def __init__(self, user=None, passwd=None, host=None, port =None, check=True): ''' Loads the utils configuration (utils.cfg) if (not os.path.isfile("../utils.cfg")): raise IOError("There is no utils.cfg file present in the project directory.") config = ConfigParser.RawConfigParser() config.read("../utils.cfg") ''' self.configReader = ConfigurationReader(user, passwd, host, port, check) # blast tools self.fastacmd = self.configReader.get_path('fastacmd') self.blastall = self.configReader.get_path('mafft') self.blastp = self.configReader.get_path('blastall') self.blastp += " -p blastp -e "+ self.configReader.get_value('blastp_e_value') # ensembl database self.ensembldb = self.configReader.get_path('ensembl_fasta') # Smith-Waterman self.sw_sharp = self.configReader.get_path('sw#') # hacked blast, to be used by swsharp to align exons while respecting the boundaries self.blosum_matrix = "{0}/{1}".format(self.configReader.get_path('resources'), self.configReader.get_value('blosum_hacked')) # mafft self.mafft = self.configReader.get_path('mafft')
def __init__(self, user=None, passwd=None, host=None, port=None, check=True): """ Loads the utils configuration (utils.cfg) if (not os.path.isfile("../utils.cfg")): raise IOError("There is no utils.cfg file present in the project directory.") config = ConfigParser.RawConfigParser() config.read("../utils.cfg") """ self.configReader = ConfigurationReader(user, passwd, host, port, check) # blast tools self.fastacmd = self.configReader.get_path("fastacmd") self._check_exists(self.fastacmd) self.blastall = self.configReader.get_path("blastall") self._check_exists(self.blastall) self.blastp = self.configReader.get_path("blastall") self.blastp += " -p blastp -e " + str(self.configReader.get_value("blastp_e_value")) # ensembl database self.ensembldb = self.configReader.get_path("ensembl_fasta") self._check_exists(self.ensembldb) # Smith-Waterman self.sw_sharp = self.configReader.get_path("sw#") self._check_exists(self.sw_sharp) # usearch self.usearch = self.configReader.get_path("usearch") self._check_exists(self.usearch) # hacked blast, to be used by swsharp to align exons while respecting the boundaries self.blosum_matrix = "{0}/{1}".format( self.configReader.get_path("resources"), self.configReader.get_value("blosum_hacked") ) # mafft self.mafft = self.configReader.get_path("mafft") self._check_exists(self.mafft) # maxent scan self.scan3 = self.configReader.get_path("score3") self.scan5 = self.configReader.get_path("score5") self.maxent_homedir = self.configReader.get_path("maxentscan")
class AlignmentCommandGenerator(object): ''' Generates commands for utilities that are used (blast, sw, genewise, fastacmd, formatdb) ''' def __init__(self, user=None, passwd=None, host=None, port =None, check=True): ''' Loads the utils configuration (utils.cfg) if (not os.path.isfile("../utils.cfg")): raise IOError("There is no utils.cfg file present in the project directory.") config = ConfigParser.RawConfigParser() config.read("../utils.cfg") ''' self.configReader = ConfigurationReader(user, passwd, host, port, check) # blast tools self.fastacmd = self.configReader.get_path('fastacmd') self.blastall = self.configReader.get_path('mafft') self.blastp = self.configReader.get_path('blastall') self.blastp += " -p blastp -e "+ self.configReader.get_value('blastp_e_value') # ensembl database self.ensembldb = self.configReader.get_path('ensembl_fasta') # Smith-Waterman self.sw_sharp = self.configReader.get_path('sw#') # hacked blast, to be used by swsharp to align exons while respecting the boundaries self.blosum_matrix = "{0}/{1}".format(self.configReader.get_path('resources'), self.configReader.get_value('blosum_hacked')) # mafft self.mafft = self.configReader.get_path('mafft') def generate_fastacmd_gene_command (self, species, seq_name, fasta_db_file, strand = None, sequence_start = None, sequence_stop = None, output_file_path = None): if (isinteger(seq_name)): seq_id_cmd = "-s 'lcl|%s' " % seq_name else: seq_id_cmd = "-s %s" % seq_name data_type_cmd = "-p F" database = "-d {0}/{1}/dna/{2}".format(self.ensembldb, species, fasta_db_file) if (strand == None or int(strand) == 1): strand_cmd = "-S 1" else: strand_cmd = "-S 2" if (sequence_start and sequence_stop): location_cmd = "-L %s,%s" % (sequence_start, sequence_stop) else: location_cmd = "" if output_file_path: output_cmd = "-o %s" % output_file_path else: output_cmd = "" fastacmd_cmd_line = self.fastacmd fastacmd_cmd_line += " {0} {1} {2} {3} {4} {5}".format(database, seq_id_cmd, data_type_cmd, strand_cmd, location_cmd, output_cmd) return fastacmd_cmd_line def generate_fastacmd_plain (self, database, seq_id, output_file_path = ''): database_cmd = "-d %s" % database if (isinteger(seq_id)): seq_id_cmd = "-s 'lcl|%s' " % seq_id else: seq_id_cmd = "-s %s" % seq_id if (output_file_path): output_cmd = "-o %s" % output_file_path else: output_cmd = "" fastacmd_cmd_line = self.fastacmd fastacmd_cmd_line += " {0} {1} {2} ".format(database_cmd, seq_id_cmd, output_cmd) return fastacmd_cmd_line def generate_fastacmd_protein_command (self, protein_id, species_name, protein_type, output_file_path): data_type_cmd = "-p T" prot_id_cmd = "-s %s" % protein_id database = "-d %s" % self._generate_proteindb_file_name(species_name, protein_type) if (output_file_path): output_cmd = "-o %s" % output_file_path else: output_cmd = "" return "fastacmd {0} {1} {2} {3}".format(prot_id_cmd, data_type_cmd, database, output_cmd) def generate_blastp_plain (self, database, input_file, output_file): # sombbody hardcoded the output format in the self.blastp blastp = self.blastp + " -m 8 " if output_file: cmd = "{0} -d {1} -i {2} -o {3}".format(blastp, database, input_file, output_file) else: cmd = "{0} -d {1} -i {2} ".format(blastp, database, input_file) return cmd def generate_blastp_command (self, database, input_file, output_file): if output_file: cmd = "{0} -d {1} -i {2} -o {3}".format(self.blastp, database, input_file, output_file) else: cmd = "{0} -d {1} -i {2} ".format(self.blastp, database, input_file) return cmd def generate_SW_nt (self, query_sequence_file, target_fasta_db_file, output_file, supress_stdout = True): # Matija's current implementation is switching the order cmd = "{0} -j {1} -i {2} --out {3}".format(self.sw_sharp, query_sequence_file, target_fasta_db_file, output_file) if supress_stdout: cmd += " > /dev/null" return cmd def generate_SW_peptide (self, query_sequence_file, target_fasta_db_file, output_file = None): cmd = "{0} --verbose 0 --matrix-file {1} ".format(self.sw_sharp, self.blosum_matrix) cmd += " -j {0} -i {1} ".format(query_sequence_file, target_fasta_db_file) cmd += " --out-type 1 --gap-open 3.0 " if output_file: cmd += " --out {0} ".format(output_file) return cmd def generate_formatdb_command (self, input_db_file, sequence_type): if sequence_type == "protein" or sequence_type == "P": cmd = "formatdb -i {0} -p T".format(input_db_file) else: cmd = "formatdb -i {0} -p F".format(input_db_file) return cmd def generate_mafft_command (self, input_file, output_file=None): ''' If there are unusual characters (e.g., U as selenocysteine in protein sequence), use the --anysymbol option. It accepts any printable characters (U, O, #, $, %, etc.; 0x21-0x7e in the ASCII code), execpt for > (0x3e). They are scored equivalently to X. Gap is - (0x2d), as in the default mode. ''' if output_file: return "{0} --quiet --anysymbol {1} > {2}".format(self.mafft, input_file, output_file) else: return "{0} --quiet --anysymbol {1} ".format(self.mafft, input_file) def _generate_genedb_file_name (self, species, sequence_type, sequence_id, masked): ''' @param species: species name @param sequence_type: scaffold / chromosome... @param sequence_id: ensembl sequence ID @param masked: 0 if dna should not be masked, 1 if it should ''' file_name = "{0}/{1}/dna".format(self.ensembldb, species.lower()) # get the template name (dependent on the assembly) tmp_file="" for f in os.listdir(file_name): # check if we've stumbled on the protein file m = re.findall(".dna", f) if not m: continue tmp_file = f m = re.findall ('(.*).dna', tmp_file) if (masked != 0): file_name = "%s/%s.dna_rm." % (file_name, m[0]) else : file_name = "%s/%s.dna." % (file_name, m[0]) if (sequence_type == 'chromosome'): file_name = "%schromosome.%s.fa" % (file_name, sequence_id) else : file_name = "%stoplevel.fa" % (file_name) if (not os.path.exists(file_name)): # find *dna.toplevel.fa file path = "{0}/{1}/dna".format(self.ensembldb, species.lower()) cmd = "ls "+path+"/*dna.toplevel.fa" retval = commands.getoutput(cmd) if (retval): file_name = retval.rstrip() # otherwise just let the thing fail, I have no better idea return file_name def _generate_proteindb_file_name (self, species, protein_type): ''' @param species: species name (ensembl) @param protein_type: all / abinitio @return: protein database name ''' file_name = "%s/%s/pep" % (self.ensembldb, species.lower()) tmp_file="" for f in os.listdir(file_name): # check if we've stumbled on the protein file m = re.findall(".pep", f) if not m: continue tmp_file = f m = re.findall ('(.*).pep', tmp_file) if (protein_type == "all"): file_name = "%s/%s.pep.all.fa" % (file_name, m[0]) else: file_name = "%s/%s.pep.abinitio.fa" % (file_name, m[0]) return file_name
class AlignmentCommandGenerator(object): """ Generates commands for utilities that are used (blast, sw, genewise, fastacmd, formatdb) """ def _check_exists(self, item): if not os.path.exists(item): print item, " not found " exit(1) def __init__(self, user=None, passwd=None, host=None, port=None, check=True): """ Loads the utils configuration (utils.cfg) if (not os.path.isfile("../utils.cfg")): raise IOError("There is no utils.cfg file present in the project directory.") config = ConfigParser.RawConfigParser() config.read("../utils.cfg") """ self.configReader = ConfigurationReader(user, passwd, host, port, check) # blast tools self.fastacmd = self.configReader.get_path("fastacmd") self._check_exists(self.fastacmd) self.blastall = self.configReader.get_path("blastall") self._check_exists(self.blastall) self.blastp = self.configReader.get_path("blastall") self.blastp += " -p blastp -e " + str(self.configReader.get_value("blastp_e_value")) # ensembl database self.ensembldb = self.configReader.get_path("ensembl_fasta") self._check_exists(self.ensembldb) # Smith-Waterman self.sw_sharp = self.configReader.get_path("sw#") self._check_exists(self.sw_sharp) # usearch self.usearch = self.configReader.get_path("usearch") self._check_exists(self.usearch) # hacked blast, to be used by swsharp to align exons while respecting the boundaries self.blosum_matrix = "{0}/{1}".format( self.configReader.get_path("resources"), self.configReader.get_value("blosum_hacked") ) # mafft self.mafft = self.configReader.get_path("mafft") self._check_exists(self.mafft) # maxent scan self.scan3 = self.configReader.get_path("score3") self.scan5 = self.configReader.get_path("score5") self.maxent_homedir = self.configReader.get_path("maxentscan") def generate_fastacmd_gene_command( self, species, seq_name, fasta_db_file, strand=None, sequence_start=None, sequence_stop=None, output_file_path=None, ): if seq_name.isdigit(): seq_id_cmd = "-s 'lcl|%s' " % seq_name else: seq_id_cmd = "-s %s" % seq_name data_type_cmd = "-p F" database = "-d {0}/{1}/dna/{2}".format(self.ensembldb, species, fasta_db_file) if strand == None or int(strand) == 1: strand_cmd = "-S 1" else: strand_cmd = "-S 2" if not sequence_start and not sequence_stop: location_cmd = "" else: location_cmd = "-L %s,%s" % ( sequence_start if sequence_start else "", sequence_stop if sequence_stop else "", ) if output_file_path: output_cmd = "-o %s" % output_file_path else: output_cmd = "" fastacmd_cmd_line = self.fastacmd fastacmd_cmd_line += " {0} {1} {2} {3} {4} {5}".format( database, seq_id_cmd, data_type_cmd, strand_cmd, location_cmd, output_cmd ) return fastacmd_cmd_line def generate_fastacmd_plain(self, database, seq_id, output_file_path=""): database_cmd = "-d %s" % database if isinteger(seq_id): seq_id_cmd = "-s 'lcl|%s' " % seq_id else: seq_id_cmd = "-s %s" % seq_id if output_file_path: output_cmd = "-o %s" % output_file_path else: output_cmd = "" fastacmd_cmd_line = self.fastacmd fastacmd_cmd_line += " {0} {1} {2} ".format(database_cmd, seq_id_cmd, output_cmd) return fastacmd_cmd_line def generate_fastacmd_protein_command(self, protein_id, species_name, protein_type, output_file_path): data_type_cmd = "-p T" prot_id_cmd = "-s %s" % protein_id database = "-d %s" % self._generate_proteindb_file_name(species_name, protein_type) if output_file_path: output_cmd = "-o %s" % output_file_path else: output_cmd = "" return "fastacmd {0} {1} {2} {3}".format(prot_id_cmd, data_type_cmd, database, output_cmd) def generate_blastp_plain(self, database, input_file, output_file): # sombbody hardcoded the output format in the self.blastp blastp = self.blastp + " -m 8 " if output_file: cmd = "{0} -d {1} -i {2} -o {3}".format(blastp, database, input_file, output_file) else: cmd = "{0} -d {1} -i {2} ".format(blastp, database, input_file) return cmd def generate_blastp_command(self, database, input_file, output_file): if output_file: cmd = "{0} -d {1} -i {2} -o {3}".format(self.blastp, database, input_file, output_file) else: cmd = "{0} -d {1} -i {2} ".format(self.blastp, database, input_file) return cmd def generate_usearch_nt( self, query_sequence_file, target_fasta_db_file, output_file, identity="0.5", strand="plus" ): # strand can also be both cmd = "{0} -threads 1 -search_local {1} -db {2} -alnout {3} -id {4} -strand {5} ".format( self.usearch, query_sequence_file, target_fasta_db_file, output_file, identity, strand ) return cmd def generate_SW_nt(self, query_sequence_file, target_fasta_db_file, output_file=None, supress_stdout=False): # Matija's current implementation is switching the order cmd = "{0} --verbose 0 -j {1} -i {2}".format(self.sw_sharp, query_sequence_file, target_fasta_db_file) if not output_file == None: cmd += " --out " + output_file if supress_stdout: cmd += " > /dev/null" return cmd def generate_SW_peptide(self, query_sequence_file, target_fasta_db_file, output_file=None): cmd = "{0} --verbose 0 --matrix-file {1} ".format(self.sw_sharp, self.blosum_matrix) cmd += " -j {0} -i {1} ".format(query_sequence_file, target_fasta_db_file) cmd += " --out-type 1 --gap-open 3.0 " if output_file: cmd += " --out {0} ".format(output_file) return cmd def generate_formatdb_command(self, input_db_file, sequence_type): if sequence_type == "protein" or sequence_type == "P": cmd = "formatdb -i {0} -p T".format(input_db_file) else: cmd = "formatdb -i {0} -p F".format(input_db_file) return cmd def generate_mafft_command(self, input_file, output_file=None): """ If there are unusual characters (e.g., U as selenocysteine in protein sequence), use the --anysymbol option. It accepts any printable characters (U, O, #, $, %, etc.; 0x21-0x7e in the ASCII code), execpt for > (0x3e). They are scored equivalently to X. Gap is - (0x2d), as in the default mode. """ if output_file: return "{0} --quiet --anysymbol {1} > {2}".format(self.mafft, input_file, output_file) else: return "{0} --quiet --anysymbol {1} ".format(self.mafft, input_file) def generate_mafft_profile(self, input_file_1, input_file_2, output_file=None): if output_file: return "{0}-profile {1} {2} > {3}".format(self.mafft, input_file_1, input_file_2, output_file) else: return "{0}-profile {1} {2} ".format(self.mafft, input_file_1, input_file_2) def generate_maxentscan_cmd(self, intron_side, input_file): if intron_side == 3: return "{0} {1} {2} ".format(self.scan3, self.maxent_homedir, input_file) elif intron_side == 5: return "{0} {1} {2} ".format(self.scan5, self.maxent_homedir, input_file) else: return "" def _generate_genedb_file_name(self, species, sequence_type, sequence_id, masked): """ @param species: species name @param sequence_type: scaffold / chromosome... @param sequence_id: ensembl sequence ID @param masked: 0 if dna should not be masked, 1 if it should """ file_name = "{0}/{1}/dna".format(self.ensembldb, species.lower()) # get the template name (dependent on the assembly) tmp_file = "" for f in os.listdir(file_name): # check if we've stumbled on the protein file m = re.findall(".dna", f) if not m: continue tmp_file = f m = re.findall("(.*).dna", tmp_file) if masked != 0: file_name = "%s/%s.dna_rm." % (file_name, m[0]) else: file_name = "%s/%s.dna." % (file_name, m[0]) if sequence_type == "chromosome": file_name = "%schromosome.%s.fa" % (file_name, sequence_id) else: file_name = "%stoplevel.fa" % (file_name) if not os.path.exists(file_name): # find *dna.toplevel.fa file path = "{0}/{1}/dna".format(self.ensembldb, species.lower()) cmd = "ls " + path + "/*dna.toplevel.fa" retval = commands.getoutput(cmd) if retval: file_name = retval.rstrip() # otherwise just let the thing fail, I have no better idea return file_name def _generate_proteindb_file_name(self, species, protein_type): """ @param species: species name (ensembl) @param protein_type: all / abinitio @return: protein database name """ file_name = "%s/%s/pep" % (self.ensembldb, species.lower()) tmp_file = "" for f in os.listdir(file_name): # check if we've stumbled on the protein file m = re.findall(".pep", f) if not m: continue tmp_file = f m = re.findall("(.*).pep", tmp_file) if protein_type == "all": file_name = "%s/%s.pep.all.fa" % (file_name, m[0]) else: file_name = "%s/%s.pep.abinitio.fa" % (file_name, m[0]) return file_name