o RŀgC@s~dZddlmZddlmZddlmZddlmZddlmZddl m Z Gd d d eZ e d kr=dd l mZed Sd S)z3Bio.SearchIO object to model a single database hit.)chain)allitems) getattr_str)optionalcascade)_BaseSearchObject)HSPc@seZdZdZdZd>ddZddZd d Zd d Zd dZ ddZ ddZ ddZ ddZ ddZddZedddZeddd Zed!d"d#Zed$d%d&Zed'd(Zed)d*Zed+d,Zed-d.Zd/d0Zd?d1d2Zd3d4Zd?d5d6Zd@d8d9ZdAd>> from Bio import SearchIO >>> qresult = next(SearchIO.parse('Blast/mirna.xml', 'blast-xml')) >>> hit = qresult[3] >>> print(hit) Query: 33211 mir_1 Hit: gi|301171322|ref|NR_035857.1| (86) Pan troglodytes microRNA mir-520c (MIR520C), microRNA HSPs: ---- -------- --------- ------ --------------- --------------------- # E-value Bit score Span Query range Hit range ---- -------- --------- ------ --------------- --------------------- 0 8.9e-20 100.47 60 [1:61] [13:73] 1 3.3e-06 55.39 60 [0:60] [13:73] You can invoke ``len`` on a Hit object to see how many HSP objects it contains:: >>> len(hit) 2 Hit objects behave very similar to Python lists. You can retrieve the HSP object inside a Hit using the HSP's integer index. Hit objects can also be sliced, which will return a new Hit objects containing only the sliced HSPs:: # HSP items inside the Hit can be retrieved using its integer index >>> hit[0] HSP(hit_id='gi|301171322|ref|NR_035857.1|', query_id='33211', 1 fragments) # slicing returns a new Hit >>> hit Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 2 hsps) >>> hit[:1] Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 1 hsps) >>> print(hit[1:]) Query: 33211 mir_1 Hit: gi|301171322|ref|NR_035857.1| (86) Pan troglodytes microRNA mir-520c (MIR520C), microRNA HSPs: ---- -------- --------- ------ --------------- --------------------- # E-value Bit score Span Query range Hit range ---- -------- --------- ------ --------------- --------------------- 0 3.3e-06 55.39 60 [0:60] [13:73] Hit objects provide ``filter`` and ``map`` methods, which are analogous to Python's built-in ``filter`` and ``map`` except that they return a new Hit object instead of a list. Here is an example of using ``filter`` to select for HSPs whose e-value is less than 1e-10:: >>> evalue_filter = lambda hsp: hsp.evalue < 1e-10 >>> filtered_hit = hit.filter(evalue_filter) >>> len(hit) 2 >>> len(filtered_hit) 1 >>> print(filtered_hit) Query: 33211 mir_1 Hit: gi|301171322|ref|NR_035857.1| (86) Pan troglodytes microRNA mir-520c (MIR520C), microRNA HSPs: ---- -------- --------- ------ --------------- --------------------- # E-value Bit score Span Query range Hit range ---- -------- --------- ------ --------------- --------------------- 0 8.9e-20 100.47 60 [1:61] [13:73] There are also other methods which are counterparts of Python lists' methods with the same names: ``append``, ``index``, ``pop``, and ``sort``. Consult their respective documentations for more details and examples of their usage. _itemsNcs||_g|_||_d|_g|_d|_i|_g|_dD]tfdd|Ddkr/t dqg|_ |D] }| || |q5dS)aInitialize a Hit object. :param hsps: HSP objects contained in the Hit object :type hsps: iterable yielding HSP :param id: hit ID :type id: string :param query_id: query ID :type query_id: string If multiple HSP objects are used for initialization, they must all have the same ``query_id``, ``query_description``, ``hit_id``, and ``hit_description`` properties. N)query_idquery_descriptionhit_idhit_descriptioncsh|]}t|qSr )getattr).0hspattrr K/var/www/html/myenv/lib/python3.10/site-packages/Bio/SearchIO/_model/hit.py szHit.__init__..rz6Hit object can not contain HSPs with more than one %s.) _id_id_alt _query_id _description_description_alt_query_description attributesdbxrefslen ValueErrorr _validate_hspappend)selfhspsidr rr rr__init__gs&  z Hit.__init__cCs d|jd|jdt|dS)z+Return string representation of Hit object.zHit(id=z , query_id=, z hsps))r&r r r$r r r__repr__s z Hit.__repr__cC t|jS)zIterate over hsps.)iterr%r)r r r__iter__ z Hit.__iter__cCr+)zReturn number of hsps.)r r%r)r r r__len__r.z Hit.__len__cCr+)zReturn True if there are hsps.)boolr%r)r r r__bool__r.z Hit.__bool__cCs ||jvS)zReturn True if hsp in items.r r$rr r r __contains__r.zHit.__contains__c Cs@g}d|j}|||jr)d|j}t|dkr"|dddn|}||d|j}z|j}Wn ty<Ynw|d|7}|||jred|j}t|dkr^|dddn|}||t|j D]\}}|d |d |ql|j r|d d |j |j s|d n|ddd}||d||dt|j D]k\} } t| ddd} t| ddd} t| d} t| d}t| d}d|d|d}t|dkr|dddn|}t| d }t| d!}d|d|d}t|d"kr |dd#dn|}||| | | | ||fqd$ |S)%z2Return a human readable summary of the Hit object.z Query: %sz %sPNMz...z Hit: %sz (%i) z: zDatabase cross-references: r(z HSPs: ?z HSPs: %s %s %s %s %s %s)z----z--------z ---------z------z---------------z---------------------z%11s %8s %9s %6s %15s %21s)#zE-valuez Bit scoreSpanz Query rangez Hit rangeevaluez%.2g)fmtbitscorez%.2faln_span query_start query_end[:] z~] hit_starthit_end )r r#rr r&seq_lenAttributeError descriptionsortedritemsrjoinr% enumerater)r$linesqid_linelinehid_linerIkeyvaluepatternidxrr9r;r<r=r> query_rangerDrE hit_ranger r r__str__sp                   " z Hit.__str__cCs2t|tr||j|}|||S|j|S)z)Return the HSP object at the given index.) isinstanceslice __class__r%_transfer_attrsr )r$rWobjr r r __getitem__s   zHit.__getitem__cCs<t|ttfr|D]}||q n||||j|<dS)zAssign hsps to index idx.N)r[listtupler"r )r$rWr%rr r r __setitem__s   zHit.__setitem__cCs |j|=dS)zDelete item of index idx.Nr )r$rWr r r __delitem__s zHit.__delitem__cCst|ts td|jrw|jdur"|j|jkr!td|j|jfn|j|_|jdur<|j|jkr;td|j|jfn|j|_|j durV|j |j krUtd|j |j fn|j |_ |j durq|j |j krotd|j |j fdS|j |_ dSdS)zValidate an HSP object (PRIVATE). Valid HSP objects have the same hit_id as the Hit object ID and the same query_id as the Hit object's query_id. z)Hit objects can only contain HSP objects.Nz.Expected HSP with hit ID %r, found %r instead.z7Expected HSP with hit description %r, found %r instead.z0Expected HSP with query ID %r, found %r instead.z9Expected HSP with query description %r, found %r instead.) r[r TypeErrorr r&rr!rKrr rr2r r rr" sP              zHit._validate_hsprrzHit descriptionrrz.Description of the query that produced the hitrrzHit ID string.rr z,ID string of the query that produced the hitz HSP objects contained in the Hit)doccC|jg|jS)zAlternative ID(s) of the Hit.)r&rr)r r rid_allKz Hit.id_allcCrg)z$Alternative descriptions of the Hit.)rKrr)r r rdescription_allPrizHit.description_allcCstt|jS)z4Access the HSPFragment objects contained in the Hit.)rarr r)r r r fragmentsUriz Hit.fragmentscCs|||j|dS)a0Add a HSP object to the end of Hit. Parameters hsp -- HSP object to append. Any HSP object appended must have the same ``hit_id`` property as the Hit object's ``id`` property and the same ``query_id`` property as the Hit object's ``query_id`` property. N)r"r r#r2r r rr#[s z Hit.appendcCs0tt||j}|r||}|||SdS)aeCreate new Hit object whose HSP objects pass the filter function. :param func: function for filtering :type func: callable, accepts HSP, returns bool ``filter`` is analogous to Python's built-in ``filter`` function, except that instead of returning a list it returns a ``Hit`` object. Here is an example of using ``filter`` to select for HSPs having bitscores bigger than 60:: >>> from Bio import SearchIO >>> qresult = next(SearchIO.parse('Blast/mirna.xml', 'blast-xml')) >>> hit = qresult[3] >>> evalue_filter = lambda hsp: hsp.bitscore > 60 >>> filtered_hit = hit.filter(evalue_filter) >>> len(hit) 2 >>> len(filtered_hit) 1 >>> print(filtered_hit) Query: 33211 mir_1 Hit: gi|301171322|ref|NR_035857.1| (86) Pan troglodytes microRNA mir-520c (MIR520C), microRNA HSPs: ---- -------- --------- ------ --------------- --------------------- # E-value Bit score Span Query range Hit range ---- -------- --------- ------ --------------- --------------------- 0 8.9e-20 100.47 60 [1:61] [13:73] N)rafilterr%r]r^r$funcr%r_r r rrlis   z Hit.filtercC |j|S)z{Return the index of a given HSP object, zero-based. :param hsp: object to look up :type hsp: HSP )r indexr2r r rrp z Hit.indexcsTdurfdd|jddD}n|jdd}|r(||}|||SdS)aKCreate new Hit object, mapping the given function to its HSPs. :param func: function for mapping :type func: callable, accepts HSP, returns HSP ``map`` is analogous to Python's built-in ``map`` function. It is applied to all HSPs contained in the Hit object and returns a new Hit object. Ncsg|]}|qSr r )rxrnr r szHit.map..)r%r]r^rmr rsrmaps   zHit.mapcCro)zRemove and returns the HSP object at the specified index. :param index: index of HSP object to pop :type index: int )r pop)r$rpr r rrwrqzHit.popFTcCsL|r |jj||ddS|jdd}|j||d||}|||S)a&Sort the HSP objects. :param key: sorting function :type key: callable, accepts HSP, returns key for sorting :param reverse: whether to reverse sorting results or no :type reverse: bool :param in_place: whether to do in-place sorting or no :type in_place: bool ``sort`` defaults to sorting in-place, to mimic Python's ``list.sort`` method. If you set the ``in_place`` argument to False, it will treat return a new, sorted Hit object and keep the initial one unsorted )rTreverseN)r sortr%r]r^)r$rTrxin_placer%r_r r rrys  zHit.sort)r NN)N)rv)NFT)!__name__ __module__ __qualname____doc___NON_STICKY_ATTRSr'r*r-r/r1r3rZr`rcrdr"rrKrr&r rr%propertyrhrjrkr#rlrprurwryr r r rr sNR +M  0      %  r __main__) run_doctestN)r~ itertoolsrBio.SearchIO._utilsrrr_baserrrr r{ Bio._utilsrr r r rs      >