def select(index_file, selected_keys_file):
command = "rs_select -index_file=" \
+ index_file \
+ " -selected_keys_file=" \
+ selected_keys_file
execute_command(command, verbose)
def simulate_reads(script_path, number_of_transcripts, readlen, error_rate,
coverage, output_dir):
remove_file_if_exists(output_dir + '/transcript_names.txt')
remove_file_if_exists(output_dir + '/num_of_reads.txt')
command = "Rscript --vanilla " \
+ script_path + " " \
+ str(number_of_transcripts) + " " \
+ str(readlen) + " " \
+ str(error_rate) + " " \
+ str(coverage) + " " \
+ str(output_dir) + " " \
execute_command(command, verbose)
transcript_names = np.genfromtxt(output_dir + '/transcript_names.txt',
names=None,
dtype=None,
usecols=(0))
num_of_reads = np.genfromtxt(output_dir + '/num_of_reads.txt',
names=None,
dtype=None,
usecols=(0))
ground_truth_map = dict(zip(transcript_names, num_of_reads))
return ground_truth_map
def select_with_k(index_file, selected_keys_file, k):
command = "rs_select -index_file=" \
+ index_file \
+ " -selected_keys_file=" \
+ selected_keys_file \
+ " -rs_length=" \
+ str(k)
execute_command(command, verbose)
def build_index_with_k(transcriptome_reference_file, k, index_output_path):
command = "kallisto index -i " \
+ index_output_path \
+ " -k " \
+ str(k) \
+ " " \
+ transcriptome_reference_file
execute_command(command, verbose)
def build_index(k, transcriptome_reference_file, index_output_path):
command = "sailfish index -t " \
+ transcriptome_reference_file \
+ " -o " \
+ index_output_path \
+ " -k " \
+ str(k)
execute_command(command,verbose)
def build_index(cluster_output, index_file, k, numthreads):
command = "rs_index -transcript_fasta=" \
+ cluster_output \
+ " -index_file=" \
+ index_file \
+ " -rs_length=" \
+ str(k) \
+ " -num_threads=" \
+ str(numthreads)
execute_command(command, verbose)
def cluster(transcriptome_reference_file, cluster_output, k, numthreads):
command = "rs_cluster -gene_fasta=" \
+ transcriptome_reference_file \
+ " -num_threads=" \
+ str(numthreads) \
+ " -output=" \
+ cluster_output \
+ " -rs_length=" \
+ str(k)
execute_command(command, verbose)
def quant(index_dir, output_dir, sample_pair1, sample_pair2):
command = "kallisto quant -i " \
+ index_dir \
+ " -t 4 -o " \
+ output_dir \
+ " " \
+ sample_pair1 \
+ " " \
+ sample_pair2 \
execute_command(command, verbose)
def quant_with_k(sample_pair1, sample_pair2, index_dir, output_dir):
command = "sailfish quant -i " \
+ index_dir \
+ " -l " \
+ "T=PE:O=><:S=SA" \
+ " -1 " \
+ sample_pair1 \
+ " -2 " \
+ sample_pair2 \
+ " -p 4 -o " \
+ output_dir
execute_command(command,verbose)
def count(selected_keys_file, count_file, sample_pair_1, sample_pair_2,
numthreads):
command = "rs_count -selected_keys_file=" \
+ selected_keys_file \
+ " -count_file=" \
+ count_file \
+ " -read_files1=" \
+ sample_pair_1 \
+ " -read_files2=" \
+ sample_pair_2 \
+ " -num_threads=" \
+ str(numthreads)
execute_command(command, verbose)
def quant_with_k(k, sample_pair1, sample_pair2, index_dir, output_dir):
command = "salmon quant -i " \
+ index_dir \
+ " -l A" \
+ " -1 " \
+ sample_pair1 \
+ " -2 " \
+ sample_pair2 \
+ " -p 4 -o " \
+ output_dir \
+ " -k " \
+ str(k)
execute_command(command, verbose)
def test_execute_command_success(self):
""" Test if execute command function returns true when command
succeeds.
"""
logging.info("test_execute_command_success")
status, ret = general_utils.execute_command("ls")
self.assertTrue(status)
def test_execute_command_fail(self):
""" Test if execute command function returns false when command fails.
"""
logging.info("test_execute_command_fail")
status, out = general_utils.execute_command("not a command")
self.assertFalse(status)
self.assertEquals(out, 'NA')
def convert_logbin_to_logtext(self):
"""This function is used to convert the binary log file to text file.
Args:
self: Instance of the class.
Returns:
True on success else False.
Raises:
NA.
"""
command = "".join(['mysqlbinlog ', self.temp_db_binlog_file, ' >> ',
self.temp_db_textlog_file])
status, ret = general_utils.execute_command(command)
if not status:
logging.error("Conversion of mysql bin log file to text failed.")
return FAILURE
return SUCCESS
