def read(self, files):
"""Read fasta files and store the names and seqs in self.names, self.seqs"""
if type(files) is str:
files = [files]
self.seqs, self.names = [], []
for fl in files:
nms, sqs = fastaread(fl)
sqs = [sq.upper() for sq in sqs]
self.names.extend(nms)
self.seqs.extend(sqs)
def files_to_OTmap(self, map_key, curr_dic):
"This function transforms a file or list of files to an OT map and sets it as an attribute in self."
print "Setting attribute: " + map_key
files = curr_dic.get('file', None)
force_list = curr_dic.get('force_list', False)
expt_table_size = curr_dic.get('table_size', 1e7)
save_file = curr_dic.get('save_file', None)
use_kmer = curr_dic.get('use_kmer', False)
if files is not None:
files_ = self.str_to_list(files)
fasta_ext = ['fa', 'fasta']
if self.check_extension(files, fasta_ext):
names, seqs = [], []
for fl in files_:
names_, seqs_ = fastaread(fl, force_upper=True)
if force_list:
names.append(names_)
seqs.append(seqs_)
else:
names.extend(names_)
seqs.extend(seqs_)
if not force_list:
names = [names]
seqs = [seqs]
OTmaps = [
OTmap(seq_,
word_size=17,
use_kmer=use_kmer,
progress_report=False,
save_file=save_file) for seq_ in seqs
]
setattr(self, map_key, OTmaps)
elif len(files_) == 1 and self.check_extension(files, '.npz'):
OTMap_ = OTmap(seq_, word_size=17)
OTMap_.load(files_[0])
OTmaps = [OTMap_]
setattr(self, map_key, OTmaps)
elif len(files_) == 1 and self.check_extension(files, 'pkl'):
OTmaps = [pickle.load(open(files_[0], 'rb'))]
setattr(self, map_key, OTmaps)
else:
print "Extension error or more than 1 npz/pkl file provided."
else:
print "No files"
setattr(self, map_key, [constant_zero_dict()])
def load_sequence_file_and_paramaters(self):
sequence_file = self.sequence_dic.get('file', None)
self.input_names, self.input_seqs = [], []
self.input_noSeqsperFile = []
if sequence_file is not None:
sequence_files = self.str_to_list(sequence_file)
for sequence_file_ in sequence_files:
names, seqs = fastaread(sequence_file_, force_upper=True)
self.input_noSeqsperFile.append(len(names))
self.input_names.extend(names)
self.input_seqs.extend(seqs)
#add additional parameters
self.params_dic['sequence_lens'] = map(len, self.input_seqs)
self.params_dic['input_noSeqsperFile'] = self.input_noSeqsperFile
self.params_dic['input_names'] = self.input_names
#internalize paramaters in params_dic
for key in self.params_dic.keys():
setattr(self, key, self.params_dic[key])
def coords_to_seq(
self,
coord,
genome_folder=r'/n/dulacfs2/Users/bbintu/Genomes/mouse/mm10',
save_file=None):
"given coords of form chr*:*-* and a genome folder, returns the sequence and saves to file if save_file not None"
import fnmatch
if fnmatch.fnmatchcase(coord, 'chr*:*-*'):
chr_ = coord.split(':')[0]
if not hasattr(self, 'seq_' + chr_):
chr_file = genome_folder + os.sep + chr_ + '.fa'
nms, seq = fastaread(chr_file)
seq = seq[0]
setattr(self, 'seq_' + chr_, seq)
else:
seq = getattr(self, 'seq_' + chr_)
start = int(coord.split(':')[-1].split('-')[0])
end = int(coord.split('-')[-1])
sq = seq[start:end]
if save_file is not None:
fastawrite(save_file, [coord], [sq])
return sq
def load_key(self, key):
"Loads a sequences from the map_dic if extension of map_dic[key]['file'] is in ['fa','fasta']. self.<key>_names,self.<key>_seqs"
curr_dic = self.map_dic['key']
files = curr_dic.get('file', None)
if files is not None:
extensions_available = ['fa', 'fasta']
if self.check_extension(files, extensions_available):
files_ = self.str_to_list(files)
names, seqs = [], []
for fl in files_:
names_, seqs_ = fastaread(fl, force_upper=True)
if curr_dic.get('force_list', False):
names.append(names_)
seqs.append(seqs_)
else:
names.extend(names_)
seqs.extend(seqs_)
setattr(self, key + '_names', names)
setattr(self, key + '_seqs', seqs)
else:
print "Error, extensions availabe: " + str(
extensions_available)
else:
print "No files"
def create_isoform_fl(self,
isoform_fls,
transcr_fl=None,
isoform_filter_name=None,
isoform_filter_seq=None):
"""
Given a list of filenames and a list of isoform_filter_name or a dictionary isoform_filter_seq
it will look through the loaded transcriptome and save isoforms to each file.
isoform_filter_name = ['*FLNA*','*(Xist)*',...]
(list with length matching seqs_RNAs)
isoform_filter_seq = {'word_size':17,'n_choice':100,'perc_keep':0.3}
(isoforms are selected if a percent of inclusion of higher than 0.3 of a random set of 100 17mers)
"""
self.isoform_filter_name = isoform_filter_name
self.isoform_filter_seq = isoform_filter_seq
self.isoform_fls = isoform_fls
if transcr_fl is not None:
self.names_transcr, self.seqs_transcr = fastaread(transcr_fl)
import fnmatch
if self.isoform_filter_name is not None:
if hasattr(self, "names_transcr"):
#Asume a list of name filters are provided
list_unfilt = self.names_transcr
list_filters = self.isoform_filter_name
#keep only a subset
self.isoform_names_list, self.isoform_seqs_list = [], []
for filter_, isoform_fl in zip(list_filters, isoform_fls):
isoform_names = fnmatch.filter(list_unfilt,
'*' + filter_ + '*')
isoform_sequences = [
self.seqs_transcr[self.names_transcr.index(is_name)]
for is_name in isoform_names
]
#make list
self.isoform_names_list.append(isoform_names)
self.isoform_seqs_list.append(isoform_sequences)
print "Writing fasta file " + str(
isoform_fl) + " with number of seqs: " + str(
len(isoform_names))
fastawrite(isoform_fl, isoform_names, isoform_sequences)
else:
print "Warning! No isoforms computed because the transciptome is not loaded."
if self.isoform_filter_seq is not None:
if hasattr(self, "names_transcr"):
word_size_ = self.isoform_filter_seq['word_size']
n_choice_ = self.isoform_filter_seq['n_choice']
perc_keep_ = self.isoform_filter_seq['perc_keep']
self.isoform_names_list, self.isoform_seqs_list = [], []
for seq_ref, isoform_fl in zip(self.seqs_RNAs, isoform_fls):
i_choice = np.random.choice(
range(len(seq_ref) - word_size_), n_choice_)
seq_choice = [
seq_ref[i_:i_ + word_size_] for i_ in i_choice
]
specs = [
np.sum([sq in seq_transcr
for sq in seq_choice]) / float(n_choice_)
for seq_transcr in self.seqs_transcr
]
index_keep = np.ravel(
np.where(np.array(specs) > perc_keep_))
isoform_names = [
self.names_transcr[i_] for i_ in index_keep
]
isoform_seqs = [self.seqs_transcr[i_] for i_ in index_keep]
self.isoform_names_list.append(isoform_names)
self.isoform_seqs_list.append(isoform_seqs)
fastawrite(isoform_fl, isoform_names, isoform_seqs)
else:
print "Warning! No isoforms computed because the transciptome is not loaded."
