U H$xeJ@sdZddlZddlZddlmZddlmZmZmZm Z m Z m Z m Z ddl m Z ddlmZddlmZmZmZmZmZmZmZmZmZmZmZeeZed d d Z eed d dZ!eee eefdddZ"GdddZ#ee eefe ee feedddZ$eee ee fe edddZ%d%eee ee feeedddZ&eeeeee ee fedddZ'eeeee ee fed d!d"Z(d#d$Z)dS)&z Parse adapter specifications N)Path)TypeOptionalListTupleAnyDictIterable)xopen) FastaReader) Adapter FrontAdapterNonInternalFrontAdapter BackAdapterNonInternalBackAdapterAnywhereAdapter PrefixAdapter SuffixAdapter LinkedAdapterInvalidCharacterRightmostFrontAdapter)specc Cszddddddddddddd }|d}t}|D]}|}|sDq2|d\}}}|}||krttd|d |dkr|d krtd |d ||dk r||}q|}|d krd }n*z t|}Wntk rt|}YnX||krtd |d|||<q2d|kr*d|kr*tdd|krFd|krFtdd|kr^d|d<|d=d|krvd|d<|d=|S)z/Parse key=value;key=value;key=value into a dictmax_error_rate max_errors min_overlapN) eZ error_raterorranywhererequiredoptionalindelsnoindels rightmost;=zUnknown parameter ''zNo value given for key 'TzKey 'z' specified twicer rz>'optional' and 'required' cannot be specified at the same timer!r"z<'indels' and 'noindels' cannot be specified at the same timeF)splitdictstrip partitionKeyError ValueErrorintfloat)rZallowed_parametersfieldsresultZfieldkeyZequalsvaluer4.lib/python3.8/site-packages/cutadapt/parser.pyparse_search_parameterssd        r6)sequencereturncCsd}d}td|D]}|dkr"q|dkrX|dkr:td|dkrJtd|}||7}q|dkrt|}d|kr|d ksntd |d qt|tr|dkrtd |dd |d |}d}q|dkrtdd}qt|ts|dkrtd|S)z Replace all occurrences of ``x{n}`` (where x is any character) with n occurrences of x. Raise ValueError if the expression cannot be parsed. >>> expand_braces('TGA{5}CT') 'TGAAAAACT' r'Nz([{}]){z""{" must be used after a character}z"}" cannot be used hereri'Value z invalidz "}" expectedz Expected "{"zUnterminated expression)rer(r-r. isinstance)r7r1prevsr4r4r5 expand_bracesXs6   rA)spec1spec2r8cCsX|dkrtd|s,|dkr"|}qPtdn$|sH|dkrBd}|}qP|}ntd||fS)Nrz2No ellipsis ("...") allowed in "anywhere" adaptersbackzInvalid adapter specificationfrontzExpected either spec1 or spec2)r-)rBrC adapter_typerr4r4r5_normalize_ellipsiss rGc@seZdZdZeeeeeeedddZddZddZ e ee eeefd d d Z e eedd d dZe ee eeeeefd ddZe ddZddZdS)AdapterSpecificationa9# noqa: E501 Description of a single non-linked adapter. These are the attributes: - name (None or str) - restriction (None, 'anchored', or 'noninternal') - sequence (nucleotide sequence as string) - search parameters (dict with keys such as 'max_errors', 'min_overlap') - adapter_type ('front' for -a, 'back' for -g and 'anywhere' for -b) >>> AdapterSpecification.parse('a_name=ACGT;anywhere', 'back') AdapterSpecification(name='a_name', restriction=None, sequence='ACGT', parameters={'anywhere': True}, adapter_type='back') )name restrictionr7rFr#cCs@|dks t|dkst||_||_||_||_||_||_dS)N)Nanchored noninternalrErDr)AssertionErrorrIrJr7 parametersrFr#)selfrIrJr7rOrFr#r4r4r5__init__s  zAdapterSpecification.__init__cCs"d|jj|j|j|j|j|jS)NzR{}(name={!r}, restriction={!r}, sequence={!r}, parameters={!r}, adapter_type={!r}))format __class____name__rIrJr7rOrFrPr4r4r5__repr__szAdapterSpecification.__repr__cCs<|j|jko:|j|jko:|j|jko:|j|jko:|j|jkSN)rIrJr7rOrF)rPotherr4r4r5__eq__s     zAdapterSpecification.__eq__)rr8cCs<|dd}d}t|dkr,|\}}|}|}||fS)z_ Parse an adapter specification given as 'name=adapt' into 'name' and 'adapt'. r%r N)r(lenr*)rr0rIr4r4r5 _extract_names  z"AdapterSpecification._extract_name)rrFr8c Csz|dkrtd|d\}}}||\}}|}t|}t|}|dd}t|ddkrv||d|i|dSz||\}} }Wntk rtd dYnX|d kr| rtd |d kr|rtd |dk r|} n| } |dkr| dk rtdd|kr| dkrtd| ddt|krFtd|dd||rh|d ks`| dk rhtd||| ||||S)af Parse an adapter specification for a non-linked adapter (without '...') and return an AdapterSpecification instance. Allow: 'back' and ADAPTER 'back' and ADAPTERX 'back' and ADAPTER$ 'front' and ADAPTER 'front' and XADAPTER 'front' and ^ADAPTER 'anywhere' and ADAPTER rM,adapter_type must be front, back or anywherer$r#FXrNzYou cannot use multiple placement restrictions for an adapter at the same time. Choose one of ^ADAPTER, ADAPTER$, XADAPTER or ADAPTERXrEzIAllowed placement restrictions for a 5' adapter are XADAPTER and ^ADAPTERrDzIAllowed placement restrictions for a 3' adapter are ADAPTERX and ADAPTER$rzPPlacement restrictions (with X, ^, $) not supported for 'anywhere' (-b) adaptersrrKz~Setting 'min_overlap=' (or 'o=') for anchored adapters is not possible because anchored adapters always need to match in full.z min_overlap=z exceeds length of adapter z1'rightmost' only allowed with regular 5' adapters) r-r+r[r*r6rApoprZ_parse_restrictionsget) clsrrFmiddleparameters_specrIrOr#front_restrictionback_restrictionrJr4r4r5parsesX   zAdapterSpecification.parsecCsd}|drd}|dd}|drJ|dk rt| rd |d|d} t| j dd| nW5d} ~ XYnXdS)zO Parse an adapter specification and yield appropriate Adapter classes. zfile:z^file:zfile$:r'rgr Nrhr$)rIzA file exists named 'zf'. To use the sequences in that file as adapter sequences, write 'file:' before the path, as in 'file:z'.r ) rir+copyupdater6read_adapters_fasta make_adapterrrexistsargs) rrFrxZanchoring_prefixZanchoring_suffixpath_rcrOrIrZ extra_messager4r4r5rzs@      rz)rrFrxrIr8cCsl|dkrtd|d\}}}|dkr@|r@|r@t|||||S|dkrZt|||\}}n|}t||||S)a Parse an adapter specification not using ``file:`` notation and return an object of an appropriate Adapter class. name -- Adapter name if not included as part of the spec. (If spec is 'name=ADAPTER', name will be 'name'.) adapter_type -- describes which commandline parameter was used (``-a`` is 'back', ``-b`` is 'anywhere', and ``-g`` is 'front'). search_parameters -- dict with default search parameters rMr\z...)r-r+_make_linked_adapterrG_make_not_linked_adapter)rrFrxrIrBrbrCr4r4r5rsr)rBrCrIrFrxr8cCs|dkrtdt|d}t|d}|dkr6|j}|jdk }|jdk }|} | |j|} | |j|dkrd} d} n|} |} | d| } | d| } | |j fdd i| } | |j fdd i| }t | || | |d S) z6Return a linked adapter from two specification stringsrz*'anywhere' (-b) adapters may not be linkedrErDNTrrIZ linked_frontZ linked_back) front_adapter back_adapterfront_required back_requiredrI) r-rHrfrIrJrrrOr^rpr7r)rBrCrIrFrxZ front_specZ back_specZfront_anchoredZ back_anchoredZfront_parametersZback_parametersrrrrr4r4r5rsP         r)rrIrFrxr8cCst||}|}|jddr:|tttfkr:d|jd<d|jkrLtd| }| |j|f|j |dkrv|j n|d|S)NrFTZforce_anywhererzA'required' and 'optional' can only be used within linked adapters)r7rI) rHrfrprOr^rrrr-rrr7rI)rrIrFrxZaspecrprOr4r4r5r s(    rc csZt|dddB}t|}|D].}|jdd}|r:|dnd}||jfVqW5QRXdS)z2 Read adapter sequences from a FASTA file rbr)modeZthreadsNr )r r rIr(r7)rfZfastarecordheaderrIr4r4r5r&s r)N)*rsr=Zloggingpathlibrtypingrrrrrrr r Z dnaio.readersr r{r rrrrrrrrrrZ getLoggerrTZloggerrtr6rArGrHr|rzrrrrr4r4r4r5sX $  4 =(Y    2    6