index_filename)
current_contig = None
contigs_seen = set()
for line in hints_file:
if line.startswith('#'):
continue
fields = line.split('\t')
assert len(fields) == 9, 'invalid hints format, expected 9 fields, got this line: {}'.format(line)
contig_name = fields[0]
if contig_name != current_contig:
contigs_seen.add(contig_name)
if contig_name.startswith('@unitig'):
match = unitig_re.match(contig_name)
output_prefix = 'unitig_' + match.group(1)
else:
output_prefix = contig_name
hints_output_file = open(output_prefix + HINTS_SUFFIX,'w')
contig_output_file = open(output_prefix + CONTIG_SUFFIX, 'w')
contig_seq = genome_dict[contig_name]
SeqIO.write(contig_seq, contig_output_file, 'fasta')
contig_output_file.close()
contig_list_output_file.write('\t'.join([contig_name, output_prefix + HINTS_SUFFIX, output_prefix + CONTIG_SUFFIX]) + '\n')
current_contig = contig_name
hints_output_file.write(line)
hints_output_file.close()
# write out all the contigs for which we have no hints,
# along with blank hints files
for contig_name in genome_dict.keys():
if not contig_name in contigs_seen:
#TODO: make this into a function, we're re-using code here
if contig_name.startswith('@unitig'):
match = unitig_re.match(contig_name)
output_prefix = 'unitig_' + match.group(1)
else:
output_prefix = contig_name
hints_output_file = open(output_prefix + HINTS_SUFFIX,'w')
hints_output_file.close() # write a blank hints file
contig_output_file = open(output_prefix + CONTIG_SUFFIX, 'w')
contig_seq = genome_dict[contig_name]
SeqIO.write(contig_seq, contig_output_file, 'fasta')
contig_output_file.close()
contig_list_output_file.write('\t'.join([contig_name, output_prefix + HINTS_SUFFIX, output_prefix + CONTIG_SUFFIX]) + '\n')
contig_list_output_file.close()
def fastq2random(outbase, files, n, verbose, seqformat='fastq'):
"""Return number of random reads from FastQ file(s)"""
#generate indexes
if verbose:
sys.stderr.write("Generating indexes...\n")
indexes = []
for i, f in enumerate(files, 1):
sys.stderr.write(" %s \r"%i)
c = Counter() #counters.append(Counter())
index = SeqIO.index_db(f.name+'.idx', f.name, seqformat, key_function=c.count)
index.close()
#get random entries
store_random_entries(outbase, files, n, verbose)
def check(self, index_file, sff_files, expt_sff_files):
if os.path.isfile(index_file):
os.remove(index_file)
# Build index...
d = SeqIO.index_db(index_file, sff_files, "sff")
self.assertEqual(395, len(d["alpha"]))
d._con.close() # hack for PyPy
d.close()
self.assertEqual([os.path.abspath(f) for f in sff_files], [os.path.abspath(f) for f in d._filenames])
# Now directly check the filenames inside the SQLite index:
filenames, flag = raw_filenames(index_file)
self.assertEqual(flag, True)
self.assertEqual(filenames, expt_sff_files)
# Load index...
d = SeqIO.index_db(index_file, sff_files)
self.assertEqual(395, len(d["alpha"]))
d._con.close() # hack for PyPy
d.close()
self.assertEqual([os.path.abspath(f) for f in sff_files], d._filenames)
os.remove(index_file)
def get_seq(args, seqname, start = 1 , end = None, strand = 1):
"""builds a biopython database file for the subject sequences and retrieves the specified
portion of the specified sequence, reverse-complementing if necessary and translating
dna sequences."""
sequence_db = SeqIO.index_db(args.index_filename, args.seqfilename, 'fasta')
#seq = sequence_db[seqname][start-1:end].seq
seq = sequence_db[seqname][start-1:end].seq
if strand < 0:
seq = seq.reverse_complement()
if args.translate and args.program == 'tblastn':
while len(seq) % 3:
seq = seq[:-1]
seq = seq.translate()
return seq
def main(argv):
blastfilename = ''
seqfilename = ''
try:
opts, args = getopt.getopt(argv,"hb:s:",["seqfile=","blastfile="])
except getopt.GetoptError:
print 'Type Blast2OrthologGroups.py -h for options'
sys.exit(2)
for opt, arg in opts:
if opt == "-h":
print 'Blast2OrthologGroups.py -b <blastfile> -s <seqfile>'
sys.exit()
elif opt in ("-b", "--blastfile"):
blastfilename = arg
elif opt in ("-s", "--seqfile"):
seqfilename = arg
#Exclude sequences that cluster with chloroplast-encoded genes
chloroplast_clusters = ("Cluster_10175", "Cluster_10226", "Cluster_10232", "Cluster_10485", "Cluster_10984", "Cluster_11190", "Cluster_11826", "Cluster_11977", "Cluster_11980", "Cluster_12324", "Cluster_12326", "Cluster_12658", "Cluster_12697", "Cluster_1272", "Cluster_12984", "Cluster_13661", "Cluster_13666", "Cluster_13836", "Cluster_14312", "Cluster_14375", "Cluster_14565", "Cluster_1826", "Cluster_2867", "Cluster_29556", "Cluster_4023", "Cluster_4421", "Cluster_5258", "Cluster_5739", "Cluster_5972", "Cluster_615", "Cluster_7013", "Cluster_7860", "Cluster_8325", "Cluster_8384")
cluster_info = path.join(path.expanduser("~"), "Bioinformatics", "Selaginella", "RefSeq", "SeqClusters.p")
seq_groups = pickle.load( open( cluster_info, "rb" ) )
indexfilename = seqfilename + ".inx"
new_seqs = SeqIO.index_db(indexfilename, seqfilename, "fasta")
used_seqs = {}
with open(blastfilename, 'rU') as f:
reader=csv.reader(f,delimiter='\t')
for row in reader:
qseqid, qlen, sacc, slen, pident, length, mismatch, gapopen, qstart, qend, qframe, sstart, send, sframe, evalue, bitscore = row
if sacc in seq_groups and not used_seqs.has_key(qseqid) and not seq_groups[sacc] in chloroplast_clusters:
used_seqs[qseqid] = 1
seq = new_seqs[qseqid]
#cluster_filename = path.join(path.expanduser("~"), "Bioinformatics", "Selaginella", "RefSeq", seq_groups[sacc] + ".fa")
cluster_filename = path.join(path.expanduser("~"), "Bioinformatics", "Selaginella", "ContigClusters", seq_groups[sacc] + ".fa")
cluster_file = open(cluster_filename, "a")
#print "saving %s to %s" % (qseqid, cluster_filename)
id = seq.id
if int(send) < int(sstart):
seq = seq.reverse_complement()
id = id + '_rc'
seq.id, seq.description = id, id
cluster_file.write(seq.format("fasta"))
cluster_file.close()
def extract_conseq(self):
'''Method to extract the CONSeq slice from a CONSeq genome file.'''
self.logger.debug("Extracting the slice from CONSeq.")
conseqOut = os.path.join(
self.dataFolder, "{0}.{1}.conseq".format(self.new_name,
self.conseq_alias))
if os.path.exists(conseqOut) and os.path.getsize(conseqOut)>0:
self.logger.warn("CONSeq file for alias {0} already present. Exiting".format(self.conseq_alias))
return
try:
index = SeqIO.index_db(self.conseq)
except Exception as error:
self.logger.exception(error)
self.logger.error("Conseq is: {0}".format(self.conseq))
self.failed=True
return
if self.chrom not in index:
self.logger.critical("Chromosome {0} not in Conseq file. Exiting.".format(self.chrom))
self.failed=True
return
#Establish boundaries
start = max(self.start-self.flank-1, 0)
end = min(len(index[self.chrom])-1,
self.end-1+self.flank)
seq=index[self.chrom][start:end]
with open(conseqOut,'w') as out:
print(seq.seq, file=out)
self.logger.debug("Finished extracting the CONSeq sequence.")
return
def distance_matrix_worker(self, seq_keys, length_threshold, dist_matrix, already_compared, lock, process_num, gb_dir):
"""
Worker process for make_distance_matrix(). Takes a list "already_compared" of sequences that have
already had all pairwise comparisons. Each worker process will work making pairwise comparisons
for a different sequence, adding them to the "already_compared" list as they are completed.
"""
# each process must load its own sqlite gb
gb = SeqIO.index_db(gb_dir + "/gb.idx")
process_num = str(process_num)
i = 0
color = Color()
for key in seq_keys:
# check whether another process is already comparing this row
compare_row = False
with lock:
if key not in already_compared:
already_compared.append(key)
compare_row = True
if compare_row:
# make the blast query
record1 = gb[key]
output_handle = open('query' + process_num + '.fasta', 'w')
SeqIO.write(record1, output_handle, 'fasta')
output_handle.close()
# make blast database
j = 0
output_handle = open('blast_db' + process_num + '.fasta', 'w')
records = []
for key2 in seq_keys:
# only add sequences that have not yet been compared
if j > i:
record = gb[key2]
records.append(record)
if j == i:
row = dist_matrix[i]
row[j] = 0.0
dist_matrix[i] = row
j += 1
SeqIO.write(records, output_handle, 'fasta')
output_handle.close()
if len(records) > 0:
# blast query against blast_db
blastn_cmd = NcbiblastnCommandline(query='query' + process_num + '.fasta', subject='blast_db' + process_num + '.fasta', \
out='blast' + process_num + '.xml', outfmt=5)
stdout, stderr = blastn_cmd()
# parse blast output
j = i + 1
blastn_xml = open('blast' + process_num + '.xml', 'r')
blast_records = NCBIXML.parse(blastn_xml)
for blast_record in blast_records:
for alignment in blast_record.alignments:
# loop through each high-scoring segment pair (HSP)
for hsp in alignment.hsps:
length1 = len(record1.seq)
length2 = alignment.length
# first check if length similarity threshold met
if (length1 < length2 * (1 + float(length_threshold))) and (length1 > length2 * (1 - float(length_threshold))):
# blast hit found, set distance to e-value
row = dist_matrix[i]
row[j] = hsp.expect
dist_matrix[i] = row
row = dist_matrix[j]
row[i] = hsp.expect
dist_matrix[j] = row
else:
# set distance to 50.0 if length similarity threshold not met
row = dist_matrix[i]
row[j] = 50.0
dist_matrix[i] = row
row = dist_matrix[j]
row[i] = 50.0
dist_matrix[j] = row
j += 1
blastn_xml.close()
i += 1
# update status
percent = str(round(100 * len(already_compared)/float(len(seq_keys)), 2))
sys.stdout.write('\r' + color.blue + 'Completed: ' + color.red + str(len(already_compared)) + '/' + str(len(seq_keys)) + ' (' + percent + '%)' + color.done)
sys.stdout.flush()
# done looping through all keys, now clean up
if os.path.exists('blast_db' + process_num + '.fasta'):
os.remove('blast_db' + process_num + '.fasta')
if os.path.exists("blast" + process_num + ".xml"):
os.remove("blast" + process_num + ".xml")
if os.path.exists("query" + process_num + ".fasta"):
os.remove("query" + process_num + ".fasta")
if os.path.exists("subject" + process_num + ".fasta"):
os.remove("subject" + process_num + ".fasta")
def extract_sequences_by_clusters(self,
dir_with_cluster_files,
dir_with_sequence_files,
output_dir,
file_with_white_list_cluster_ids=None,
mode="families",
sequence_file_extension="fasta",
sequence_file_format="fasta",
label_species=False,
separator_for_labeling="@",
species_label_first=True):
"""
basenames of cluster and sequence files must be same
mode:
clusters - extract sequences from clusters in separate files,
species - extract sequences from species to separate files
"""
white_list_ids = None
if file_with_white_list_cluster_ids:
white_list_ids = IdSet()
white_list_ids.read(file_with_white_list_cluster_ids)
clusters_dict = self.read_cluster_files_from_dir(
dir_with_cluster_files)
cluster_names = self.get_cluster_names(clusters_dict,
white_list_ids=white_list_ids)
sequence_super_dict = OrderedDict()
out_dir = self.check_path(output_dir)
for species in clusters_dict:
idx_file = "%s_tmp.idx" % species
sequence_file = "%s%s.%s" % (self.check_path(
dir_with_sequence_files), species, sequence_file_extension)
sequence_super_dict[species] = SeqIO.index_db(
idx_file, sequence_file, format=sequence_file_format)
if mode == "species":
seqeuence_names = self.get_sequence_names(
clusters_dict,
write_ids=False,
out_prefix=None,
white_list_ids=white_list_ids)
for species in seqeuence_names:
out_file = "%s%s.%s" % (out_dir, species,
sequence_file_extension)
SeqIO.write(SequenceRoutines.record_by_id_generator(
sequence_super_dict[species], seqeuence_names[species]),
out_file,
format=sequence_file_format)
elif mode == "families":
def per_family_record_generator(seq_super_dict, clust_dict,
cluster_id):
if species_label_first:
label_sequence = lambda label, name: "%s%s%s" % (
label, separator_for_labeling, name)
else:
label_sequence = lambda label, name: "%s%s%s" % (
name, separator_for_labeling, label)
for species in seq_super_dict:
#print species, cluster_id
for record_id in clust_dict[species][cluster_id]:
if label_species:
record = deepcopy(
seq_super_dict[species][record_id])
record.id = label_sequence(species, record_id)
yield record
else:
yield seq_super_dict[species][record_id]
for cluster_name in cluster_names:
out_file = "%s%s.%s" % (out_dir, cluster_name,
sequence_file_extension)
SeqIO.write(per_family_record_generator(
sequence_super_dict, clusters_dict, cluster_name),
out_file,
format=sequence_file_format)
for species in clusters_dict:
os.remove("%s_tmp.idx" % species)
def test_old_same_dir(self):
"""Load existing index with no options (from same directory)."""
os.chdir("Roche")
d = SeqIO.index_db("triple_sff.idx")
self.assertEqual(54, len(d))
self.assertEqual(395, len(d["alpha"]))
def key_check(self, filename, format, alphabet, comp):
"""Check indexing with a key function."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [
rec.id for rec in SeqIO.parse(filename, format, alphabet)
]
key_list = [add_prefix(id) for id in id_list]
rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
if not sqlite3:
return
#In memory,
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
#check error conditions
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
format="dummy",
key_function=add_prefix)
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
filenames=["dummy"],
key_function=add_prefix)
rec_dict.close()
del rec_dict
#Saving to file...
index_tmp = filename + ".key.idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp,
alphabet=alphabet,
key_function=add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
os.remove(index_tmp)
def simple_check(self, filename, format, alphabet, comp):
"""Check indexing (without a key function)."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [
rec.id for rec in SeqIO.parse(filename, format, alphabet)
]
with warnings.catch_warnings():
if "_alt_index_" in filename:
# BiopythonParserWarning: Could not parse the SFF index:
# Unknown magic number b'.diy' in SFF index header:
# b'.diy1.00'
warnings.simplefilter('ignore', BiopythonParserWarning)
rec_dict = SeqIO.index(filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
if not sqlite3:
return
# In memory,
# note here give filenames as list of strings
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
# check error conditions
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
format="dummy")
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
filenames=["dummy"])
# Saving to file...
index_tmp = self.index_tmp
if os.path.isfile(index_tmp):
os.remove(index_tmp)
# To disk,
# note here we give the filename as a single string
# to confirm that works too (convience feature).
rec_dict = SeqIO.index_db(index_tmp, filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
# Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
# Now reload without passing filenames and format
# and switch directory to check paths still work
index_tmp = os.path.abspath(index_tmp)
os.chdir(os.path.dirname(filename))
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
os.remove(index_tmp)
def get_raw_check(self, filename, format, alphabet, comp):
# Also checking the key_function here
if comp:
h = gzip.open(filename, "rb")
raw_file = h.read()
h.close()
h = gzip_open(filename, format)
id_list = [
rec.id.lower() for rec in SeqIO.parse(h, format, alphabet)
]
h.close()
else:
h = open(filename, "rb")
raw_file = h.read()
h.close()
id_list = [
rec.id.lower()
for rec in SeqIO.parse(filename, format, alphabet)
]
if format in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonParserWarning)
rec_dict = SeqIO.index(filename,
format,
alphabet,
key_function=lambda x: x.lower())
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:",
filename,
format,
alphabet,
key_function=lambda x: x.lower())
else:
rec_dict = SeqIO.index(filename,
format,
alphabet,
key_function=lambda x: x.lower())
if sqlite3:
rec_dict_db = SeqIO.index_db(":memory:",
filename,
format,
alphabet,
key_function=lambda x: x.lower())
self.assertEqual(set(id_list), set(rec_dict))
if sqlite3:
self.assertEqual(set(id_list), set(rec_dict_db))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertIn(key, rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(isinstance(raw, bytes),
"Didn't get bytes from %s get_raw" % format)
self.assertTrue(raw.strip())
self.assertIn(raw, raw_file)
if sqlite3:
raw_db = rec_dict_db.get_raw(key)
# Via index using format-specific get_raw which scans the file,
# Via index_db in general using raw length found when indexing.
self.assertEqual(
raw, raw_db,
"index and index_db .get_raw() different for %s" % format)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(_bytes_to_string(raw))
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(b"<entry "))
self.assertTrue(raw.endswith(b"</entry>"))
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % _bytes_to_string(raw)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
def simple_check(self, filename, fmt, alphabet, comp):
"""Check indexing (without a key function)."""
msg = "Test failure parsing file %s with format %s" % (filename, fmt)
if comp:
mode = "r" + self.get_mode(fmt)
with gzip.open(filename, mode) as handle:
id_list = [rec.id for rec in SeqIO.parse(handle, fmt, alphabet)]
else:
id_list = [rec.id for rec in SeqIO.parse(filename, fmt, alphabet)]
with warnings.catch_warnings():
if "_alt_index_" in filename:
# BiopythonParserWarning: Could not parse the SFF index:
# Unknown magic number b'.diy' in SFF index header:
# b'.diy1.00'
warnings.simplefilter("ignore", BiopythonParserWarning)
rec_dict = SeqIO.index(filename, fmt, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
rec_dict.close()
if not sqlite3:
return
# In memory,
# note here give filenames as list of strings
rec_dict = SeqIO.index_db(":memory:", [filename], fmt, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
rec_dict.close()
# check error conditions
with self.assertRaises(ValueError, msg=msg):
SeqIO.index_db(":memory:", format="dummy")
with self.assertRaises(ValueError, msg=msg):
SeqIO.index_db(":memory:", filenames=["dummy"])
# Saving to file...
index_tmp = self.index_tmp
if os.path.isfile(index_tmp):
os.remove(index_tmp)
# To disk,
# note here we give the filename as a single string
# to confirm that works too.
rec_dict = SeqIO.index_db(index_tmp, filename, fmt, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
# Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], fmt, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
# Now reload without passing filenames and format
# and switch directory to check paths still work
index_tmp = os.path.abspath(index_tmp)
os.chdir(os.path.dirname(filename))
try:
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
finally:
os.chdir(CUR_DIR)
self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
os.remove(index_tmp)
def key_check(self, filename, fmt, alphabet, comp):
"""Check indexing with a key function."""
msg = "Test failure parsing file %s with format %s" % (filename, fmt)
if comp:
mode = "r" + self.get_mode(fmt)
with gzip.open(filename, mode) as handle:
id_list = [rec.id for rec in SeqIO.parse(handle, fmt, alphabet)]
else:
id_list = [rec.id for rec in SeqIO.parse(filename, fmt, alphabet)]
key_list = [self.add_prefix(id) for id in id_list]
with warnings.catch_warnings():
if "_alt_index_" in filename:
# BiopythonParserWarning: Could not parse the SFF index:
# Unknown magic number b'.diy' in SFF index header:
# b'.diy1.00'
warnings.simplefilter("ignore", BiopythonParserWarning)
rec_dict = SeqIO.index(filename, fmt, alphabet, self.add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
rec_dict.close()
if not sqlite3:
return
# In memory,
rec_dict = SeqIO.index_db(
":memory:", [filename], fmt, alphabet, self.add_prefix
)
self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
# check error conditions
with self.assertRaises(ValueError, msg=msg):
SeqIO.index_db(":memory:", format="dummy", key_function=self.add_prefix)
with self.assertRaises(ValueError, msg=msg):
SeqIO.index_db(
":memory:", filenames=["dummy"], key_function=self.add_prefix
)
rec_dict.close()
# Saving to file...
index_tmp = filename + ".key.idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
rec_dict = SeqIO.index_db(
index_tmp, [filename], fmt, alphabet, self.add_prefix
)
self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
# Now reload it...
rec_dict = SeqIO.index_db(
index_tmp, [filename], fmt, alphabet, self.add_prefix
)
self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
# Now reload without passing filenames and format
rec_dict = SeqIO.index_db(
index_tmp, alphabet=alphabet, key_function=self.add_prefix
)
self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
os.remove(index_tmp)
import sys
import tempfile
# set up log
logging.basicConfig(level=logging.DEBUG)
# debug biopython issue
logging.debug('sys.version')
logging.debug(sys.version)
logging.debug('sqlite3.version')
logging.debug(sqlite3.version)
logging.debug('platform.python_implementation()')
logging.debug(platform.python_implementation())
logging.debug('platform.platform()')
logging.debug(platform.platform())
logging.debug('Bio.__version__')
logging.debug(Bio.__version__)
logging.debug('os.environ')
logging.debug(os.environ)
read_file = '/r1.fq'
outdir = tempfile.mkdtemp(dir=os.environ.get('PWD'))
db_file = os.path.join(outdir, 'r1.idx')
try:
read_index = SeqIO.index_db(db_file, read_file, 'fastq')
except Exception as e:
logging.exception('')
raise e
def gfftosequence(gff, sequencedir):
seqdirectory = os.path.abspath(sequencedir)
seqfiles = [
os.path.join(seqdirectory, file) for file in os.listdir(seqdirectory)
]
#Make index of fasta files
print 'Indexing sequences...'
seqdb = SeqIO.index_db('seqdb.idx', seqfiles, 'fasta')
print '{0} sequences indexed'.format(len(seqdb))
#Make gff database
gff_fn = gff
db_fn = os.path.basename(gff_fn) + '.db'
if os.path.isfile(db_fn) == False:
gffutils.create_db(gff_fn, db_fn)
db = gffutils.FeatureDB(db_fn)
seqs = {} #dictionary where key is ID and value is sequence
counter = 0
UTRs = db.features_of_type('5UTR')
for UTR in UTRs:
counter += 1
chrm = UTR.chrom
strand = UTR.strand
ID = UTR.attributes['ID']
exoncoords = []
UTRsequence = ''
for exon in db.children(UTR, featuretype='exon'):
exoncoords.append([exon.start, exon.stop])
number_of_exons = len(exoncoords)
if strand == '+':
for idx, exonstartstop in enumerate(exoncoords):
if idx + 1 < number_of_exons:
UTRsequence += seqdb[chrm].seq[exonstartstop[0] -
1:exonstartstop[1]].upper()
elif idx + 1 == number_of_exons: #if at the last exon
#To check for start codon, take three more nucleotides (change [1]-1 to [1]+2)
UTRsequence += seqdb[chrm].seq[exonstartstop[0] -
1:exonstartstop[1] -
1].upper()
elif strand == '-':
for idx, exonstartstop in enumerate(reversed(
exoncoords)): #reverse exon order since this is - strand
if idx + 1 < number_of_exons:
UTRsequence += seqdb[chrm].seq[exonstartstop[0] -
1:exonstartstop[1]].upper(
).reverse_complement()
elif idx + 1 == number_of_exons: #if at the last exon
#To check for start codon, take three more nucleotides (change [0] to [0]-3)
UTRsequence += seqdb[chrm].seq[
exonstartstop[0]:exonstartstop[1]].upper(
).reverse_complement()
seqs[ID] = UTRsequence
if counter <= 50 and counter % 10 == 0:
print 'Retrieving sequence %i' % (counter)
elif counter > 50 and counter % 50 == 0:
print 'Retrieving sequence %i' % (counter)
print 'Retrieved {0} sequences.'.format(len(seqs))
os.remove(db_fn)
os.remove('seqdb.idx')
return seqs
def go(input, output, raw_reads, linear_refs, circular_refs, coverage_file):
if raw_reads:
assert os.path.isfile(raw_reads)
idx = raw_reads + ".idx"
if os.path.isfile(idx):
sys.stderr.write("Loading %s\n" % idx)
raw = SeqIO.index_db(idx)
else:
sys.stderr.write("Creating %s\n" % idx)
raw = SeqIO.index_db(idx, raw_reads, "fastq")
sys.stderr.write(
"Have %i raw reads (used for unmapped partners)\n" % len(raw))
else:
raw = dict()
ref_len_linear = dict()
if linear_refs:
for f in linear_refs:
ref_len_linear.update(get_fasta_ids_and_lengths(f))
ref_len_circles = dict()
if circular_refs:
for f in circular_refs:
ref_len_circles.update(get_fasta_ids_and_lengths(f))
# print ref_len_circles
if input is None:
input_handle = sys.stdin
elif isinstance(input, basestring):
input_handle = open(input)
else:
input_handle = input
if output is None:
output_handle = sys.stdout
elif isinstance(output, basestring):
output_handle = open(output, "w")
else:
output_handle = output
line = input_handle.readline()
while line[0] == "@":
# SAM header
if line[0:4] == "@SQ\t":
parts = line[4:].strip().split("\t")
rname = None
length = None
for p in parts:
if p.startswith("SN:"):
rname = p[3:]
if p.startswith("LN:"):
length = int(p[3:])
if rname in ref_len_linear:
assert length == ref_len_linear[rname]
# print "Found @SQ line for linear reference %s" % rname
elif rname in ref_len_circles:
if length == 2 * ref_len_circles[rname]:
# Return the length to its correct value (should have
# happened already)
sys.stderr.write("Fixing @SQ line for %s, length %i --> %i\n" %
(rname, length, ref_len_circles[rname]))
line = "@SQ\tSN:%s\tLN:%i\n" % (
rname, ref_len_circles[rname])
else:
assert length == ref_len_circles[rname]
elif rname is None:
sys_exit("Bad @SQ line:\n%s" % line)
else:
sys_exit("This reference was not given!:\n%s" % line)
output_handle.write(line)
line = input_handle.readline()
global solo0, solo1, solo2, solo12
solo0 = solo1 = solo2 = solo12 = 0
global coverage
coverage = dict()
if coverage_file:
import numpy
for lengths in [ref_len_linear, ref_len_circles]:
for ref, length in lengths.iteritems():
coverage[ref] = numpy.zeros((5, length), numpy.float)
cur_read_name = None
reads = set()
while line:
# SAM read
qname, flag, rname, pos, rest = line.split("\t", 4)
flag = int(flag)
if " " in qname:
# Stupid mrfast!
qname = qname.split(None, 1)[0]
if rname in ref_len_circles and pos != "0":
length = ref_len_circles[rname]
if length <= int(pos) - 1:
sys_exit("Have POS %s yet length of %s is %i (circular)\n" %
(pos, rname, length))
elif rname in ref_len_linear and pos != "0":
length = ref_len_linear[rname]
if length <= int(pos) - 1:
sys_exit("Have POS %s yet length of %s is %i (linear)\n" %
(pos, rname, length))
if qname[-2:] == "/1":
qname = qname[:-2]
frag = 1
elif qname[-2:] == "/2":
qname = qname[:-2]
frag = 2
elif not (flag & 0x1):
frag = 0 # Single read
elif flag & 0x40:
frag = 1
elif flag & 0x80:
frag = 2
else:
frag = 0 # Assume unpaired
if qname == cur_read_name:
# Cache this, as a tuple - ordered to allow sorting on position:
# Using a set will eliminate duplicates after adjusting POS
reads.add((qname, frag, rname, pos, flag, rest))
else:
if coverage_file:
count_coverage(coverage, reads)
flush_cache(output_handle, reads, raw,
ref_len_linear, ref_len_circles)
reads = set([(qname, frag, rname, pos, flag, rest)])
cur_read_name = qname
# Next line...
line = input_handle.readline()
if reads:
if coverage_file:
count_coverage(coverage, reads)
flush_cache(output_handle, reads, raw, ref_len_linear, ref_len_circles)
if isinstance(input, basestring):
input_handle.close()
if isinstance(output, basestring):
output_handle.close()
if coverage_file:
handle = open(coverage_file, "w")
for lengths in [ref_len_linear, ref_len_circles]:
for ref, length in lengths.iteritems():
handle.write(">%s length %i\n" % (ref, length))
for row in coverage[ref]:
assert len(row) == length
handle.write("\t".join("%.1f" % v for v in row) + "\n")
handle.close()
sys.stderr.write("%i singletons; %i where only /1, %i where only /2, %i where both present\n" %
(solo0, solo1, solo2, solo12))
#!/usr/bin/env python
import os
from Bio import SeqIO
from RouToolPa.Routines import FileRoutines
workdir = "/home/mahajrod/Genetics/Projects/nxf/nxf_arthropoda/"
data_dir = "/home/mahajrod/Genetics/Projects/nxf/nxf_arthropoda/data/"
os.chdir(workdir)
data_files = FileRoutines.make_list_of_path_to_files([data_dir])
record_dict = SeqIO.index_db("tmp.idx", data_files, format="genbank")
print("#organism\ttaxonomy\tregion_id\ttranscript_id\tproduct\texon_len")
for record_id in record_dict:
for feature in record_dict[record_id].features:
if feature.type == "mRNA":
mRNA_string = ""
mRNA_string += "%s" % record_dict[record_id].annotations["organism"]
mRNA_string += "\t%s" % (";".join(
record_dict[record_id].annotations["taxonomy"]))
mRNA_string += "\t%s" % record_id
mRNA_string += "\t%s" % (feature.qualifiers["transcript_id"][0]
if "transcript_id" in feature.qualifiers
else ".")
mRNA_string += "\t%s" % (feature.qualifiers["product"][0] if
"product" in feature.qualifiers else ".")
location_lenths = []
#!/usr/bin/env python
import numpy as np
import sys
from Bio import SeqIO
paf_file = sys.argv[1]
unitigs = sys.argv[2]
output_stats = sys.argv[3]
output_file = sys.argv[4]
unitigs_corrected = open(output_file, 'w')
stats_file = open(output_stats, 'a')
# open up sequence map for illumina
illumina_dict = SeqIO.index_db(unitigs + ".idx", unitigs, "fasta")
def find_sequence_illumina(seqid, start, end):
return illumina_dict[seqid].seq[start:end + 1]
def write_sequence(f, seq):
for i in range(0, len(seq), 60):
f.write(str(seq[i:i + 60]) + "\n")
############ read input paf file #######################################################################################
mapping_freq = {}
nano_lengths = {}
def test_old_files(self):
"""Load existing index with correct files."""
d = SeqIO.index_db(
"Roche/triple_sff.idx",
["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"])
self.assertEqual(54, len(d))
def get_raw_check(self, filename, fmt, alphabet, comp):
# Also checking the key_function here
msg = "Test failure parsing file %s with format %s" % (filename, fmt)
if comp:
with gzip.open(filename, "rb") as handle:
raw_file = handle.read()
mode = "r" + self.get_mode(fmt)
with gzip.open(filename, mode) as handle:
id_list = [rec.id.lower() for rec in SeqIO.parse(handle, fmt, alphabet)]
else:
with open(filename, "rb") as handle:
raw_file = handle.read()
id_list = [rec.id.lower() for rec in SeqIO.parse(filename, fmt, alphabet)]
if fmt in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonParserWarning)
rec_dict = SeqIO.index(filename, fmt, alphabet, key_function=str.lower)
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:", filename, fmt, alphabet, key_function=str.lower,
)
else:
rec_dict = SeqIO.index(filename, fmt, alphabet, key_function=str.lower)
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:", filename, fmt, alphabet, key_function=str.lower,
)
self.assertEqual(set(id_list), set(rec_dict), msg=msg)
if sqlite3:
self.assertEqual(set(id_list), set(rec_dict_db), msg=msg)
self.assertEqual(len(id_list), len(rec_dict), msg=msg)
for key in id_list:
self.assertIn(key, rec_dict, msg=msg)
self.assertEqual(key, rec_dict[key].id.lower(), msg=msg)
self.assertEqual(key, rec_dict.get(key).id.lower(), msg=msg)
raw = rec_dict.get_raw(key)
self.assertIsInstance(raw, bytes, msg=msg)
self.assertTrue(raw.strip(), msg=msg)
self.assertIn(raw, raw_file, msg=msg)
if sqlite3:
raw_db = rec_dict_db.get_raw(key)
# Via index using format-specific get_raw which scans the file,
# Via index_db in general using raw length found when indexing.
self.assertEqual(raw, raw_db, msg=msg)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
mode = self.get_mode(fmt)
if mode == "b":
handle = BytesIO(raw)
elif mode == "t":
handle = StringIO(raw.decode())
else:
raise RuntimeError("Unexpected mode %s" % mode)
if fmt == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False,
)
elif fmt == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True,
)
elif fmt == "uniprot-xml":
self.assertTrue(raw.startswith(b"<entry "), msg=msg)
self.assertTrue(raw.endswith(b"</entry>"), msg=msg)
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = (
"""<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
"""
% raw.decode()
)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, fmt, alphabet)
else:
rec2 = SeqIO.read(handle, fmt, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
def test_old_rel(self):
"""Load existing index (with relative paths) with no options (from parent directory)."""
d = SeqIO.index_db("Roche/triple_sff_rel_paths.idx")
self.assertEqual(54, len(d))
self.assertEqual(395, len(d["alpha"]))
def test_order_index_db(self):
"""Check index_db preserves ordering indexed file."""
d = SeqIO.index_db(":memory:", [self.f], "fasta")
self.assertEqual(self.ids, list(d))
def key_check(self, filename, format, alphabet, comp):
"""Check indexing with a key function."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [
rec.id for rec in SeqIO.parse(filename, format, alphabet)
]
key_list = [add_prefix(id) for id in id_list]
with warnings.catch_warnings():
if "_alt_index_" in filename:
# BiopythonParserWarning: Could not parse the SFF index:
# Unknown magic number b'.diy' in SFF index header:
# b'.diy1.00'
warnings.simplefilter('ignore', BiopythonParserWarning)
rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
del rec_dict
if not sqlite3:
return
# In memory,
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
# check error conditions
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
format="dummy",
key_function=add_prefix)
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
filenames=["dummy"],
key_function=add_prefix)
rec_dict.close()
del rec_dict
# Saving to file...
index_tmp = filename + ".key.idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
# Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
# Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp,
alphabet=alphabet,
key_function=add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
os.remove(index_tmp)
def make_index(input_file, output_file):
SeqIO.index_db(output_file, input_file, 'fasta')
def index_gb():
print "indexing genbank file"
gb_index = SeqIO.index_db(index_file, gb_file, "genbank")
print "done indexing file\n"
return gb_index
### Set up the logger
# create logger with 'spam_application'
logger = logging.getLogger('BuildBioIndex')
logger.setLevel(logging.DEBUG)
# create file handler which logs even debug messages
# create console handler with a higher log level
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) #WARN
# create formatter and add it to the handlers
formatter = logging.Formatter('%(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
# add the handlers to the logger
logger.addHandler(ch)
logger.debug(" ".join(sys.argv))
if len(sys.argv) != 3:
logger.error("2 arguments are required (index, file fasta file")
sys.exit(1)
index_file = sys.argv[1]
fasta_file = sys.argv[2]
logger.debug("Index file: %s", index_file)
logger.debug("Fasta file: %s", fasta_file)
if os.path.isfile(fasta_file):
IndexDB = SeqIO.index_db(index_file, fasta_file, "fasta")
else:
logger.error("Fasta file (%s) is not a file", fasta_file)
sys.exit(1)
def simple_check(self, filename, format, alphabet, comp):
"""Check indexing (without a key function)."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [
rec.id for rec in SeqIO.parse(filename, format, alphabet)
]
rec_dict = SeqIO.index(filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
if not sqlite3:
return
#In memory,
#note here give filenames as list of strings
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
#check error conditions
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
format="dummy")
self.assertRaises(ValueError,
SeqIO.index_db,
":memory:",
filenames=["dummy"])
#Saving to file...
index_tmp = self.index_tmp
if os.path.isfile(index_tmp):
os.remove(index_tmp)
#To disk,
#note here we give the filename as a single string
#to confirm that works too (convience feature).
rec_dict = SeqIO.index_db(index_tmp, filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() # hack for PyPy
del rec_dict
os.remove(index_tmp)
type=FileRoutines.make_list_of_path_to_files_from_string,
help="Comma-separated list of input files/directories with sequences")
parser.add_argument("-o", "--output_directory", action="store", dest="output", type=FileRoutines.check_path,
help="Directory to output groups_of sequences")
parser.add_argument("-f", "--format", action="store", dest="format", default="fasta",
help="Format of input and output files. Allowed formats genbank, fasta(default)")
parser.add_argument("-e", "--extension", action="store", dest="extension",
help="Extension of output files. Default: equal to -f")
parser.add_argument("-d", "--id_file", action="store", dest="id_file",
help="File with groups of sequences to extract(.fam file).")
args = parser.parse_args()
FileRoutines.safe_mkdir(args.output)
args.extension = args.extension if args.extension else args.format
tmp_index_file = "temp.idx"
#id_list = read_ids(args.id_file)
id_list = IdSet(filename=args.id_file)
sequence_groups_id = SynDict()
sequence_groups_id.read(args.id_file, split_values=True)
#print("Parsing %s..." % args.input_file)
sequence_dict = SeqIO.index_db(tmp_index_file, args.input, format=args.format)
for group in sequence_groups_id:
SeqIO.write(SequenceRoutines.record_by_id_generator(sequence_dict, sequence_groups_id[group],
verbose=True),
"%s%s.%s" % (args.output, group, args.extension), format=args.format)
os.remove(tmp_index_file)
def test_old(self):
"""Load existing index with no options (from parent directory)."""
d = SeqIO.index_db("Roche/triple_sff.idx")
self.assertEqual(54, len(d))
self.assertRaises(FileNotFoundError, d.get_raw, "alpha")
"--dont_extract_kmer_list",
action="store_true",
dest="dont_extract_kmer_list",
help="Don't extract kmer list")
args = parser.parse_args()
args.input = make_list_of_path_to_files(args.input)
if args.count_both_strands and args.add_rev_com:
raise ValueError(
"Options -b/--count_both_strands and -r/--add_reverse_complement are not compatible"
)
if args.add_rev_com:
file_with_rev_com = args.base_prefix + "_with_rev_com.fasta"
record_dict = SeqIO.index_db("temp_index.idx", args.input, format="fasta")
SeqIO.write(rev_com_generator(record_dict, yield_original_record=True),
file_with_rev_com, "fasta")
args.base_prefix += "_with_rev_com"
base_file = "%s_%i_mer.jf" % (args.base_prefix, args.kmer_length)
kmer_table_file = "%s_%i_mer.counts" % (args.base_prefix, args.kmer_length)
kmer_file = "%s_%i_mer.kmer" % (args.base_prefix, args.kmer_length)
Jellyfish.threads = args.threads
Jellyfish.path = args.jellyfish_path if args.jellyfish_path else ""
Jellyfish.count(args.input if not args.add_rev_com else file_with_rev_com,
base_file,
kmer_length=args.kmer_length,
hash_size=args.hash_size,
count_both_strands=args.count_both_strands)
def test_old_format(self):
"""Load existing index with correct format."""
d = SeqIO.index_db("Roche/triple_sff.idx", format="sff")
self.assertEqual(54, len(d))
def test_old(self):
"""Load existing index with no options."""
d = SeqIO.index_db("Roche/triple_sff.idx")
self.assertEqual(54, len(d))
parser.add_argument("-f",
"--format",
action="store",
dest="format",
default="fasta",
help="format of file with sequences - default: fasta.")
parser.add_argument("-i",
"--input",
action="store",
dest="input",
help="file with sequences")
parser.add_argument("-o",
"--output",
action="store",
dest="output",
default="out.t",
help="output file - default: out.t.")
args = parser.parse_args()
out_fd = sys.stdout if args.output == "stdout" else open(args.output, "w")
record_dict = SeqIO.index_db("temp_index.idx", [args.input],
format=args.format)
lengths_dict = SequenceRoutines.get_lengths(record_dict, out_file=out_fd)
print("Longest sequence: %i" % max(lengths_dict.values()))
print("Shortest sequence: %i" % min(lengths_dict.values()))
print("Total length: %i" % sum(lengths_dict.values()))
os.remove("temp_index.idx")
def distance_matrix_worker_old(self, seq_keys, length_threshold, dist_matrix, already_compared, lock, process_num, gb_dir):
"""
Worker process for make_distance_matrix(). Takes a list "already_compared" of sequences that have
already had all pairwise comparisons. Each worker process will work making pairwise comparisons
for a different sequence, adding them to the "already_compared" list as they are completed.
"""
# each process must load its own sqlite gb
gb = SeqIO.index_db(gb_dir + "/gb.idx")
process_num = str(process_num)
i = 0
color = Color()
for key in seq_keys:
# check whether another process is already comparing this row
compare_row = False
with lock:
if key not in already_compared:
already_compared.append(key)
compare_row = True
if compare_row:
# get the sequence record to compare
record1 = gb[key]
output_handle = open('query' + process_num + '.fasta', 'w')
SeqIO.write(record1, output_handle, 'fasta')
output_handle.close()
j = 0
for key2 in seq_keys:
# only calculate e-values for pairs that have not yet been compared
if dist_matrix[i][j] == 99:
if key == key2:
row = dist_matrix[i]
row[j] = 0.0
dist_matrix[i] = row
# check sequence lengths
else:
# print("proc # = "+process_num+" i = "+str(i)+ " j = "+str(j))
record2 = gb[key2]
length1 = len(record1.seq)
length2 = len(record2.seq)
# set distance to 50.0 if length similarity threshold not met
if (length2 < length1 * (1 + float(length_threshold))) and (length2 > length1 * (1 - float(length_threshold))):
row = dist_matrix[i]
row[j] = 50.0
dist_matrix[i] = row
row = dist_matrix[j]
row[i] = 50.0
dist_matrix[j] = row
else:
# do the blast comparison
output_handle = open('query' + process_num + '.fasta', 'w')
SeqIO.write(record2, output_handle, 'fasta')
output_handle.close()
blastn_cmd = NcbiblastnCommandline(query='query' + process_num + '.fasta', subject='subject' + process_num + \
'.fasta', out='blast' + process_num + '.xml', outfmt=5)
stdout, stderr = blastn_cmd()
blastn_xml = open('blast' + process_num + '.xml', 'r')
blast_records = NCBIXML.parse(blastn_xml)
for blast_record in blast_records:
if blast_record.alignments:
if blast_record.alignments[0].hsps:
# blast hit found, set distance to e-value
row = dist_matrix[i]
row[j] = blast_record.alignments[0].hsps[0].expect
dist_matrix[i] = row
row = dist_matrix[j]
row[i] = blast_record.alignments[0].hsps[0].expect
dist_matrix[j] = row
else:
# no blast hit found, set distance to default 10.0
row = dist_matrix[i]
row[j] = 10.0
dist_matrix[i] = row
row = dist_matrix[j]
row[i] = 10.0
dist_matrix[j] = row
blastn_xml.close()
j += 1
i += 1
# update status
percent = str(round(100 * len(already_compared)/float(len(seq_keys)), 2))
sys.stdout.write('\r' + color.blue + 'Completed: ' + color.red + str(len(already_compared)) + '/' + str(len(seq_keys)) + ' (' + percent + '%)' + color.done)
sys.stdout.flush()
# done looping through all keys, now clean up
os.remove("blast" + process_num + ".xml")
os.remove("query" + process_num + ".fasta")
os.remove("subject" + process_num + ".fasta")
def get_raw_check(self, filename, format, alphabet, comp):
# Also checking the key_function here
if comp:
h = gzip.open(filename, "rb")
raw_file = h.read()
h.close()
h = gzip_open(filename, format)
id_list = [rec.id.lower() for rec in
SeqIO.parse(h, format, alphabet)]
h.close()
else:
h = open(filename, "rb")
raw_file = h.read()
h.close()
id_list = [rec.id.lower() for rec in
SeqIO.parse(filename, format, alphabet)]
if format in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonParserWarning)
rec_dict = SeqIO.index(filename, format, alphabet,
key_function=lambda x: x.lower())
rec_dict_db = SeqIO.index_db(":memory:", filename, format, alphabet,
key_function=lambda x: x.lower())
else:
rec_dict = SeqIO.index(filename, format, alphabet,
key_function=lambda x: x.lower())
rec_dict_db = SeqIO.index_db(":memory:", filename, format, alphabet,
key_function=lambda x: x.lower())
self.assertEqual(set(id_list), set(rec_dict))
self.assertEqual(set(id_list), set(rec_dict_db))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertIn(key, rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(isinstance(raw, bytes),
"Didn't get bytes from %s get_raw" % format)
self.assertTrue(raw.strip())
self.assertIn(raw, raw_file)
raw_db = rec_dict_db.get_raw(key)
# Via index using format-specific get_raw which scans the file,
# Via index_db in general using raw length found when indexing.
self.assertEqual(raw, raw_db,
"index and index_db .get_raw() different for %s" % format)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(_bytes_to_string(raw))
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(b"<entry "))
self.assertTrue(raw.endswith(b"</entry>"))
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % _bytes_to_string(raw)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
#!/usr/bin/env python3 # -*- coding: utf-8 -*- # Author: Kevin Lamkiewicz # Email: [email protected] from Bio import SeqIO import time import sys import pickle import glob import re files = glob.glob(f"{sys.argv[1]}/gbvrl*.seq") gb_vrl = SeqIO.index_db(f"{sys.argv[1]}/gbvrl.idx", files, "genbank") countryRegex = re.compile(r'country="([^"]+)"') accessionDateRegex = re.compile(r'collection_date="([^"]+)"') d_metaInformation = {} for accession in gb_vrl: genbankEntry = gb_vrl.get_raw(accession).decode("utf-8") country = re.findall(countryRegex, genbankEntry) if country: country = country[0].replace('\n', ' ').replace(' ', '_') else: country = '--' accessionDate = re.findall(accessionDateRegex, genbankEntry)
