primer_blast_dx package¶
Submodules¶
primer_blast_dx.version module¶
Module contents¶
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primer_blast_dx.
createBetterResult
(result)¶ Create a primer3 result in a better format Args:
result: primer3 result- Returns:
- better result
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primer_blast_dx.
findPrimers
(inputData, resultFormat='better')¶ return primer3 result with given format Args:
inputData: input data resultFormat: result format (raw/better)- Returns:
- result
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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
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primer_blast_dx.
findPrimersFromTask
(task)¶ return primer3 result from task. Checks exception Args:
inputData: input data- Returns:
- task result
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primer_blast_dx.
get_masked_seq
(primer_seq, genome_seq)¶
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primer_blast_dx.
get_offtarget_attrs
(off_target, side, idx, data, side_cols, target_cols, pysam_fasta)¶
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primer_blast_dx.
get_target_attrs
(target, side, idx, data, side_cols, target_cols, pysam_fasta)¶
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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
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primer_blast_dx.
specCheck
(task, taskResult)¶ Dealing with input files both task and task results
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primer_blast_dx.
transformInput
(data)¶ separate input to seq_args and global_args Args:
data: input data- Returns:
- separated input data