old_contents: #!usr/bin/python
  
  import pytest
  import random
  import os.path
  
  from tool import bwa_indexer
  
  def test_bwa_indexer ():
      
      resource_path = os.path.join(os.path.dirname(__file__), "data/")
      genome_fa = resource_path + "macs2.Human.GCA_000001405.22.fasta"
      fastqFile = resource_path + "macs2.Human.DRR000150.22.fastq"
      
      files = [
          genome_fa,
          genome_fa + ".amb",
          genome_fa + ".ann",
          genome_fa + ".bwt",
          genome_fa + ".pac",
          genome_fa + ".sa"
      ]
      
      bwa_amb = files[1]
      bwa_ann = files[2]
      bwa_bwt = files[3]
      bwa_pac = files[4]
      bwa_sa  = files[5]
      
      print (bwa_amb)
      print (bwa_ann)
      print (bwa_bwt)
      print (bwa_pac)
      print (bwa_sa)
      
      bwaT = bwa_indexer.bwaIndexerTool()
      bwaT.run([genome_fa], {'assembly' : 'test'}) 
      
  def test_bwa_indexer_02 ():
      
      resource_path = os.path.join(os.path.dirname(__file__), "data/")
      genome_fa = resource_path + "inps.Mouse.GRCm38.fasta"
      fastqFile = resource_path + "inps.Mouse.DRR000386.fastq"
      
      files = [
          genome_fa,
          genome_fa + ".amb",
          genome_fa + ".ann",
          genome_fa + ".bwt",
          genome_fa + ".pac",
          genome_fa + ".sa"
      ]
      
      bwa_amb = files[1]
      bwa_ann = files[2]
      bwa_bwt = files[3]
      bwa_pac = files[4]
      bwa_sa  = files[5]
      
      print (bwa_amb)
      print (bwa_ann)
      print (bwa_bwt)
      print (bwa_pac)
      print (bwa_sa)
      
      bwaT = bwa_indexer.bwaIndexerTool()
      bwaT.run([genome_fa], {'assembly' : 'test'}) 
      
  
new_contents: #!usr/bin/python
  
  import pytest
  import random
  import os.path
  
  from tool import bwa_indexer
  
  def test_bwa_indexer ():
      
      resource_path = os.path.join(os.path.dirname(__file__), "data/")
      genome_fa = resource_path + "macs2.Human.GCA_000001405.22.fasta"
      fastqFile = resource_path + "macs2.Human.DRR000150.22.fastq"
      
      files = [
          genome_fa,
          genome_fa + ".amb",
          genome_fa + ".ann",
          genome_fa + ".bwt",
          genome_fa + ".pac",
          genome_fa + ".sa"
      ]
      
      bwa_amb = files[1]
      bwa_ann = files[2]
      bwa_bwt = files[3]
      bwa_pac = files[4]
      bwa_sa  = files[5]
      
      print(bwa_amb)
      print(bwa_ann)
      print(bwa_bwt)
      print(bwa_pac)
      print(bwa_sa)
      
      bwaT = bwa_indexer.bwaIndexerTool()
      bwaT.run([genome_fa], {'assembly' : 'test'}) 
      
  def test_bwa_indexer_02 ():
      
      resource_path = os.path.join(os.path.dirname(__file__), "data/")
      genome_fa = resource_path + "inps.Mouse.GRCm38.fasta"
      fastqFile = resource_path + "inps.Mouse.DRR000386.fastq"
      
      files = [
          genome_fa,
          genome_fa + ".amb",
          genome_fa + ".ann",
          genome_fa + ".bwt",
          genome_fa + ".pac",
          genome_fa + ".sa"
      ]
      
      bwa_amb = files[1]
      bwa_ann = files[2]
      bwa_bwt = files[3]
      bwa_pac = files[4]
      bwa_sa  = files[5]
      
      print(bwa_amb)
      print(bwa_ann)
      print(bwa_bwt)
      print(bwa_pac)
      print(bwa_sa)
      
      bwaT = bwa_indexer.bwaIndexerTool()
      bwaT.run([genome_fa], {'assembly' : 'test'}) 
      
  
subject: Create test_bwa_indexer.py