| |
|
|
| """ |
| Create HMMs. |
| """ |
|
|
| __author__ = 'Donovan Parks' |
| __copyright__ = 'Copyright 2013' |
| __credits__ = ['Donovan Parks'] |
| __license__ = 'GPL3' |
| __version__ = '1.0.0' |
| __maintainer__ = 'Donovan Parks' |
| __email__ = 'donovan.parks@gmail.com' |
| __status__ = 'Development' |
|
|
| import os |
| import argparse |
|
|
| class CreateHMMs(object): |
| def __init__(self): |
| self.prokSeqs = '/srv/whitlam/bio/db/mothur/gg_12_10/aligned_seqs/94_otu.align.fna' |
| self.taxonomyFile = '/srv/whitlam/bio/db/mothur/gg_12_10/taxonomy/94_otu_taxonomy.txt' |
| self.eukSeqs = '/srv/whitlam/bio/db/mothur/silva/silva.eukarya.fasta' |
|
|
| self.nuc = {'A':'T','T':'A','G':'C','C':'G','K':'M','M':'K','R':'Y','Y':'R','S':'W','W':'W','B':'V','V':'B','H':'G','D':'C','X':'N','N':'N','*':'N','-':'-', '.':'-'} |
| pass |
|
|
| def readTaxonomy(self, taxonomyFile): |
| taxonomy = {} |
| for line in open(taxonomyFile): |
| lineSplit = line.split('\t') |
| ggId = lineSplit[0] |
| taxa = [x.strip() for x in lineSplit[1].split(';')] |
|
|
| taxonomy[ggId] = taxa |
|
|
| return taxonomy |
|
|
| def createSeqFile(self, taxonomy, outputFile, taxa): |
| fout = open(outputFile, 'w') |
|
|
| bKeep = False |
| for line in open(self.prokSeqs): |
| if line[0] == '>': |
| ggId = line[1:].rstrip() |
| if taxa == taxonomy[ggId][0]: |
| fout.write(line) |
| bKeep = True |
| else: |
| bKeep = False |
| elif bKeep: |
| fout.write(line) |
| fout.close() |
|
|
| self.revComplementFastaFile(outputFile) |
|
|
| def run(self, output_dir, threads): |
| taxonomy = self.readTaxonomy(self.taxonomyFile) |
|
|
| self.createSeqFile(taxonomy, 'bacteria.fasta', 'k__Bacteria') |
| os.system('hmmbuild --cpu ' + str(threads) + ' --informat afa ' + output_dir + '/SSU_bacteria.hmm bacteria.fasta') |
|
|
| self.createSeqFile(taxonomy, 'archaea.fasta', 'k__Archaea') |
| os.system('hmmbuild --cpu ' + str(threads) + ' --informat afa ' + output_dir + '/SSU_archaea.hmm archaea.fasta') |
|
|
| self.revComplementFastaFile(self.eukSeqs) |
| os.system('hmmbuild --cpu ' + str(threads) + ' --informat afa ' + output_dir + '/SSU_euk.hmm ' + self.eukSeqs) |
|
|
| if __name__ == '__main__': |
| parser = argparse.ArgumentParser(description="Create HMMs.", formatter_class=argparse.ArgumentDefaultsHelpFormatter) |
|
|
| parser.add_argument('output_dir', help='output directory') |
| parser.add_argument('-t', '--threads', help='number of threads', type=int, default = 1) |
|
|
| args = parser.parse_args() |
|
|
| createHMMs = CreateHMMs() |
| createHMMs.run(args.output_dir, args.threads) |
|
|
