o Rŀg0@sdZddlZddlZddlZddlZddlmZddlmZddl m Z ddl m Z ddl m Z ddl m Z dd l mZdd l mZdd lmZddlZdd lmZdd lmZddlmZddlmZddlmZddlmZdZdZdZ dZ!Gddde"Z#Gddde"Z$GdddeZ%GdddeZ&Gddde'Z(Gdd d eZ)d!d"Z*d#d$Z+d3d&d'Z,ee ddddd(d)dddd*dddddddddddddddddddd+dd+dddddd%ddddddd,df/d-d.Z-de-_.d/d0Z/e0d1krdd2lm1Z1e1dSdS)4aCode to parse and store BLAST XML output, and to invoke the NCBI BLAST web server. This module provides code to parse and store BLAST XML output, following its definition in the associated BLAST XML DTD file: https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd This module also provides code to invoke the BLAST web server provided by NCBI. https://blast.ncbi.nlm.nih.gov/ Variables: - email Set the Blast email parameter (default is None). - tool Set the Blast tool parameter (default is ``biopython``). N)UserList) urlencode) build_opener)HTTPBasicAuthHandler)HTTPPasswordMgrWithDefaultRealm)install_opener)Request)urlopen)expat)BiopythonWarning)StreamModeError)function_with_previous) Alignment) Alignments)_writers biopythonz(https://blast.ncbi.nlm.nih.gov/Blast.cgiic@ eZdZdZddZddZdS) NotXMLErrorzFailed to parse file as XML.cC ||_dSzInitialize the class.NmsgselfmessagerF/var/www/html/myenv/lib/python3.10/site-packages/Bio/Blast/__init__.py__init__< zNotXMLError.__init__cC d|jS))Return a string summary of the exception.zZFailed to parse the XML data (%s). Please make sure that the input data are in XML format.rrrrr__str__@zNotXMLError.__str__N__name__ __module__ __qualname____doc__rr"rrrrr9 rc@r)CorruptedXMLErrorzCorrupted XML.cCrrrrrrrrKrzCorruptedXMLError.__init__cCr)r zZFailed to parse the XML data (%s). Please make sure that the input data are not corrupted.rr!rrrr"Or#zCorruptedXMLError.__str__Nr$rrrrr*Hr)r*cs(eZdZdZddZfddZZS)HSPagStores an alignment of one query sequence against a target sequence. An HSP (High-scoring Segment Pair) stores the alignment of one query sequence segment against one target (hit) sequence segment. The ``Bio.Blast.HSP`` class inherits from the ``Bio.Align.Alignment`` class. In addition to the ``target`` and ``query`` attributes of a ``Bio.Align.Alignment``, a ``Bio.Blast.HSP`` object has the following attributes: - score: score of HSP; - annotations: a dictionary that may contain the following keys: - 'bit score': score (in bits) of HSP (float); - 'evalue': e-value of HSP (float); - 'identity': number of identities in HSP (integer); - 'positive': number of positives in HSP (integer); - 'gaps': number of gaps in HSP (integer); - 'midline': formatting middle line. A ``Bio.Blast.HSP`` object behaves the same as a `Bio.Align.Alignment`` object and can be used as such. However, when printing a ``Bio.Blast.HSP`` object, the BLAST e-value and bit score are included in the output (in addition to the alignment itself). See the documentation of ``Bio.Blast.Record`` for a more detailed explanation of how the information in BLAST records is stored in Biopython. c Cs8|j}|j}|j\}}d|jd|jd|d|d S)Nz)querytargetshapeid)rr.r/nmrrr__repr__us "z HSP.__repr__cst}|j}|j}|jd|jdkrdnd}|jd|jdkr%dnd}d}tj|jd||d }tj|jd||d }|jd } |jd } |j } t |jd } t t | d } g}|jd}td|| }d|| |f}|||jd}|durtd|| }d|| |f}||z|jd}Wn tyYnwtd|| }d|| |f}||d|}d|jt||||jt|||| | | ||f S)Nrr6PlusMinusrrrr8z Pwidthinitial_indentsubsequent_indentevalue bit scorer6ridentitygY@zIdentities:%d/%d(%d%%)positivezPositives:%d/%d(%d%%)gapszGaps:%d.%d(%d%%)z, zpQuery : %s Length: %d Strand: %s %s Target: %s Length: %d Strand: %s %s Score:%d bits(%d), Expect:%.1g, %s %s )superr"r.r/ coordinatestextwrapfill description annotationsscorenpdiffsumabsmaxroundappendgetKeyErrorjoinr1len)ralignment_textr.r/ query_strand target_strandindentquery_descriptiontarget_descriptionrBbitscorerMstepsaln_spantermsrDidentity_percentage identity_textrEpositive_percentage positive_textrFgaps_percentage gaps_text counts_line __class__rrr"{s           z HSP.__str__)r%r&r'r(r4r" __classcell__rrrjrr+Wsr+cs0eZdZdZfddZddZddZZS)HitaStores a single BLAST hit of one single query against one target. The ``Bio.Blast.Hit`` class inherits from the ``Bio.Align.Alignments`` class, which is a subclass of a Python list. The ``Bio.Blast.Hit`` class stores ``Bio.Blast.HSP`` objwcts, which inherit from ``Bio.Align.Alignment``. A ``Bio.Blast.Hit`` object is therefore effectively a list of ``Bio.Align.Alignment`` objects. Most hits consist of only 1 or a few Alignment objects. Each ``Bio.Blast.Hit`` object has a ``target`` attribute containing the following information: - target.id: seqId of subject; - target.description: definition line of subject; - target.name: accession of subject; - len(target.seq): sequence length of subject. See the documentation of ``Bio.Blast.Record`` for a more detailed explanation of the information stored in the alignments contained in the ``Bio.Blast.Hit`` object. csLzt|}Wn tytddwt|tr$t|}|j|_|S|S)Nindex out of range)rG __getitem__ IndexError isinstanceslicermr/)rkeyvaluehitrjrrros   zHit.__getitem__c Csv|j}z|d}Wntyd|jdYSw|j}t|}|dkr(d}nd}d|jd|jd|d |d S) Nrzr6r+HSPsr,r- >)r/rpr1r.rX)rr/ alignmentr.nhspsunitrrrr4s  "z Hit.__repr__c Csg}|dj}d|j}||d}tj|jd||d}|||j}d|jt|f}||tj|jd||d}|||ddd }||d ||dt |D]w\} } t | j d d } t | j d d} t | jd} tt| d}| jd}| jd}d|d|d}t|dkr|dddn|}| jd}| jd}d|d|d}t|dkr|dddn|}||| | | |||fq]d|S)z2Return a human readable summary of the Hit object.rz Query: %sz r=r>z Hit: %s (length=%i)z HSPs: %s %s %s %s %s %s)----z--------z ---------z------z---------------z---------------------z%11s %8s %9s %6s %15s %21s)#zE-valuez Bit scoreSpanz Query rangez Hit rangerBz.2grCz.2fr6r5r7[:]N z~]r;r< )r.r1rTrIwraprKextendr/rX enumerateformatrLrNrOrHrPrQrRrW)rlinesr.qid_liner\description_linesr/hid_linepatternidxhsprBr_r`ra query_start query_end query_range hit_starthit_end hit_rangerrrr"sd            z Hit.__str__)r%r&r'r(ror4r"rlrrrjrrms   rmcsPeZdZdZddZddZddZfdd Zd d Zd d Z ddZ Z S)RecordaStores the BLAST results for a single query. A ``Bio.Blast.Record`` object is a list of ``Bio.Blast.Hit`` objects, each corresponding to one hit for the query in the BLAST output. The ``Bio.Blast.Record`` object may have the following attributes: - query: A ``SeqRecord`` object which may contain some or all of the following information: - query.id: SeqId of query; - query.description: Definition line of query; - len(query.seq): Length of the query sequence. - stat: A dictionary with summary statistics of the BLAST run. It may contain the following keys: - 'db-num': number of sequences in BLAST db (integer); - 'db-len': length of BLAST db (integer); - 'hsp-len': effective HSP length (integer); - 'eff-space': effective search space (float); - 'kappa': Karlin-Altschul parameter K (float); - 'lambda': Karlin-Altschul parameter Lambda (float); - 'entropy': Karlin-Altschul parameter H (float). - message: Some (error?) information. Each ``Bio.Blast.Hit`` object has a ``target`` attribute containing the following information: - target.id: seqId of subject; - target.description: definition line of subject; - target.name: accession of subject; - len(target.seq): sequence length of subject. The ``Bio.Blast.Hit`` class inherits from the ``Bio.Align.Alignments`` class, which inherits from a Python list. In this list, the ``Bio.Blast.Hit`` object stores ``Bio.Blast.HSP`` objects, which inherit from the ``Bio.Align.Alignment`` class. A ``Bio.Blast.Hit`` object is therefore effectively a list of alignment objects. Each HSP in a ``Bio.Blast.Hit`` object has the attributes ``target`` and ``query`` attributes, as usual for of a ``Bio.Align.Alignment`` object storing a pairwise alignment, pointing to a ``SeqRecord`` object representing the target and query, respectively. For translated BLAST searches, the ``features`` attribute of the target or query may contain a ``SeqFeature`` of type CDS that stores the amino acid sequence region. The ``qualifiers`` attribute of such a feature is a dictionary with a single key 'coded_by'; the corresponding value specifies the nucleotide sequence region, in a GenBank-style string with 1-based coordinates, that encodes the amino acid sequence. Each ``Bio.Blast.HSP`` object has the following additional attributes: - score: score of HSP; - annotations: a dictionary that may contain the following keys: - 'bit score': score (in bits) of HSP (float); - 'evalue': e-value of HSP (float); - 'identity': number of identities in HSP (integer); - 'positive': number of positives in HSP (integer); - 'gaps': number of gaps in HSP (integer); - 'midline': formatting middle line. >>> from Bio import Blast >>> record = Blast.read("Blast/xml_2212L_blastx_001.xml") >>> record.query SeqRecord(seq=Seq(None, length=556), id='gi|1347369|gb|G25137.1|G25137', name='', description='human STS EST48004, sequence tagged site', dbxrefs=[]) >>> record.stat {'db-num': 2934173, 'db-len': 1011751523, 'hsp-len': 0, 'eff-space': 0, 'kappa': 0.041, 'lambda': 0.267, 'entropy': 0.14} >>> len(record) 78 >>> hit = record[0] >>> type(hit) >>> from Bio.Align import Alignments >>> isinstance(hit, Alignments) True >>> hit.target SeqRecord(seq=Seq(None, length=319), id='gi|12654095|gb|AAH00859.1|', name='AAH00859', description='Unknown (protein for IMAGE:3459481) [Homo sapiens]', dbxrefs=[]) Most hits consist of only 1 or a few Alignment objects: >>> len(hit) 1 >>> alignment = hit[0] >>> type(alignment) >>> alignment.score 630.0 >>> alignment.annotations {'bit score': 247.284, 'evalue': 1.69599e-64, 'identity': 122, 'positive': 123, 'gaps': 0, 'midline': 'DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+'} Target and query information are stored in the respective attributes of the alignment: >>> alignment.target SeqRecord(seq=Seq({155: 'DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDP...TKK'}, length=319), id='gi|12654095|gb|AAH00859.1|', name='AAH00859', description='Unknown (protein for IMAGE:3459481) [Homo sapiens]', dbxrefs=[]) >>> alignment.query SeqRecord(seq=Seq('DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDP...XKE'), id='gi|1347369|gb|G25137.1|G25137', name='', description='human STS EST48004, sequence tagged site', dbxrefs=[]) This was a BLASTX run, so the query sequence was translated: >>> len(alignment.target.features) 0 >>> len(alignment.query.features) 1 >>> feature = alignment.query.features[0] >>> feature SeqFeature(SimpleLocation(ExactPosition(0), ExactPosition(133)), type='CDS', qualifiers=...) >>> feature.qualifiers {'coded_by': 'gi|1347369|gb|G25137.1|G25137:1..399'} i.e., nucleotides 0:399 (in zero-based coordinates) encode the amino acids of the query in the alignment. For an alignment against the reverse strand, the location in the qualifier is shown as in this example: >>> record[72][0].query.features[0].qualifiers {'coded_by': 'complement(gi|1347369|gb|G25137.1|G25137:345..530)'} cCs d|_dS)zInitialize the Record object.N)r.r!rrrrrzRecord.__init__cCsj|j}z|j}Wn tyd}Ynwt|}|dkr"d|dS|dkr,d|dSd|d|dS) Nunknownrzr-z hits>)r.r1AttributeErrorrX)rr.query_idnhitsrrrr4s    zRecord.__repr__c Csg}z|j}Wn tyYn w|d|z|j}Wn ty'Yn w|d||jdurU|d|jjt|jfd}tj|jj d||d}| |t|dkra|dn|d d d }||d ||d t |D]i\}}t|} |d krd|j j|j j f} t| dkr| ddd} |||t|| fq||t|dkrd|j j|j j f} t| dkr| ddd} |||t|| fq||d kr|ddq|d |S)Nz Program: z db: z Query: %s (length=%d)z r=r>rz Hits: No hits foundz Hits: %s %s %s)r}z-----z:----------------------------------------------------------z %13s %5s %s)r~z# HSPzID + descriptionz%s %s:7z...z%14sz~~~r)versionrrTdbr.r1rXrIrrKrrr/rW) rrrrr\rrrrur2rrrrr"sZ           zRecord.__str__c szt|}Wn1tytddty9t|ts$tdd|D]}|jj|kr4|YSq&t|wt|t ryt }| |z|j }Wn t yUYnw||_ d}|D]}zt||}Wn t yoYq]wt|||q]|S|S)Nrnz%key must be an integer, slice, or strsourceprogramr referencerparammbstat)rGrorp TypeErrorrqstrr/r1rVrrrrr.rgetattrsetattr)rrsrtrurecordr.keysrjrrros@             zRecord.__getitem__cCsdd|DS)z+Return a list of the target.id of each hit.cSsg|]}|jjqSrr/r1).0rurrr *szRecord.keys..rr!rrrr(sz Record.keyscCs |D] }|jj|kr dSqdS)NTFr)rrsrurrr __contains__,s  zRecord.__contains__cCs6t|D]\}}|jj|kr|Sqtd|d)zHReturn the index of the hit for which the target.id is equal to the key.'z ' not found)rr/r1 ValueError)rrsirurrrindex2s  z Record.index) r%r&r'r(rr4r"rorrrrlrrrjrrBsv 0-rcsleZdZdZddZddZddZdd Zd d Zd d Z fddZ e ddZ ddZ ddZZS)RecordsuStores the BLAST results of a single BLAST run. A ``Bio.Blast.Records`` object is an iterator. Iterating over it returns returns ``Bio.Blast.Record`` objects, each of which corresponds to one BLAST query. Common attributes of a ``Bio.Blast.Records`` object are - source: The input data from which the ``Bio.Blast.Records`` object was constructed. - program: The specific BLAST program that was used (e.g., 'blastn'). - version: The version of the BLAST program (e.g., 'BLASTN 2.2.27+'). - reference: The literature reference to the BLAST publication. - db: The BLAST database against which the query was run (e.g., 'nr'). - query: A ``SeqRecord`` object which may contain some or all of the following information: - query.id: SeqId of the query; - query.description: Definition line of the query; - query.seq: The query sequence. The query sequence. The query sequence. - param: A dictionary with the parameters used for the BLAST run. You may find the following keys in this dictionary: - 'matrix': the scoring matrix used in the BLAST run (e.g., 'BLOSUM62') (string); - 'expect': threshold on the expected number of chance matches (float); - 'include': e-value threshold for inclusion in multipass model in psiblast (float); - 'sc-match': score for matching nucleotides (integer); - 'sc-mismatch': score for mismatched nucleotides (integer); - 'gap-open': gap opening cost (integer); - 'gap-extend': gap extension cost (integer); - 'filter': filtering options applied in the BLAST run (string); - 'pattern': PHI-BLAST pattern (string); - 'entrez-query': Limit of request to Entrez query (string). - mbstat: A dictionary with Mega BLAST search statistics. As this information is stored near the end of the XML file, this attribute can only be accessed after the file has been read completely (by iterating over the records until a ``StopIteration`` is issued. This dictionary can contain the same keys as the dictionary stored under the ``stat`` attribute of a ``Record`` object. >>> from Bio import Blast >>> path = "Blast/xml_2218_blastp_002.xml" In a script, you would use a ``with`` block, as in >>> with Blast.parse(path) as records: ... print(records.source) ... Blast/xml_2218_blastp_002.xml to ensure that the file is closed at the end of the block. Here, we will simply do >>> records = Blast.parse("Blast/xml_2218_blastp_002.xml") so we can see the output of each command right away. >>> type(records) >>> records.source 'Blast/xml_2218_blastp_002.xml' >>> records.program 'blastp' >>> records.version 'BLASTP 2.2.18+' >>> records.reference 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.' >>> records.db 'gpipe/9606/Previous/protein' >>> records.param {'matrix': 'BLOSUM62', 'expect': 0.01, 'gap-open': 11, 'gap-extend': 1, 'filter': 'm L; R -d repeat/repeat_9606;'} Iterating over the records returns Bio.Blast.Record objects: >>> record = next(records) >>> type(record) >>> record.query.id 'gi|585505|sp|Q08386|MOPB_RHOCA' >>> record = next(records) >>> type(record) >>> record.query.id 'gi|129628|sp|P07175.1|PARA_AGRTU' >>> record = next(records) # doctest:+ELLIPSIS Traceback (most recent call last): ... StopIteration You can also use the records as a list, for example by extracting a record by index, or by calling ``len`` or ``print`` on the records. The parser will then automatically iterate over the records and store them: >>> records = Blast.parse("Blast/wnts.xml") >>> record = records[3] # this causes all records to be read in and stored >>> record.query.id 'Query_4' >>> len(records) 5 After the records have been read in, you can still iterate over them: >>> for i, record in enumerate(records): ... print(i, record.query.id) ... 0 Query_1 1 Query_2 2 Query_3 3 Query_4 4 Query_5 cCst|tr||_d|_d|_dS||_zt|d}Wnty1|ddkr-t dd|}Ynw||_ | g|_d|_dS)zInitialize the Records object.TrNrbz1BLAST output files must be opened in binary mode.F) rqlist_records_loaded_indexropenrreadr _stream _read_header)rrstreamrrrrs*   zRecords.__init__c Csddlm}|j}|j}zhtjdd}||_||}||_ |t }|dkr?z|jWn t y5Yn>wt d|j dz| |d Wntjya}z |jrXt|dt|dd}~wwz|jWn t ypYnwnqWnty||ur|wd|_dS) Nr) XMLHandlerrx)namespace_separatorTr)premature end of XML file (after reading  bytes)F)Bio.Blast._parserrrrr ParserCreate_parserrrBLOCKrrCurrentByteIndexParse ExpatErrorStartElementHandlerr*r_cache Exceptioncloser)rrrrparserhandlerdataerrrrsR            zRecords._read_headercC|SNrr!rrr __enter__zRecords.__enter__cCs:z|j}Wn tyYdSw||jur||`dSr)rrrr)rexc_type exc_value exc_tracebackrrrr__exit__s   zRecords.__exit__cCrrrr!rrr__iter__rzRecords.__iter__c Cs|jdur!z|j|j}Wn tytdw|jd7_|Sz|j}Wn ty0tdw|j}|j} z|j }Wn tyHYn w|jd7_|S| t }|dkro|`|`|j durmt d|jdtz||dWntjy}zt|dd}~wwq8)NTr6rrrF)rrrrp StopIterationrrrrpopleftrrrrrrr rr*)rrcacherrrrrrr__next__sN         zRecords.__next__csFt|}|tdddkr!|jD] \}}|dvr ||j|<q|S)N)rrr)rGrorr__dict__items)rritemrsrtrjrrro,s  zRecords.__getitem__cCs|jdurG|j}|dkr(z|jdWn tjy tdw|d|_|D]}|j |q*|j}||j ur?| |`d|_||_|jS)z)Overrides the data attribute of UserList.FrzQlist-like access after iterating is supported only if the input data is seekable.T) rrrseekioUnsupportedOperationrrrrTrr)rrrrrrrr4s*  z Records.datac Cs&d|jd|jd|jd|jd S)Nz>> from Bio import Blast >>> stream = open("Blast/wnts.xml", "rb") # opened in binary mode >>> records = Blast.parse(stream) >>> for record in records: ... print(record.query.id, record.query.description) ... Query_1 gi|195230749:301-1383 Homo sapiens wingless-type MMTV integration site family member 2 (WNT2), transcript variant 1, mRNA Query_2 gi|325053704:108-1166 Homo sapiens wingless-type MMTV integration site family, member 3A (WNT3A), mRNA Query_3 gi|156630997:105-1160 Homo sapiens wingless-type MMTV integration site family, member 4 (WNT4), mRNA Query_4 gi|371502086:108-1205 Homo sapiens wingless-type MMTV integration site family, member 5A (WNT5A), transcript variant 2, mRNA Query_5 gi|53729353:216-1313 Homo sapiens wingless-type MMTV integration site family, member 6 (WNT6), mRNA >>> stream.close() )r)rrrrparse]src Cst|-}zt|}Wn tytddwzt|tdty)YnwWdn1s4wYdD]}zt||}Wn tyMYq;wt|||q;|S)a*Parse an XML file containing BLAST output for a single query and return it. Internally, this function uses Bio.Blast.parse to obtain an iterator over BLAST records. The function then reads one record from the iterator, ensures that there are no further records, and returns the record it found as a Bio.Blast.Record object. An exception is raised if no records are found, or more than one record is found. The source can be a file stream or the path to an XML file containing the BLAST output. If a file stream, source must be in binary mode. This allows the parser to detect the encoding from the XML file,and to use it to convert any text in the XML to the correct Unicode string. The qblast function in Bio.Blast returns a file stream in binary mode. For files, please use mode "rb" when opening the file, as in >>> from Bio import Blast >>> stream = open("Blast/xml_21500_blastn_001.xml", "rb") # opened in binary mode >>> record = Blast.read(stream) >>> record.query.id 'Query_78041' >>> record.query.description 'G26684.1 human STS STS_D11570, sequence tagged site' >>> len(record) 11 >>> stream.close() Use the Bio.Blast.parse function if you want to read a file containing BLAST output for more than one query. zNo BLAST output found.Nz+BLAST output for more than one query found.r)rnextrrrrr)rrrrsrtrrrr{s,       rXMLc Cs|}|dkr tj}n|dkrtj}ntd|dzt|d}WntyBz|dWn ty=tddw|}Ynw||}z||}W||urV| |S||ura| ww) aWrite BLAST records as an XML file, and return the number of records. Arguments: - records - A ``Bio.Blast.Records`` object. - destination - File or file-like object to write to, or filename as string. The File object must have been opened for writing in binary mode, and must be closed (or flushed) by the caller after this function returns to ensure that all records are written. - fmt - string describing the file format to write (case-insensitive). Currently, only "XML" and "XML2" are accepted. Returns the number of records written (as an integer). rXML2zUnknown format z; expected 'XML' or 'XML2'wbrz/File must be opened in binary mode for writing.N) upperr XMLWriter XML2Writerrrrwriter r)r destinationfmtWriterrwritercountrrrrs:     rz(none)g$@2iblastc2BCsjgd}2||2vrtd|dd|2| r3|dkr3d} t|dkr3d} d }d }d} d}td tid |d |d|d|d|d|d| d| d| d| d| d|d|d|d|-d|d|id|d|d|d |d!|d"|d#|d$|d%|d&|d'|d(|d)| d*|.d+|/d,|d-||d.d/}3|1durt}4|4d||0|1t|4}5t |5}6t |6|t kr|3 t td0d1d2|3D}3t|3}7t||7d3d4i}8t|8}9t|9\}:};|!|"|#|$|%|&|'|(|)|*|:|+||,d5d6}3d7d2|3D}3t|3}7d8}tj|<|>}?|?d:kr-t|?|>|?t_n|>t_|tt||7d3d4i}8t|8}9|9}A|)d?krmd@|Avrmq|AdAruq |)dBkr|AdCsJn)|)d?kr|AdDsJn|)dEvr|AdFsJn |)dGvr|AdHsJ|:|9_|;|9_|9S)Ia BLAST search using NCBI's QBLAST server or a cloud service provider. Supports all parameters of the old qblast API for Put and Get. Please note that NCBI uses the new Common URL API for BLAST searches on the internet (http://ncbi.github.io/blast-cloud/dev/api.html). Thus, some of the parameters used by this function are not (or are no longer) officially supported by NCBI. Although they are still functioning, this may change in the future. The Common URL API (http://ncbi.github.io/blast-cloud/dev/api.html) allows doing BLAST searches on cloud servers. To use this feature, please set ``url_base='http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi'`` and ``format_object='Alignment'``. For more details, please see https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast Some useful parameters: - program blastn, blastp, blastx, tblastn, or tblastx (lower case) - database Which database to search against (e.g. "nr"). - sequence The sequence to search. - ncbi_gi TRUE/FALSE whether to give 'gi' identifier. - descriptions Number of descriptions to show. Def 500. - alignments Number of alignments to show. Def 500. - expect An expect value cutoff. Def 10.0. - matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45). - filter "none" turns off filtering. Default no filtering - format_type "XML" (default), "HTML", "Text", "XML2", "JSON2", or "Tabular". - entrez_query Entrez query to limit Blast search - hitlist_size Number of hits to return. Default 50 - megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only) - short_query TRUE/FALSE whether to adjust the search parameters for a short query sequence. Note that this will override manually set parameters like word size and e value. Turns off when sequence length is > 30 residues. Default: None. - service plain, psi, phi, rpsblast, megablast (lower case) This function does no checking of the validity of the parameters and passes the values to the server as is. More help is available at: https://ncbi.github.io/blast-cloud/dev/api.html The http.client.HTTPResponse object returned by this function has the additional attributes rid and rtoe with the Request ID and Request Time Of Execution for this BLAST search. )blastnblastpblastxtblastntblastxzProgram specified is z. Expected one of z, rNir6z"SHORT_QUERY_ADJUST" is incorrectly implemented (by NCBI) for blastn. We bypass the problem by manually adjusting the search parameters. Thus, results may slightly differ from web page searches. AUTO_FORMATCOMPOSITION_BASED_STATISTICSDATABASEDB_GENETIC_CODE ENDPOINTS ENTREZ_QUERYEXPECTFILTERGAPCOSTS GENETIC_CODE HITLIST_SIZEI_THRESHLAYOUT LCASE_MASK MEGABLAST MATRIX_NAME NUCL_PENALTY NUCL_REWARDOTHER_ADVANCED PERC_IDENT PHI_PATTERNPROGRAMQUERY QUERY_FILEQUERY_BELIEVE_DEFLINE QUERY_FROMQUERY_TO SEARCHSP_EFFSERVICESHORT_QUERY_ADJUST TEMPLATE_TYPETEMPLATE_LENGTH THRESHOLDUNGAPPED_ALIGNMENTPut) WORD_SIZECMD)emailtoolcSi|] \}}|dur||qSrrrrsrtrrr zqblast..z User-AgentBiopythonClientGet) ALIGNMENTSALIGNMENT_VIEW DESCRIPTIONSENTREZ_LINKS_NEW_WINDOW EXPECT_LOW EXPECT_HIGHFORMAT_ENTREZ_QUERY FORMAT_OBJECT FORMAT_TYPENCBI_GIRID RESULTS_FILEr  SHOW_OVERVIEWr(cSr+rrr,rrrr-r.Tr<iXzBLAST request z9 is taking longer than 10 minutes, consider re-issuing itHTMLsNCBI Blast:s