diff --git a/examples/bioinformatics/tel_search.py b/examples/bioinformatics/tel_search.py index bfb9b87..42cecbe 100644 --- a/examples/bioinformatics/tel_search.py +++ b/examples/bioinformatics/tel_search.py @@ -11,7 +11,7 @@ import functools import multiprocessing -import pandas, pandera +import pandas import funix @@ -127,10 +127,6 @@ def test(): return search_telomeres(sRNAs, repeat) -class InputSchema(pandera.DataFrameModel): - sRNAs: pandera.typing.Series[str] - - @funix.funix( description = "A telomere is a region of repetitive DNA sequences at the end of a chromosome. Enter a repeating unit, and a list of sRNAs in the table below, this telomere checker will tell whether each of the sRNAs is a telomere.", # destination = "column", @@ -152,7 +148,7 @@ def telomere_check( # "CCCTAAACCCTAAACCCTAAAC", # True, 22-nt # "CTAAACCCTAAACCCTAAACCCT" # True, 25-nt # ], - sRNAs: pandera.typing.DataFrame[InputSchema] = + sRNAs: pandas.DataFrame = pandas.DataFrame({"sRNAs": [ "CCCTAAACCCTAAACCCTAT", # False diff --git a/examples/bioinformatics/vector_strip.py b/examples/bioinformatics/vector_strip.py index 4b1a004..5ae623b 100644 --- a/examples/bioinformatics/vector_strip.py +++ b/examples/bioinformatics/vector_strip.py @@ -6,7 +6,7 @@ import functools import multiprocessing -import pandas, pandera +import pandas import funix @@ -95,14 +95,6 @@ def test(): print(code, ":", seq) -class InputSchema(pandera.DataFrameModel): - sRNAs: pandera.typing.Series[str] - - -class OutputSchema(pandera.DataFrameModel): - original_sRNA: pandera.typing.Series[str] - adapter_removed: pandera.typing.Series[str] - @funix.funix( description="Remove 3' prime adapter from the end of an RNA-seq", @@ -111,7 +103,7 @@ def remove_3_prime_adapter( # adapter_3_prime: str="TCGTATGCCGTCTTCTGCTT", adapter_3_prime: str = "TCGTA", minimal_match_length: int = 8, - sRNAs: pandera.typing.DataFrame[InputSchema] = pandas.DataFrame( + sRNAs: pandas.DataFrame = pandas.DataFrame( { "sRNAs": [ "AAGCTCAGGAGGGATAGCGCCTCGTATGCCGTCTTCTGC", # shorter than full 3' adapter