PyDNApsenac module

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A class used for computing different types of DNA descriptors!

You can freely use and distribute it. If you have any problem,

you could contact with us timely.

Authors: Zhijiang Yao and Dongsheng Cao.

Date: 2016.06.14

Email: gadsby@163.com and oriental-cds@163.com

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PyDNApsenac.CheckPsenac(lamada, w, k)

Check the validation of parameter lamada, w and k.

PyDNApsenac.GetPCPseDNC(input_data, **kwargs)

Make a PCPseDNC dictionary.

Parameters:

• input_data – file object or sequence list.
• phyche_index – physicochemical properties list.
• all_property – choose all physicochemical properties or not.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetPCPseTNC(input_data, **kwargs)

Make a PCPseDNC dictionary.

Parameters:

• input_data – file object or sequence list.
• phyche_index – physicochemical properties list.
• all_property – choose all physicochemical properties or not.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetPseDNC(input_data, **kwargs)

Make PseDNC dictionary.

Parameters:

• input_data – file type or handle.
• k – k-tuple.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetPseKNC(input_data, **kwargs)

Make PseKNC dictionary.

Parameters:

• input_data – file type or handle.
• k – k-tuple.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetSCPseDNC(input_data, **kwargs)

Make a SCPseDNC dictionary.

Parameters:

• input_data – file object or sequence list.
• phyche_index – physicochemical properties list.
• all_property – choose all physicochemical properties or not.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetSCPseTNC(input_data, **kwargs)

Make a SCPseTNC dictionary.

Parameters:

• input_data – file object or sequence list.
• phyche_index – physicochemical properties list.
• all_property – choose all physicochemical properties or not.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetSequenceListAndPhycheValue(input_data, k, phyche_index, extra_phyche_index, all_property)

For PseKNC-general make sequence_list and phyche_value.

Parameters:

• input_data – file type or handle.
• k – int, the value of k-tuple.
• k – physicochemical properties list.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

• all_property – bool, choose all physicochemical properties or not.

PyDNApsenac.GetSequenceListAndPhycheValuePsednc(input_data, extra_phyche_index=None)

For PseDNC, PseKNC, make sequence_list and phyche_value.

Parameters:

• input_data – file type or handle.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.

PyDNApsenac.GetSequenceListAndPhycheValuePseknc(input_data, extra_phyche_index=None)

For PseDNC, PseKNC, make sequence_list and phyche_value.

Parameters:

• input_data – file type or handle.
• extra_phyche_index –

  dict, the key is the dinucleotide (string),

  the value is its physicochemical property value (list).

  It means the user-defined physicochemical indices.