primer_blast_dx package

Submodules

primer_blast_dx.version module

Module contents

primer_blast_dx.createBetterResult(result)

Create a primer3 result in a better format Args:

result: primer3 result
Returns:
better result
primer_blast_dx.findPrimers(inputData, resultFormat='better')

return primer3 result with given format Args:

inputData: input data resultFormat: result format (raw/better)
Returns:
result
primer_blast_dx.findPrimersFile(taskPath, taskResultPath)

find primers from the task file and store the result to a task result file Args:

taskPath: location of the task file taskResultPath: location of the task result file to store
primer_blast_dx.findPrimersFromTask(task)

return primer3 result from task. Checks exception Args:

inputData: input data
Returns:
task result
primer_blast_dx.get_masked_seq(primer_seq, genome_seq)
primer_blast_dx.get_offtarget_attrs(off_target, side, idx, data, side_cols, target_cols, pysam_fasta)
primer_blast_dx.get_target_attrs(target, side, idx, data, side_cols, target_cols, pysam_fasta)
primer_blast_dx.run(task)

run findPrimers and specCheck Args:

task (dic): task data saveTmp (bool): true if user wants to save temporary files
Returns:
dic: result dictionary
primer_blast_dx.specCheck(task, taskResult)

Dealing with input files both task and task results

primer_blast_dx.transformInput(data)

separate input to seq_args and global_args Args:

data: input data
Returns:
separated input data