gtAI package

Submodules

gtAI.CA_RSCU module

CA_RSCU.RSCU(allseq, allseq_name, The_Genetic_Codes_number)[source]

calculate RSCU values

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 codons and RSCU values

gtAI.Run_gtAI module

gtAI.gtAI module

gtAI.GtRNAdb(url)[source]
Get the tRNA genes count from GtRNAdb database

Args:

url (string): a url to anticodon table for organism from GtRNAdb database (http://gtrnadb.ucsc.edu/)

Returns:

A dictionary of each anticodon and its gene count

Raises:

ValueError if the URL, not a valid for GtRNAdb database

Example:

gtAI.abs_Wi(dict_anticodon_number, Sug, Sci, Sai, Sgu, Sal, bacteria=False)[source]

Calculate the absolute adaptiveness values for each codon.

Args:

dict_anticodon_number (dict): a merged dictionary of anticodon-codon with each anticodon tRNA gene copy number returned from dict_codon_anticodon_count() function.

Sug (int): the S-value for codon with (U) in the third position and (G) in first anticodon position

Sci (int): the S-value for codon with (C) in the third position and (I) in first anticodon position

Sai (int): the S-value for codon with (A) in the third position and (I) in first anticodon position

Sgu (int): the S-value for codon with (G) in the third position and (U) in first anticodon position

Sal (int): the S-value for codon with (A) in the third position and (L) in first anticodon position ( if bacteria = True)

bacteria (bool): True If the tested organism is prokaryotic or archaea, else equal to False ( default = False )

Returns:

A dictionary of the absolute adaptiveness values for each codon

Note:

All Sij values (as Sug) should be a number from 0 to 1

Raises:

ValueError if the length of dict_anticodon_number equal to zero ValueError if any of Sij values are less than 0 or greater than 1

Example:

> anticodon_dict = tRNADB_CE(“trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/whole_anticodon.cgi?GID=|CP001631&DTYPE=CMP&VTYPE=1”) # Return an anticodon table of Acidimicrobium ferrooxidans DSM 10331 > anticodon_codon = dict_codon_anticodon ( anticanticodon_dictodon ) > dict_codon_anticodon_count = dict_codon_anticodon_count(anticodon_codon,anticodon_dict,bacteria = True) > abs_Wi(dict_codon_anticodon_count, Sug=1, Sci=1, Sai=1, Sgu=1, Sal=1, bacteria=True)
gtAI.calc_Tai(DNA, rel_dict_wi, genetic_code_number=1)[source]

Calculate the tRNA adaptation index of a gene.

Args:

DNA (str): a coding sequence of DNA ( should only contain A, C, T, and G )

rel_dict_wi (dict): dictionary of the relative adaptiveness values for each codon returned from rel_Wi() function

genetic_code_number (int): default = 1, The Genetic Codes number described by NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)

Returns:

the tRNA adaptation index of a gene

Raises:

ValueError if the length of dict_anticodon_number equal to zero

Example:

> anticodon_dict = tRNADB_CE(“trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/whole_anticodon.cgi?GID=|CP001631&DTYPE=CMP&VTYPE=1”) # Return an anticodon table of Acidimicrobium ferrooxidans DSM 10331 > anticodon_codon = dict_codon_anticodon ( anticanticodon_dictodon ) > dict_codon_anticodon_count = dict_codon_anticodon_count(anticodon_codon,anticodon_dict,bacteria = True) > abs_Wi = abs_Wi(dict_codon_anticodon_count, Sug=1, Sci=1, Sai=1, Sgu=1, Sal=1, bacteria=True) > rel_Wi(abs_Wi, 11)
gtAI.dict_codon_anticodon(anti_codon_dict)[source]

Identify all potential anticodons for each codon

Args:

anti_codon_dict (dict): a dictionary of all anticodons for an organism ( returned from ( tRNADB_CE() ) or ( GtRNAdb() ) )

Returns:

A dictionary of all potential anticodons for each codon

Raises:

ValueError if the length of anti_codon_dict equal to zero

Example:

> anticodon_dict = tRNADB_CE(“trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/whole_anticodon.cgi?GID=|CP001631&DTYPE=CMP&VTYPE=1”) # Return an anticodon table of Acidimicrobium ferrooxidans DSM 10331 > dict_codon_anticodon ( anticanticodon_dictodon )
gtAI.dict_codon_anticodon_count(dic_codon_anticodon, dict_tGCN_main, bacteria=False)[source]

Merge anticodon-codon dictionary with each anticodon tRNA gene copy number.

Args:

dic_codon_anticodon (dict): A dictionary of all potential anticodons for each codon returned from dict_codon_anticodon() function.

dict_tGCN_main (dict): a dictionary of all anticodons for an organism ( returned from ( tRNADB_CE() function ) or ( GtRNAdb() function ) )

bacteria (bool): True If the tested organism is prokaryotic or archaea, else equal to False ( default = False )

Returns:

a merged dictionary of anticodon-codon with each anticodon tRNA gene copy number.

Raises:

ValueError if the length of anti_codon_dict equal to zero ValueError if the length of dict_tGCN_main equal to zero

Example:

> anticodon_dict = tRNADB_CE(“trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/whole_anticodon.cgi?GID=|CP001631&DTYPE=CMP&VTYPE=1”) # Return an anticodon table of Acidimicrobium ferrooxidans DSM 10331 > anticodon_codon = dict_codon_anticodon ( anticanticodon_dictodon ) > dict_codon_anticodon_count(anticodon_codon,anticodon_dict,bacteria = True)
gtAI.rel_Wi(dict_abs_Wi, genetic_code_number=1)[source]

Calculate the relative adaptiveness values for each codon.

Args:

dict_abs_Wi (dict): dictionary of the absolute adaptiveness values for each codon returned from abs_Wi() function

genetic_code_number (int): default = 1, The Genetic Codes number described by NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)

Returns:

a dictionary of the relative adaptiveness values for each codon

Raises:

ValueError if the length of dict_abs_Wi equal to zero

Example:

> anticodon_dict = tRNADB_CE(“trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/whole_anticodon.cgi?GID=|CP001631&DTYPE=CMP&VTYPE=1”) # Return an anticodon table of Acidimicrobium ferrooxidans DSM 10331 > anticodon_codon = dict_codon_anticodon ( anticanticodon_dictodon ) > dict_codon_anticodon_count = dict_codon_anticodon_count(anticodon_codon,anticodon_dict,bacteria = True) > abs_Wi = abs_Wi(dict_codon_anticodon_count, Sug=1, Sci=1, Sai=1, Sgu=1, Sal=1, bacteria=True) > rel_Wi(abs_Wi, 11)
gtAI.tRNADB_CE(url)[source]

Get the tRNA genes count from tRNADB-CE database

Args:

url (string): a url to anticodon table for organism from tRNADB_CE database (http://trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/index.cgi)

Returns:

A dictionary of each anticodon and its gene count

Raises:

ValueError if the URL, not a valid for tRNADB-CE database

Example:

> tRNADB_CE(“trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/whole_anticodon.cgi?GID=|CP001631&DTYPE=CMP&VTYPE=1”) # Return an anticodon table of Acidimicrobium ferrooxidans DSM 10331