Remove .bim reader/writer

Pedigree.py

@@ -765,42 +765,6 @@ def check_allele_coding(self, filename):
  print('Allele coding OK')
 
 
- def readInBim(self, filename, startsnp=None, stopsnp=None):
- """Read allele coding from PLINK plain text .bim format.
- Only allele 1 and allele 2 fields are used, remaining are ignored
- Fields
- Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name
- Variant identifier
- Position in morgans or centimorgans (safe to use dummy value of '0')
- Base-pair coordinate (1-based; limited to 231-2)
- Allele 1 (corresponding to clear bits in .bed; usually minor)
- Allele 2 (corresponding to set bits in .bed; usually major)"""
- code0 = []
- code1 = []
- with open(filename, 'r') as f:
- for line in f:
- fields = line.split()
- code0.append(fields[4])
- code1.append(fields[5])
- coding = np.vstack([np.array(code0, dtype=np.bytes_), np.array(code1, dtype=np.bytes_)])
- if startsnp is not None:
- coding = coding[:, startsnp: stopsnp+1]
-
- nLoci = coding.shape[1]
- if self.nLoci == 0:
- self.nLoci = nLoci
- if self.nLoci != nLoci:
- print(f"ERROR: inconsistent number of markers in {filename}. Expected {self.nLoci} got {nLoci}.")
- sys.exit(2)
-
- self.check_allele_coding(filename)
- if self.allele_coding is None:
- self.allele_coding = coding
- if not np.alltrue(self.allele_coding == coding):
- print(f'ERROR: inconsistent allele coding in {filename}')
- sys.exit(2)
-
-
  def readInPed(self, filename, startsnp=None, stopsnp=None, haps=False, update_coding=False):
  """Read in genotypes, and optionally haplotypes, from a PLINK plain text formated file, usually .ped
  If update_coding is True, the allele coding is interpreted from the .ped file and any coding
@@ -1043,23 +1007,6 @@ def writePhasePed(self, outputFile):
  MultiThreadIO.writeLinesPlinkPlainTxt(outputFile, data_list)
 
 
- def writeBim(self, outputFile):
- """Write allele coding to PLINK plain text .bim format.
- Only base-pair, allele 1 and allele 2 are written, remaining fields are set to 0
- Fields
- Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name
- Variant identifier
- Position in morgans or centimorgans (safe to use dummy value of '0')
- Base-pair coordinate (1-based; limited to 231-2)
- Allele 1 (corresponding to clear bits in .bed; usually minor)
- Allele 2 (corresponding to set bits in .bed; usually major)"""
- with open(outputFile, 'w+') as f:
- for i in range(self.nLoci):
- allele0 = self.allele_coding[0, i].astype(str)
- allele1 = self.allele_coding[1, i].astype(str)
- f.write(f'0 0 0 {i+1} {allele0} {allele1}\n')
-
-
  def writeLine(self, f, idx, data, func) :
  f.write(idx + ' ' + ' '.join(map(func, data)) + '\n')
 
@@ -1078,7 +1025,6 @@ def addIfNotMissing(array1, counts, array2):
  counts[i] += 2
 
 
-
 @jit(nopython=True)
 def addIfMissing(array1, array2):
  for i in range(len(array1)):