B h}\ [@s2dZddlmZddlZdddddd d d d d dddddddd gZGdddeZeddZededdZededdZ ededdZ ededd Z ed!ed"d#Z ed$ed%d&Z ed'ed(d'Zed)ed*d)Zed+ed,d-Zed.d/ZGd0ddeZGd1d d eZd2dZd3dZd4dZdS)5a Alphabetic sequences and associated tools and data. Seq is a subclass of a python string with additional annotation and an alphabet. The characters in string must be contained in the alphabet. Various standard alphabets are provided. Classes :: Alphabet -- A subset of non-null ascii characters Seq -- An alphabetic string SeqList -- A collection of Seq's Alphabets :: o generic_alphabet -- A generic alphabet. Any printable ASCII character. o protein_alphabet -- IUCAP/IUB Amino Acid one letter codes. o nucleic_alphabet -- IUPAC/IUB Nucleic Acid codes 'ACGTURYSWKMBDHVN-' o dna_alphabet -- Same as nucleic_alphabet, with 'U' (Uracil) an alternative for 'T' (Thymidine). o rna_alphabet -- Same as nucleic_alphabet, with 'T' (Thymidine) an alternative for 'U' (Uracil). o reduced_nucleic_alphabet -- All ambiguous codes in 'nucleic_alphabet' are alternative to 'N' (aNy) o reduced_protein_alphabet -- All ambiguous ('BZJ') and non-canonical amino acids codes ( 'U', Selenocysteine and 'O', Pyrrolysine) in 'protein_alphabet' are alternative to 'X'. o unambiguous_dna_alphabet -- 'ACGT' o unambiguous_rna_alphabet -- 'ACGU' o unambiguous_protein_alphabet -- The twenty canonical amino acid one letter codes, in alphabetic order, 'ACDEFGHIKLMNPQRSTVWY' Amino Acid Codes:: Code Alt. Meaning ----------------- A Alanine B Aspartic acid or Asparagine C Cysteine D Aspartate E Glutamate F Phenylalanine G Glycine H Histidine I Isoleucine J Leucine or Isoleucine K Lysine L Leucine M Methionine N Asparagine O Pyrrolysine P Proline Q Glutamine R Arginine S Serine T Threonine U Selenocysteine V Valine W Tryptophan Y Tyrosine Z Glutamate or Glutamine X ? any * translation stop - .~ gap Nucleotide Codes:: Code Alt. Meaning ------------------------------ A Adenosine C Cytidine G Guanine T Thymidine U Uracil R G A (puRine) Y T C (pYrimidine) K G T (Ketone) M A C (aMino group) S G C (Strong interaction) W A T (Weak interaction) B G T C (not A) (B comes after A) D G A T (not C) (D comes after C) H A C T (not G) (H comes after G) V G C A (not T, not U) (V comes after U) N X? A G C T (aNy) - .~ A gap Refs: http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html Authors: GEC 2004,2005 )arrayNAlphabetSeqrnadnaproteinSeqListgeneric_alphabetprotein_alphabetnucleic_alphabet dna_alphabet rna_alphabetreduced_nucleic_alphabetreduced_protein_alphabetunambiguous_dna_alphabetunambiguous_rna_alphabetunambiguous_protein_alphabetc@seZdZdZddddgZd)ddZd d Zd d Zd dZddZ ddZ ddZ ddZ ddZ ddZddZddZdd Zd!d"Zd#d$Zd%d&Zed*d'd(ZdS)+rzoAn ordered subset of printable ascii characters. Status: Beta Authors: - GEC 2005 _letters _alternatives _ord_table _chr_tableNcCslt|}dddtddD}|dkr0|}||_tdd}|dkrL|}td gd }xHt|D]<\}}t|} | d krt d || d krt d ||| <qdWg} g} xP|D]H\} } | |krt| } || d kr|t| || <| | | | qWd| d| f|_ |d d ks&t ||_ td gd }x"t|D]\}}t|||<qDW||_|S)aXCreate a new, immutable Alphabet. e.g. Alphabet( 'ACDEFGHIKLMNPQRSTVUWY', zip('acdefghiklmnpqrstvuwy', 'ACDEFGHIKLMNPQRSTVUWY') ) arguments: - letters -- the letters in the alphabet. The ordering determines the ordinal position of each character in this alphabet. - alt -- A list of (alternative, canonical) letters. The alternatives are given the same ordinal position as the canonical characters. e.g. (('?','X'),('x', 'X')) states that '?' and 'x' are synonomous with 'X'. Values that are not in 'letters' are ignored. Alternatives that are already in 'letters' are also ignored. If the same alternative character is used twice then the alternative is assigned to the canonical character that occurs first in 'letters'. The default is to assume that upper and lower case characters are equivalent, unless both cases are included in 'letters'. raises: ValueError : Repetitive or otherwise illegal set of letters. cSsg|] }t|qS)chr).0Z _Alphabet__irrU/home/fristb/BIRCH/lib-linux-x86_64/python/lib/python3.7/site-packages/weblogo/seq.py sz$Alphabet.__new__.. NabcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZrz)Alphabet cannot contain null character \0zRepetitive alphabet)object__new__joinrangerzip bytearray enumerateord ValueErrorappendrAssertionErrorrdecoder)clsletters alternativesself ascii_lettersZequivalent_by_caseZ ord_tableianZ_fromZ_toecZ chr_tablerrrr$sD      zAlphabet.__new__cCs0|j}x$t|D]}|t|dkrdSqWdS)z:True if all characters of the string are in this alphabet.r!FT)rstrr*)r2stringtablesrrr alphabetics zAlphabet.alphabeticcCs |j|S)z9 The n'th character in the alphabet (zero indexed) or \0 )r)r2r6rrrrsz Alphabet.chrcCs|jt|S)zgThe ordinal position of the character c in this alphabet, or 255 if no such character. )rr*)r2r8rrrr*sz Alphabet.ordcs&fdd|D}d|}t|S)z9Convert a sequence of ordinals into an alphabetic string.csg|]}j|qSr)r)rr6)r2rrrsz!Alphabet.chrs..r)r%r)r2Zsequence_of_intsr8r<r)r2rchrss z Alphabet.chrscCs,t|}||j}tdt|d}|S)z;Convert an alphabetic string into a byte array of ordinals.Br)r9 translaterrcodecslatin_1_encode)r2r:r<r5rrrords s z Alphabet.ordscCs"||std|||S)zNormalize an alphabetic string by converting all alternative symbols to the canonical equivalent in 'letters'. zNot an alphabetic string.)r=r+r>rC)r2r:rrr normalizes zAlphabet.normalizecCst|S)z% Letters of the alphabet as a string.)r9)r2rrrr0szAlphabet.letterscCsd|jdt|jdS)Nz Alphabet( 'z', zipz ))rreprr)r2rrr__repr__$szAlphabet.__repr__cCs t|jS)N)r9r)r2rrr__str__'szAlphabet.__str__cCs t|jS)N)lenr)r2rrr__len__*szAlphabet.__len__cCst|dsdS|j|jkS)NrF)hasattrr)r2otherrrr__eq__-s zAlphabet.__eq__cCs || S)N)rL)r2rKrrr__ne__2szAlphabet.__ne__cCs t|jS)N)iterr)r2rrr__iter__5szAlphabet.__iter__cCs |j|S)N)r)r2keyrrr __getitem__8szAlphabet.__getitem__cCstt|jS)N)hashtupler)r2rrr__hash__;szAlphabet.__hash__csH|dkrtttf}ddlfdd|D}|t|}||}|S)a Returns the most appropriate unambiguous protein, RNA or DNA alphabet for a Seq or SeqList. If a list of alphabets is supplied, then the best alphabet is selected from that list. The heuristic is to count the occurrences of letters for each alphabet and downweight longer alphabets by the log of the alphabet length. Ties go to the first alphabet in the list. Nrcs(g|] }t|t|qSr)sumtallylogrH)rr5)mathseqsrrrOsz"Alphabet.which..)rrrrXindexmax)rYZ alphabetsZscorebestr5r)rXrYrwhich>s zAlphabet.which)N)N)__name__ __module__ __qualname____doc__ __slots__r$r=rr*r>rCrDr0rFrGrIrLrMrOrQrT staticmethodr]rrrrrs(  K zACDEFGHIKLMNOPQRSTUVWYBJZX*-zacdefghiklmnopqrstuvwybjzx?.~zACDEFGHIKLMNOPQRSTUVWYBJZXX--zACGTURYSWKMBDHVN-zacgturyswkmbdhvnXx?.~zACGTURYSWKMBDHVNNNN--zACGTRYSWKMBDHVN-zacgtryswkmbdhvnXx?.~UuzACGTRYSWKMBDHVNNNN--TTzACGURYSWKMBDHVN-zacguryswkmbdhvnXx?.~TtzACGURYSWKMBDHVNNNN--UUzACGTN-z acgtryswkmbdhvnXx?.~TtRYSWKMBDHVz ACGTNNNNNNNNNNNNNN--TTNNNNNNNNNNzACDEFGHIKLMNPQRSTVWYX*-zacdefghiklmnpqrstvwyx?.~BbZzUuzACDEFGHIKLMNPQRSTVWYXX--XXXXCCZACGTZacgtZACGUZacguZACDEFGHIKLMNPQRSTVWYZacdefghiklmnopqrstuvwyZACDEFGHIKLMNOPQRSTUVWYz&ACGTRYSWKMBDHVN-acgtUuryswkmbdhvnXx?.~z&TGCAYRSWMKVHDBN-tgcaAayrswmkvhdbnXx?.~cseZdZdZeddfddZeddZddZd3d d Z d d Z d dZ ddZ fddZ ddZddZddZddZddZddZdd Zd!d"Zd4d%d&Zd'd(Zd)d*Zd+d,Zd-d.Zd5d/d0Zd6d1d2ZZS)7raY An alphabetic string. A subclass of "str" consisting solely of letters from the same alphabet. Attributes: alphabet -- A string or Alphabet of allowed characters. name -- A short string used to identify the sequence. description -- A string describing the sequence Authors : GEC 2005 NcCsZt||}|dkrt}t|ts*t|}||sDtd||f||_||_||_ |S)Nz Sequence not alphabetic %s, '%s') r9r$r isinstancerr=r+ _alphabetname description)r/objalphabetrfrgr2rrrr$s   z Seq.__new__cCs|jS)N)re)r2rrrrisz Seq.alphabetcCs |j|S)z[ Convert sequence to an array of integers in the range [0, len(alphabet) ) )rirC)r2rrrrCszSeq.ordscCsP|s |j}t|}dg|}||}x$|D]}||kr,||d7<q,W|S)zCounts the occurrences of alphabetic characters. Arguments: - alphabet -- an optional alternative alphabet Returns : A list of character counts in alphabetic order. r)rirHrC)r2riLcountsrCr6rrrrVs    z Seq.tallycCs|j}|t|||jS)N) __class__r9rQri)r2rPr/rrrrQszSeq.__getitem__cCs|j}|t|||jS)N)rmr9__add__ri)r2rKr/rrrrnsz Seq.__add__cCs|j}|t|||jS)N)rmr9rnri)r2rKr/rrr__radd__sz Seq.__radd__cs|j}|tt|||jS)N)rmsuperrr%ri)r2Zstr_listr/)rmrrr%szSeq.joincCs*t|dsdS|j|jkrdSt||S)NriF)rJrir9rL)r2rKrrrrLs   z Seq.__eq__cCs || S)N)rL)r2rKrrrrMsz Seq.__ne__cCst|S)z' Converts Seq to a raw string. )r9)r2rrrtostringsz Seq.tostringcCs|j}||ddd|jS)zReturn the reversed sequence. Note that this method returns a new object, in contrast to the in-place reverse() method of list objects. N)rmri)r2r/rrrreversesz Seq.reversecCs |dS)Nz-.~)remove)r2rrrungapsz Seq.ungapcs<|j}dfddt|D}||tdd|jS)z]Return a new alphabetic sequence with all characters in 'delchars' removed. rc3s|]}|tkr|VqdS)N)set)rchar)delcharsrr szSeq.remove..)rmr%r9r@ maketransri)r2rxr/Zcleanseqr)rxrrtsz Seq.removecCs(|j}tdd}|t|||jS)z*Return a lower case copy of the sequence. r r)rmr9rzr@ri)r2r/transrrrlowers z Seq.lowercCs(|j}tdd}|t|||jS)z*Return a lower case copy of the sequence. rr )rmr9rzr@ri)r2r/r{rrruppers z Seq.upperrXcCsLt|}t|dkrtd||}t||}|j}|t|||jS)zReplace all occurrences of letters with the mask character. The default is to replace all lower case letters with 'X'. rjzMask should be single character)rHr+r9rzrmr@ri)r2r0maskZLLtor{r/rrrr s  zSeq.maskcCsddlm}||S)zTranslate a nucleotide sequence to a polypeptide using full IUPAC ambiguities in DNA/RNA and amino acid codes, using the standard genetic code. See weblogo.transform.GeneticCode for details and more options. rj) GeneticCode) transformrstdr@)r2rrrrr@s z Seq.translatecCsddlm}||S)zTranslate a protein sequence back into coding DNA, using the standard genetic code. See weblogo.transform.GeneticCode for details and more options. rj)r)rrrback_translate)r2rrrrr#s zSeq.back_translatecCs |S)zpReturns reversed complementary nucleic acid sequence (i.e. the other strand of a DNA sequence.) )rs complement)r2rrrreverse_complement+szSeq.reverse_complementcCs:t|jstdt|t}|j}|||j|j|j S)z,Returns complementary nucleic acid sequence.zIncompatable alphabets) r r=rir+r9r@_complement_tablermrfrg)r2r<r/rrrr1s   zSeq.complementccslt||krdS|j|}xFtdt||dD],}||||}|dks^||r8|Vq8WdS)zReturn an iteration over all subwords of length k in the sequence. If an optional alphabet is provided, only words from that alphabet are returned. >>> list(Seq("abcabc").words(3)) ['abc', 'bca', 'cab', 'abc'] Nrrj)rHrirDrqr&r=)r2kriseqr4wordrrrwords9s z Seq.wordscCs$ddlm}t|||}||S)zReturn a count of all subwords in the sequence. >>> from weblogo.seq import * >>> Seq("abcabc").word_count(3) [('abc', 2), ('bca', 1), ('cab', 1)] rj) group_count)utilsrsortedr)r2rrirrrrr word_countMs zSeq.word_count)N)rr~)N)N)r^r_r`rar r$propertyrirCrVrQrnror%rLrMrqrsrurtr|r}rr@rrrrr __classcell__rr)rmrrs2         c@sReZdZdZdddgZgdddfddZdd Zdd d Zdd d ZdddZ dS)rz A list of sequences. rirfrgNcCs"t||||_||_||_dS)N)list__init__rirfrg)r2Zalistrirfrgrrrrbs zSeqList.__init__cCsdt|dkrdS|j}|dkr(|dj}t|d}x*|D]"}t||krNdS|j|kr:dSq:WdS)z2Are all sequences of the same length and alphabet?rTNF)rHri)r2Arkr<rrr isalignedms      zSeqList.isalignedcCs<|s |j}|stdg}x|D]}|||q W|S)z< Convert sequence list into a 2D array of ordinals. z No alphabet)rir+r,rC)r2rirr<rrrrC}s z SeqList.ordscs:s |jstdddtfdd|DD}|S)zCounts the occurrences of alphabetic characters. Arguments: - alphabet -- an optional alternative alphabet Returns : A list of character counts in alphabetic order. z No alphabetcSsg|] }t|qSr)rU)rr8rrrrsz!SeqList.tally..csg|]}|qSr)rV)rr<)rirrrs)rir+r')r2rirlr)rirrVs  z SeqList.tallyc s|s |j}|stdt|||}t|d}fddtd|D}xR|D]J}t||krjtdx0t|D]$\}}|krt|||d7<qtWqRWddlm}|||S)zgCounts the occurrences of characters in each column. Returns: Motif(counts, alphabet) z No alphabetrcsg|]}dgqS)rr)rl)Nrrrsz#SeqList.profile..z6Sequences are of incommensurate lengths. Cannot tally.rj)Motif)rir+rHrCr&r)Zmatrixr) r2rirCrkrlojr6rr)rrprofiles      zSeqList.profile)N)N)N) r^r_r`rarbrrrCrVrrrrrr\s   cCs t|tdS)zACreate an alphabetic sequence representing a stretch of DNA. )ri)rr )r:rrrrscCs t|tdS)zACreate an alphabetic sequence representing a stretch of RNA. )ri)rr )r:rrrrscCs t|tdS)zICreate an alphabetic sequence representing a stretch of polypeptide. )ri)rr )r:rrrrs)rarrA__all__r#rr r'r r r r rrrrrr9rzrrrrrrrrrrrzsh @ ][