BCAWT package¶
BCAWT.BCAWT module¶
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BCAWT.
BCAW
(main_fasta_file, save_path='', ref_fasta_file=None, genetic_code_=1, Auto=False)¶ BCAWT ( Bio Codon Analysis Workflow Tool ), it manages a complete workflow to analysis the codon usage bias for genes and genomes of any organism..
Args:
main_fasta_file (list): list of string of the file’s path or file-like object
save_path (str): absolute path to the directory to save the result in, default = the current directory
ref_fasta_file (list): list of string of the file’s path or file-like object, default = None
genetic_code_(int): default = 1, The Genetic Codes number described by NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
Auto (bool): default = False, if ref_fasta_file not None.
Notes:
- Auto (bool): should be = True to auto-generate a reference set, when arg (ref_fasta_file) not available ( = None )
Returns:
BCAWT.BCAWT_auto_test module¶
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BCAWT_auto_test.
auto_check_files
(path)¶ Check the expected outputs.
- Args:
- path: absolute path to the directory to save the result in
Returns:
None
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BCAWT_auto_test.
auto_test
(path='', test_file='')¶ Run a demo test with 23 results ( see the documentation for more details about the expected output )
Args:
path: absolute path to the directory to save the result in test_file: absolute path to the fasta file that will be tested- Returns:
- None
BCAWT.ATCG3 module¶
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ATCG3.
ACTG3
(sequ, A=False, T=False, C=False, G=False)¶ Calculate A, T, G, and C content at the third position.
Args:
sequ (str): DNA sequence A (bool): default = False T (bool): default = False C (bool): default = False G (bool): default = False- Returns:
- A3 content if arg(A) is True
- T3 content if arg(T) is True
- C3 content if arg(C) is True
- G3 content if arg(G) is True
- None if all args are False
BCAWT.CA module¶
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CA.
CA
(file)¶ correspondence analysis.
Args:
file (directory): csv file contains genes’ RSCU values- Returns:
- csv file contains genes’ values for the first 4 axes of the correspondence analysis result
- csv file contains codons’ values for the first 4 axes of the correspondence analysis result
- plot the genes first 2 axes values of the correspondence analysis result
- plot the codons first 2 axes values of the correspondence analysis result
BCAWT.CA_RSCU module¶
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CA_RSCU.
CA_RSCU
(allseq, allseq_name, The_Genetic_Codes_number=1)¶ calculate RSCU values for correspondence analysis.
Args:
allseq (str): DNA sequence allseq_name (str) : gene name The_Genetic_Codes_number (int) : default = 1, The Genetic Codes number described by NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)- Returns:
- DataFrame: DataFrame contains [gene_name and RSCU values]
BCAWT.GC123 module¶
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GC123.
GC1
(sequ)¶ Calculates the GC content an the first codon position.
Args:
sequ (str): DNA sequence- Returns:
- int: GC1 value
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GC123.
GC12
(sequ)¶ Calculates the GC content average at the 1st and 2nd codon positions.
Args:
sequ (str): DNA sequence- Returns:
- int: GC12 value
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GC123.
GC2
(sequ)¶ Calculates the GC content an the 2nd codon position..
Args:
sequ (str): DNA sequence- Returns:
- int: GC2 value
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GC123.
GC3
(sequ)¶ Calculates the GC content an the 3rd codon position..
Args:
sequ (str): DNA sequence- Returns:
- int: GC3 value
BCAWT.GRAVY_AROMO module¶
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GRAVY_AROMO.
GRAvy_ARomo
(seq, genetic_code_=1, G=False, A=False)¶ calculating Gravy and Aroma for DNA sequence.
- Args:
- seq (str):DNA sequence genetic_code_(int): default = 1, The Genetic Codes number described by NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) G (bool): default = False A (bool): default = False
- Returns:
- Gravy value if arg(G) is True
- Aroma value if arg(A) is True
- None if both args are False
BCAWT.Optimal_codon_corr_method module¶
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Optimal_codon_corr_method.
op_corr
(ENc_file_name, RSCU_file_name)¶ determine the optimal codons using the correlation method described here: https://doi.org/10.1371/journal.pgen.1000556
Args:
ENc_file_name (file): file contains the ENc values for a set of genes RSCU_file_name (file): file contains the RSCU values for a set of genes- Returns:
- DataFrame contains the optimal codons
BCAWT.P2_index module¶
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P2_index.
P2_index
(sequ, wwc=False, sst=False, wwy=False, ssy=False, p2=False)¶ calculate P2 index.
- Args:
- sequ (str): DNA sequence wwc (bool): default = False sst (bool): default = False wwy (bool): default = False ssy (bool): default = False p2 (bool): default = False
- Returns:
- wwc value if arg(wwc) is True
- sst value if arg(sst) is True
- wwy value if arg(wwy) is True
- ssy value if arg(ssy) is True
- p2 value if arg(p2) is True