.. py:function:: pytrf.version()
Get current version of pytrf
:return: version
:rtype: str
.. py:class:: pytrf.STRFinder(chrom, seq, mono=12, di=7, tri=5, tetra=4, penta=4, hexa=4)
Find all exact or perfect short tandem repeats (STRs), simple sequence repeats (SSRs) or microsatellites that meet the minimum repeats on the input sequence
:param str chrom: the sequence name
:param str seq: the input DNA sequence
:param int mono: the minimum tandem repeats for mono-nucleotide repeats
:param int di: the minimum tandem repeats for di-nucleotide repeats
:param int tri: the minimum tandem repeats for tri-nucleotide repeats
:param int tetra: the minimum tandem repeats for tetra-nucleotide repeats
:param int penta: the minimum tandem repeats for penta-nucleotide repeats
:param int hexa: the minimum tandem repeats for hexa-nucleotide repeats
:return: STRFinder object
.. py:method:: as_list()
Put all SSRs in a list and return, each SSR in list has 7 columns including [sequence name, start position, end position, motif sequence, motif length, repeats, SSR length]
:return: all SSRs found
:rtype: list
.. py:class:: pytrf.GTRFinder(chrom, seq, min_motif=1, max_motif=100, min_repeat=3, min_length=10)
Find all exact or perfect generic tandem repeats (GTRs) that meet the minimum repeat and minimum length on the input sequence
:param str chrom: the sequence name
:param str seq: the input DNA sequence
:param int min_motif: minimum length of motif sequence
:param int max_motif: maximum length of motif sequence
:param int min_repeat: minimum number of tandem repeats
:param int min_length: minimum length of tandem repeats
:return: GTRFinder object
.. py:method:: as_list()
Put all GTRs in a list and return, each GTR in list has 7 columns including [sequence name, start position, end position, motif sequence, motif length, repeats, GTR length]
:return: all GTRs found
:rtype: list
.. py:class:: pytrf.ATRFinder(chrom, seq, min_motif_size=1, max_motif_size=6, min_seed_repeat=3, min_seed_length=10, max_consecutive_error=3, min_extend_identity=70, max_extend_length=2000)
Find all approximate or imperfect tandem repeats (ATRs) from the input sequence
:param str chrom: the sequence name
:param str seq: the input DNA sequence
:param int min_motif_size: minimum length of motif
:param int max_motif_size: maximum length of motif
:param int min_seed_repeat: minimum number of repeat for seed
:param int min_seed_length: minimum length of seed
:param int max_consecutive_error: maximum number of allowed consecutive aligned errors
:param float min_extend_identity: minimum identity of extended alignment (0~1)
:param int max_extend_length: maximum length allowed to extend
:return: ATRFinder object
.. py:method:: as_list()
Put all ATRs in a list and return, each ATR in list has 14 columns including [sequence name, seed start position, seed end position, motif sequence, motif length, seed repeat, ATR start position, ATR end position, ATR repeat, ATR length, extend matches, extend substitutions, extend insertions, extend deletions, extend identity]
.. py:class:: pytrf.ETR
Readonly exact tandem repeat (ETR) object generated by iterating over STRFinder or GTRFinder object
.. py:attribute:: chrom
chromosome or sequence name where ETR located on
.. py:attribute:: start
ETR one-based start position on sequence
.. py:attribute:: end
ETR one-based end position on sequence
.. py:attribute:: motif
motif sequence
.. py:attribute:: type
motif length
.. py:attribute:: repeat
number of repeats
.. py:attribute:: length
length of ETR
.. py:attribute:: seq
get the sequence of ETR
.. py:method:: as_list()
convert ETR object to a list
.. py:method:: as_dict()
convert ETR object to a dict
.. py:method:: as_gff(terminator='')
convert ETR object to a gff formatted string
.. py:method:: as_string(separator='\t', terminator='')
convert ETR object to a TSV or CSV string by using separator and terminator
:param str separator: a separator between columns
:param str terminator: a terminator added to the end of string
:return: a formatted string
:rtype: str
.. py:class:: pytrf.ATR
Readonly imperfect or approximate tandem repeat (ATR) object generated by iterating over ATRFinder object
.. py:attribute:: chrom
chromosome or sequence name where ATR located on
.. py:attribute:: start
ATR one-based start position on sequence
.. py:attribute:: end
ATR one-based end position on sequence
.. py:attribute:: seed_start
start position of seed
.. py:attribute:: seed_end
end position of seed
.. py:attribute:: seed_repeat
repeat number of seed
.. py:attribute:: motif
motif sequence
.. py:attribute:: type
motif length
.. py:attribute:: repeat
repeat number of perfect counterpart
.. py:attribute:: length
length of ITR
.. py:attribute:: matches
number of matches for extend
.. py:attribute:: substitutions
number of substitutions for extend
.. py:attribute:: insertions
number of insertions for extend
.. py:attribute:: deletions
number of deletions for extend
.. py:attribute:: identity
extend identity
.. py:attribute:: seq
get the sequence of ATR
.. py:method:: as_list()
convert ATR object to a list
.. py:method:: as_dict()
convert ATR object to a dict
.. py:method:: as_gff(terminator='')
convert ATR object to a gff formatted string
.. py:method:: as_string(separator='\t', terminator='')
convert ATR object to a TSV or CSV string by using separator and terminator
:param str separator: a separator between columns
:param str terminator: a terminator added to the end of string
:return: a formatted string
:rtype: str