Python SequenceBasics.read_fasta_into_hash Examples

Example #1

File: GenePredBasics.py Project: jason-weirather/Au-public

def write_genepred_to_fasta_directionless(gpd_filename,ref_fasta,out_fasta):
  ofile = open(out_fasta,'w')
  ref = SequenceBasics.read_fasta_into_hash(ref_fasta)
  with open(gpd_filename) as f:
    for line in f:
      if re.match('^#',line): continue
      d = line_to_entry(line)
      if d['chrom'] in ref:
        seq = ''
        for i in range(0,d['exonCount']):
          seq = seq+ref[d['chrom']][d['exonStarts'][i]:d['exonEnds'][i]]
        ofile.write(">"+str(d['name'])+"\n"+seq+"\n")
  ofile.close()

Example #2

File: SimulationBasics.py Project: songjiajia2018/Manual-for-running-IDP-pipeline

 def __init__(self,genomefasta,vcffile):
   self.var_by_chr = {}
   with open(vcffile) as inf:
     for line in inf:
       line = line.rstrip()
       if re.match('^#',line): continue
       f = line.split("\t")
       chrom = f[0]
       pos = int(f[1])
       reference = f[3]
       alternate = f[4]
       if not chrom in self.var_by_chr:
         self.var_by_chr[chrom] = {}
       self.var_by_chr[chrom][pos] = {}
       self.var_by_chr[chrom][pos]['ref'] = reference
       self.var_by_chr[chrom][pos]['alt'] = alternate
   self.ref_genome = SequenceBasics.read_fasta_into_hash(genomefasta)

Example #3

File: SamBasics.py Project: jason-weirather/Au-public

 def set_genome(self,fasta):
   self.genome = SequenceBasics.read_fasta_into_hash(fasta)

Example #4

 def set_genome(self, fasta):
     self.genome = SequenceBasics.read_fasta_into_hash(fasta)