o Rŀg|80@sdZddlZddlZddlmZddlmZddlmZddlm Z ddlm Z ddlm Z dd lm Z dd lm Z dd lmZdd lmZdZd ZdZeeddddddddddddddddddddddddddddddddddddddddddddddf/ddZde_ddZdS)aMCode to invoke the NCBI BLAST server over the internet. This module provides code to work with the WWW version of BLAST provided by the 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)StringIO) urlencode) build_opener)HTTPBasicAuthHandler)HTTPPasswordMgrWithDefaultRealm)install_opener)Request)urlopen)BiopythonWarning)function_with_previous biopythonz(https://blast.ncbi.nlm.nih.gov/Blast.cgiz(none)g$@2iXMLblastc2ECs2gd}2||2vrtd|dd|2| r3|dkr3d} t|dkr3d} d }d }d} d}td tid |d |d|d|d|d|d| d| d| d| d| d|d|d|d|-d|d|id|d|d|d |d!|d"|d#|d$|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|Ad?krjqd@|Avrt t|AS|Ad@}B|AdA|B}C|A|Btd@|C}D|DdBkr t|ASq)Ca 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 "HTML", "Text", "ASN.1", or "XML". Def. "XML". - 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 )blastnblastpblastxtblastntblastxzProgram specified is z. Expected one of z, rNiz"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||qSN.0keyvaluerArAE/var/www/html/myenv/lib/python3.10/site-packages/Bio/Blast/NCBIWWW.py zqblast..z User-AgentBiopythonClientGet) ALIGNMENTSALIGNMENT_VIEW DESCRIPTIONSENTREZ_LINKS_NEW_WINDOW EXPECT_LOW EXPECT_HIGHFORMAT_ENTREZ_QUERY FORMAT_OBJECT FORMAT_TYPENCBI_GIRID RESULTS_FILEr4 SHOW_OVERVIEWr<cSr?r@rArBrArArFrGrHTr<iXzBLAST request z9 is taking longer than 10 minutes, consider re-issuing itz zStatus= READY) ValueErrorjoinlenwarningswarnr r add_passwordrrrNCBI_BLAST_URLupdater=r>itemsrencoderr _parse_qblast_ref_pagetimeqblastprevioussleepreaddecodeindexstripupperr)Eprogramdatabasesequenceurl_base auto_formatcomposition_based_statisticsdb_genetic_code endpoints entrez_queryexpectfiltergapcosts genetic_code hitlist_sizei_threshlayout lcase_mask matrix_name nucl_penalty nucl_rewardother_advanced perc_ident phi_pattern query_filequery_believe_defline query_fromquery_to searchsp_effservice thresholdungapped_alignment word_size short_query alignmentsalignment_view descriptionsentrez_links_new_window expect_low expect_highformat_entrez_query format_object format_typencbi_gi results_file show_overview megablast template_typetemplate_lengthusernamepasswordprograms parameters password_mgrhandleropenermessagerequesthandleridrtoedelay start_timecurrentwaitelapsedresultsijstatusrArArFrh,s0_         !"#$%)             rhcCs|}|d}|dkrd}n|d|}||td|}|d}|dkr0d}n|d|}||td|}|s|s|d}|dkrt||tdd}|ddd ddd }|rttd ||d }|dkr||td d}|d dd ddd }|rtd ||d }|dkr||dddd ddd }td |td|std|d|std|dz|t|fWStytd|dw)zExtract a tuple of RID, RTOE from the 'please wait' page (PRIVATE). The NCBI FAQ pages use TOE for 'Time of Execution', so RTOE is probably 'Request Time of Execution' and RID would be 'Request Identifier'. zRID =NrZzRTOE =z
z
rrzError message from NCBI: z

z

z Message ID#rbrhrirfrArArArFs