Bio.Blast包¶
子模块¶
- Bio.Blast.Applications模块
NcbiblastpCommandlineNcbiblastpCommandline.__init__()NcbiblastpCommandline.best_hit_overhangNcbiblastpCommandline.best_hit_score_edgeNcbiblastpCommandline.comp_based_statsNcbiblastpCommandline.culling_limitNcbiblastpCommandline.dbNcbiblastpCommandline.db_hard_maskNcbiblastpCommandline.db_soft_maskNcbiblastpCommandline.dbsizeNcbiblastpCommandline.entrez_queryNcbiblastpCommandline.evalueNcbiblastpCommandline.export_search_strategyNcbiblastpCommandline.gapextendNcbiblastpCommandline.gapopenNcbiblastpCommandline.gilistNcbiblastpCommandline.hNcbiblastpCommandline.helpNcbiblastpCommandline.htmlNcbiblastpCommandline.import_search_strategyNcbiblastpCommandline.lcase_maskingNcbiblastpCommandline.line_lengthNcbiblastpCommandline.matrixNcbiblastpCommandline.max_hspsNcbiblastpCommandline.max_hsps_per_subjectNcbiblastpCommandline.max_target_seqsNcbiblastpCommandline.negative_gilistNcbiblastpCommandline.negative_seqidlistNcbiblastpCommandline.num_alignmentsNcbiblastpCommandline.num_descriptionsNcbiblastpCommandline.num_threadsNcbiblastpCommandline.outNcbiblastpCommandline.outfmtNcbiblastpCommandline.parse_deflinesNcbiblastpCommandline.qcov_hsp_percNcbiblastpCommandline.queryNcbiblastpCommandline.query_locNcbiblastpCommandline.remoteNcbiblastpCommandline.searchspNcbiblastpCommandline.segNcbiblastpCommandline.seqidlistNcbiblastpCommandline.show_gisNcbiblastpCommandline.soft_maskingNcbiblastpCommandline.subjectNcbiblastpCommandline.subject_locNcbiblastpCommandline.sum_statisticsNcbiblastpCommandline.sum_statsNcbiblastpCommandline.taskNcbiblastpCommandline.thresholdNcbiblastpCommandline.ungappedNcbiblastpCommandline.use_sw_tbackNcbiblastpCommandline.versionNcbiblastpCommandline.window_sizeNcbiblastpCommandline.word_sizeNcbiblastpCommandline.xdrop_gapNcbiblastpCommandline.xdrop_gap_finalNcbiblastpCommandline.xdrop_ungap
NcbiblastnCommandlineNcbiblastnCommandline.__init__()NcbiblastnCommandline.best_hit_overhangNcbiblastnCommandline.best_hit_score_edgeNcbiblastnCommandline.culling_limitNcbiblastnCommandline.dbNcbiblastnCommandline.db_hard_maskNcbiblastnCommandline.db_soft_maskNcbiblastnCommandline.dbsizeNcbiblastnCommandline.dustNcbiblastnCommandline.entrez_queryNcbiblastnCommandline.evalueNcbiblastnCommandline.export_search_strategyNcbiblastnCommandline.filtering_dbNcbiblastnCommandline.gapextendNcbiblastnCommandline.gapopenNcbiblastnCommandline.gilistNcbiblastnCommandline.hNcbiblastnCommandline.helpNcbiblastnCommandline.htmlNcbiblastnCommandline.import_search_strategyNcbiblastnCommandline.index_nameNcbiblastnCommandline.lcase_maskingNcbiblastnCommandline.line_lengthNcbiblastnCommandline.max_hspsNcbiblastnCommandline.max_hsps_per_subjectNcbiblastnCommandline.max_target_seqsNcbiblastnCommandline.min_raw_gapped_scoreNcbiblastnCommandline.negative_gilistNcbiblastnCommandline.negative_seqidlistNcbiblastnCommandline.no_greedyNcbiblastnCommandline.num_alignmentsNcbiblastnCommandline.num_descriptionsNcbiblastnCommandline.num_threadsNcbiblastnCommandline.off_diagonal_rangeNcbiblastnCommandline.outNcbiblastnCommandline.outfmtNcbiblastnCommandline.parse_deflinesNcbiblastnCommandline.penaltyNcbiblastnCommandline.perc_identityNcbiblastnCommandline.qcov_hsp_percNcbiblastnCommandline.queryNcbiblastnCommandline.query_locNcbiblastnCommandline.remoteNcbiblastnCommandline.rewardNcbiblastnCommandline.searchspNcbiblastnCommandline.seqidlistNcbiblastnCommandline.show_gisNcbiblastnCommandline.soft_maskingNcbiblastnCommandline.strandNcbiblastnCommandline.subjectNcbiblastnCommandline.subject_locNcbiblastnCommandline.sum_statisticsNcbiblastnCommandline.sum_statsNcbiblastnCommandline.taskNcbiblastnCommandline.template_lengthNcbiblastnCommandline.template_typeNcbiblastnCommandline.ungappedNcbiblastnCommandline.use_indexNcbiblastnCommandline.versionNcbiblastnCommandline.window_masker_dbNcbiblastnCommandline.window_masker_taxidNcbiblastnCommandline.window_sizeNcbiblastnCommandline.word_sizeNcbiblastnCommandline.xdrop_gapNcbiblastnCommandline.xdrop_gap_finalNcbiblastnCommandline.xdrop_ungap
NcbiblastxCommandlineNcbiblastxCommandline.__init__()NcbiblastxCommandline.best_hit_overhangNcbiblastxCommandline.best_hit_score_edgeNcbiblastxCommandline.comp_based_statsNcbiblastxCommandline.culling_limitNcbiblastxCommandline.dbNcbiblastxCommandline.db_hard_maskNcbiblastxCommandline.db_soft_maskNcbiblastxCommandline.dbsizeNcbiblastxCommandline.entrez_queryNcbiblastxCommandline.evalueNcbiblastxCommandline.export_search_strategyNcbiblastxCommandline.frame_shift_penaltyNcbiblastxCommandline.gapextendNcbiblastxCommandline.gapopenNcbiblastxCommandline.gilistNcbiblastxCommandline.hNcbiblastxCommandline.helpNcbiblastxCommandline.htmlNcbiblastxCommandline.import_search_strategyNcbiblastxCommandline.lcase_maskingNcbiblastxCommandline.line_lengthNcbiblastxCommandline.matrixNcbiblastxCommandline.max_hspsNcbiblastxCommandline.max_hsps_per_subjectNcbiblastxCommandline.max_intron_lengthNcbiblastxCommandline.max_target_seqsNcbiblastxCommandline.negative_gilistNcbiblastxCommandline.negative_seqidlistNcbiblastxCommandline.num_alignmentsNcbiblastxCommandline.num_descriptionsNcbiblastxCommandline.num_threadsNcbiblastxCommandline.outNcbiblastxCommandline.outfmtNcbiblastxCommandline.parse_deflinesNcbiblastxCommandline.qcov_hsp_percNcbiblastxCommandline.queryNcbiblastxCommandline.query_gencodeNcbiblastxCommandline.query_locNcbiblastxCommandline.remoteNcbiblastxCommandline.searchspNcbiblastxCommandline.segNcbiblastxCommandline.seqidlistNcbiblastxCommandline.show_gisNcbiblastxCommandline.soft_maskingNcbiblastxCommandline.strandNcbiblastxCommandline.subjectNcbiblastxCommandline.subject_locNcbiblastxCommandline.sum_statisticsNcbiblastxCommandline.sum_statsNcbiblastxCommandline.taskNcbiblastxCommandline.thresholdNcbiblastxCommandline.ungappedNcbiblastxCommandline.use_sw_tbackNcbiblastxCommandline.versionNcbiblastxCommandline.window_sizeNcbiblastxCommandline.word_sizeNcbiblastxCommandline.xdrop_gapNcbiblastxCommandline.xdrop_gap_finalNcbiblastxCommandline.xdrop_ungap
NcbitblastnCommandlineNcbitblastnCommandline.__init__()NcbitblastnCommandline.best_hit_overhangNcbitblastnCommandline.best_hit_score_edgeNcbitblastnCommandline.comp_based_statsNcbitblastnCommandline.culling_limitNcbitblastnCommandline.dbNcbitblastnCommandline.db_gencodeNcbitblastnCommandline.db_hard_maskNcbitblastnCommandline.db_soft_maskNcbitblastnCommandline.dbsizeNcbitblastnCommandline.entrez_queryNcbitblastnCommandline.evalueNcbitblastnCommandline.export_search_strategyNcbitblastnCommandline.frame_shift_penaltyNcbitblastnCommandline.gapextendNcbitblastnCommandline.gapopenNcbitblastnCommandline.gilistNcbitblastnCommandline.hNcbitblastnCommandline.helpNcbitblastnCommandline.htmlNcbitblastnCommandline.import_search_strategyNcbitblastnCommandline.in_pssmNcbitblastnCommandline.lcase_maskingNcbitblastnCommandline.line_lengthNcbitblastnCommandline.matrixNcbitblastnCommandline.max_hspsNcbitblastnCommandline.max_hsps_per_subjectNcbitblastnCommandline.max_intron_lengthNcbitblastnCommandline.max_target_seqsNcbitblastnCommandline.negative_gilistNcbitblastnCommandline.negative_seqidlistNcbitblastnCommandline.num_alignmentsNcbitblastnCommandline.num_descriptionsNcbitblastnCommandline.num_threadsNcbitblastnCommandline.outNcbitblastnCommandline.outfmtNcbitblastnCommandline.parse_deflinesNcbitblastnCommandline.qcov_hsp_percNcbitblastnCommandline.queryNcbitblastnCommandline.query_locNcbitblastnCommandline.remoteNcbitblastnCommandline.searchspNcbitblastnCommandline.segNcbitblastnCommandline.seqidlistNcbitblastnCommandline.show_gisNcbitblastnCommandline.soft_maskingNcbitblastnCommandline.subjectNcbitblastnCommandline.subject_locNcbitblastnCommandline.sum_statisticsNcbitblastnCommandline.sum_statsNcbitblastnCommandline.taskNcbitblastnCommandline.thresholdNcbitblastnCommandline.ungappedNcbitblastnCommandline.use_sw_tbackNcbitblastnCommandline.versionNcbitblastnCommandline.window_sizeNcbitblastnCommandline.word_sizeNcbitblastnCommandline.xdrop_gapNcbitblastnCommandline.xdrop_gap_finalNcbitblastnCommandline.xdrop_ungap
NcbitblastxCommandlineNcbitblastxCommandline.__init__()NcbitblastxCommandline.best_hit_overhangNcbitblastxCommandline.best_hit_score_edgeNcbitblastxCommandline.culling_limitNcbitblastxCommandline.dbNcbitblastxCommandline.db_gencodeNcbitblastxCommandline.db_hard_maskNcbitblastxCommandline.db_soft_maskNcbitblastxCommandline.dbsizeNcbitblastxCommandline.entrez_queryNcbitblastxCommandline.evalueNcbitblastxCommandline.export_search_strategyNcbitblastxCommandline.gapextendNcbitblastxCommandline.gapopenNcbitblastxCommandline.gilistNcbitblastxCommandline.hNcbitblastxCommandline.helpNcbitblastxCommandline.htmlNcbitblastxCommandline.import_search_strategyNcbitblastxCommandline.lcase_maskingNcbitblastxCommandline.line_lengthNcbitblastxCommandline.matrixNcbitblastxCommandline.max_hspsNcbitblastxCommandline.max_hsps_per_subjectNcbitblastxCommandline.max_intron_lengthNcbitblastxCommandline.max_target_seqsNcbitblastxCommandline.negative_gilistNcbitblastxCommandline.negative_seqidlistNcbitblastxCommandline.num_alignmentsNcbitblastxCommandline.num_descriptionsNcbitblastxCommandline.num_threadsNcbitblastxCommandline.outNcbitblastxCommandline.outfmtNcbitblastxCommandline.parse_deflinesNcbitblastxCommandline.qcov_hsp_percNcbitblastxCommandline.queryNcbitblastxCommandline.query_gencodeNcbitblastxCommandline.query_locNcbitblastxCommandline.remoteNcbitblastxCommandline.searchspNcbitblastxCommandline.segNcbitblastxCommandline.seqidlistNcbitblastxCommandline.show_gisNcbitblastxCommandline.soft_maskingNcbitblastxCommandline.strandNcbitblastxCommandline.subjectNcbitblastxCommandline.subject_locNcbitblastxCommandline.sum_statisticsNcbitblastxCommandline.sum_statsNcbitblastxCommandline.thresholdNcbitblastxCommandline.versionNcbitblastxCommandline.window_sizeNcbitblastxCommandline.word_sizeNcbitblastxCommandline.xdrop_gapNcbitblastxCommandline.xdrop_gap_finalNcbitblastxCommandline.xdrop_ungap
NcbipsiblastCommandlineNcbipsiblastCommandline.__init__()NcbipsiblastCommandline.best_hit_overhangNcbipsiblastCommandline.best_hit_score_edgeNcbipsiblastCommandline.comp_based_statsNcbipsiblastCommandline.culling_limitNcbipsiblastCommandline.dbNcbipsiblastCommandline.dbsizeNcbipsiblastCommandline.entrez_queryNcbipsiblastCommandline.evalueNcbipsiblastCommandline.export_search_strategyNcbipsiblastCommandline.gap_triggerNcbipsiblastCommandline.gapextendNcbipsiblastCommandline.gapopenNcbipsiblastCommandline.gilistNcbipsiblastCommandline.hNcbipsiblastCommandline.helpNcbipsiblastCommandline.htmlNcbipsiblastCommandline.ignore_msa_masterNcbipsiblastCommandline.import_search_strategyNcbipsiblastCommandline.in_msaNcbipsiblastCommandline.in_pssmNcbipsiblastCommandline.inclusion_ethreshNcbipsiblastCommandline.lcase_maskingNcbipsiblastCommandline.line_lengthNcbipsiblastCommandline.matrixNcbipsiblastCommandline.max_hspsNcbipsiblastCommandline.max_hsps_per_subjectNcbipsiblastCommandline.max_target_seqsNcbipsiblastCommandline.msa_master_idxNcbipsiblastCommandline.negative_gilistNcbipsiblastCommandline.negative_seqidlistNcbipsiblastCommandline.num_alignmentsNcbipsiblastCommandline.num_descriptionsNcbipsiblastCommandline.num_iterationsNcbipsiblastCommandline.num_threadsNcbipsiblastCommandline.outNcbipsiblastCommandline.out_ascii_pssmNcbipsiblastCommandline.out_pssmNcbipsiblastCommandline.outfmtNcbipsiblastCommandline.parse_deflinesNcbipsiblastCommandline.phi_patternNcbipsiblastCommandline.pseudocountNcbipsiblastCommandline.qcov_hsp_percNcbipsiblastCommandline.queryNcbipsiblastCommandline.query_locNcbipsiblastCommandline.remoteNcbipsiblastCommandline.save_each_pssmNcbipsiblastCommandline.save_pssm_after_last_roundNcbipsiblastCommandline.searchspNcbipsiblastCommandline.segNcbipsiblastCommandline.seqidlistNcbipsiblastCommandline.show_gisNcbipsiblastCommandline.soft_maskingNcbipsiblastCommandline.subjectNcbipsiblastCommandline.subject_locNcbipsiblastCommandline.sum_statisticsNcbipsiblastCommandline.sum_statsNcbipsiblastCommandline.thresholdNcbipsiblastCommandline.use_sw_tbackNcbipsiblastCommandline.versionNcbipsiblastCommandline.window_sizeNcbipsiblastCommandline.word_sizeNcbipsiblastCommandline.xdrop_gapNcbipsiblastCommandline.xdrop_gap_finalNcbipsiblastCommandline.xdrop_ungap
NcbirpsblastCommandlineNcbirpsblastCommandline.__init__()NcbirpsblastCommandline.best_hit_overhangNcbirpsblastCommandline.best_hit_score_edgeNcbirpsblastCommandline.comp_based_statsNcbirpsblastCommandline.culling_limitNcbirpsblastCommandline.dbNcbirpsblastCommandline.dbsizeNcbirpsblastCommandline.entrez_queryNcbirpsblastCommandline.evalueNcbirpsblastCommandline.export_search_strategyNcbirpsblastCommandline.gilistNcbirpsblastCommandline.hNcbirpsblastCommandline.helpNcbirpsblastCommandline.htmlNcbirpsblastCommandline.import_search_strategyNcbirpsblastCommandline.lcase_maskingNcbirpsblastCommandline.line_lengthNcbirpsblastCommandline.max_hspsNcbirpsblastCommandline.max_hsps_per_subjectNcbirpsblastCommandline.max_target_seqsNcbirpsblastCommandline.negative_gilistNcbirpsblastCommandline.negative_seqidlistNcbirpsblastCommandline.num_alignmentsNcbirpsblastCommandline.num_descriptionsNcbirpsblastCommandline.num_threadsNcbirpsblastCommandline.outNcbirpsblastCommandline.outfmtNcbirpsblastCommandline.parse_deflinesNcbirpsblastCommandline.qcov_hsp_percNcbirpsblastCommandline.queryNcbirpsblastCommandline.query_locNcbirpsblastCommandline.remoteNcbirpsblastCommandline.searchspNcbirpsblastCommandline.segNcbirpsblastCommandline.seqidlistNcbirpsblastCommandline.show_gisNcbirpsblastCommandline.soft_maskingNcbirpsblastCommandline.sum_statisticsNcbirpsblastCommandline.sum_statsNcbirpsblastCommandline.use_sw_tbackNcbirpsblastCommandline.versionNcbirpsblastCommandline.window_sizeNcbirpsblastCommandline.word_sizeNcbirpsblastCommandline.xdrop_gapNcbirpsblastCommandline.xdrop_gap_finalNcbirpsblastCommandline.xdrop_ungap
NcbirpstblastnCommandlineNcbirpstblastnCommandline.__init__()NcbirpstblastnCommandline.comp_based_statsNcbirpstblastnCommandline.dbNcbirpstblastnCommandline.dbsizeNcbirpstblastnCommandline.entrez_queryNcbirpstblastnCommandline.evalueNcbirpstblastnCommandline.export_search_strategyNcbirpstblastnCommandline.gilistNcbirpstblastnCommandline.hNcbirpstblastnCommandline.helpNcbirpstblastnCommandline.htmlNcbirpstblastnCommandline.import_search_strategyNcbirpstblastnCommandline.lcase_maskingNcbirpstblastnCommandline.line_lengthNcbirpstblastnCommandline.max_hspsNcbirpstblastnCommandline.max_hsps_per_subjectNcbirpstblastnCommandline.max_target_seqsNcbirpstblastnCommandline.negative_gilistNcbirpstblastnCommandline.negative_seqidlistNcbirpstblastnCommandline.num_alignmentsNcbirpstblastnCommandline.num_descriptionsNcbirpstblastnCommandline.num_threadsNcbirpstblastnCommandline.outNcbirpstblastnCommandline.outfmtNcbirpstblastnCommandline.parse_deflinesNcbirpstblastnCommandline.qcov_hsp_percNcbirpstblastnCommandline.queryNcbirpstblastnCommandline.query_gencodeNcbirpstblastnCommandline.query_locNcbirpstblastnCommandline.remoteNcbirpstblastnCommandline.searchspNcbirpstblastnCommandline.segNcbirpstblastnCommandline.seqidlistNcbirpstblastnCommandline.show_gisNcbirpstblastnCommandline.soft_maskingNcbirpstblastnCommandline.strandNcbirpstblastnCommandline.sum_statisticsNcbirpstblastnCommandline.sum_statsNcbirpstblastnCommandline.ungappedNcbirpstblastnCommandline.use_sw_tbackNcbirpstblastnCommandline.versionNcbirpstblastnCommandline.window_sizeNcbirpstblastnCommandline.word_sizeNcbirpstblastnCommandline.xdrop_gapNcbirpstblastnCommandline.xdrop_gap_finalNcbirpstblastnCommandline.xdrop_ungap
NcbiblastformatterCommandlineNcbiblastformatterCommandline.__init__()NcbiblastformatterCommandline.archiveNcbiblastformatterCommandline.hNcbiblastformatterCommandline.helpNcbiblastformatterCommandline.htmlNcbiblastformatterCommandline.line_lengthNcbiblastformatterCommandline.max_target_seqsNcbiblastformatterCommandline.num_alignmentsNcbiblastformatterCommandline.num_descriptionsNcbiblastformatterCommandline.outNcbiblastformatterCommandline.outfmtNcbiblastformatterCommandline.parse_deflinesNcbiblastformatterCommandline.ridNcbiblastformatterCommandline.show_gisNcbiblastformatterCommandline.version
NcbideltablastCommandlineNcbideltablastCommandline.__init__()NcbideltablastCommandline.best_hit_overhangNcbideltablastCommandline.best_hit_score_edgeNcbideltablastCommandline.comp_based_statsNcbideltablastCommandline.culling_limitNcbideltablastCommandline.dbNcbideltablastCommandline.dbsizeNcbideltablastCommandline.domain_inclusion_ethreshNcbideltablastCommandline.entrez_queryNcbideltablastCommandline.evalueNcbideltablastCommandline.export_search_strategyNcbideltablastCommandline.gap_triggerNcbideltablastCommandline.gapextendNcbideltablastCommandline.gapopenNcbideltablastCommandline.gilistNcbideltablastCommandline.hNcbideltablastCommandline.helpNcbideltablastCommandline.htmlNcbideltablastCommandline.import_search_strategyNcbideltablastCommandline.inclusion_ethreshNcbideltablastCommandline.lcase_maskingNcbideltablastCommandline.line_lengthNcbideltablastCommandline.matrixNcbideltablastCommandline.max_hspsNcbideltablastCommandline.max_hsps_per_subjectNcbideltablastCommandline.max_target_seqsNcbideltablastCommandline.negative_gilistNcbideltablastCommandline.negative_seqidlistNcbideltablastCommandline.num_alignmentsNcbideltablastCommandline.num_descriptionsNcbideltablastCommandline.num_iterationsNcbideltablastCommandline.num_threadsNcbideltablastCommandline.outNcbideltablastCommandline.out_ascii_pssmNcbideltablastCommandline.out_pssmNcbideltablastCommandline.outfmtNcbideltablastCommandline.parse_deflinesNcbideltablastCommandline.pseudocountNcbideltablastCommandline.qcov_hsp_percNcbideltablastCommandline.queryNcbideltablastCommandline.query_locNcbideltablastCommandline.remoteNcbideltablastCommandline.rpsdbNcbideltablastCommandline.save_each_pssmNcbideltablastCommandline.save_pssm_after_last_roundNcbideltablastCommandline.searchspNcbideltablastCommandline.segNcbideltablastCommandline.seqidlistNcbideltablastCommandline.show_domain_hitsNcbideltablastCommandline.show_gisNcbideltablastCommandline.soft_maskingNcbideltablastCommandline.subjectNcbideltablastCommandline.subject_locNcbideltablastCommandline.sum_statisticsNcbideltablastCommandline.sum_statsNcbideltablastCommandline.thresholdNcbideltablastCommandline.use_sw_tbackNcbideltablastCommandline.versionNcbideltablastCommandline.window_sizeNcbideltablastCommandline.word_sizeNcbideltablastCommandline.xdrop_gapNcbideltablastCommandline.xdrop_gap_finalNcbideltablastCommandline.xdrop_ungap
NcbimakeblastdbCommandlineNcbimakeblastdbCommandline.__init__()NcbimakeblastdbCommandline.blastdb_versionNcbimakeblastdbCommandline.dbtypeNcbimakeblastdbCommandline.gi_maskNcbimakeblastdbCommandline.gi_mask_nameNcbimakeblastdbCommandline.hNcbimakeblastdbCommandline.hash_indexNcbimakeblastdbCommandline.helpNcbimakeblastdbCommandline.input_fileNcbimakeblastdbCommandline.input_typeNcbimakeblastdbCommandline.logfileNcbimakeblastdbCommandline.mask_dataNcbimakeblastdbCommandline.mask_descNcbimakeblastdbCommandline.mask_idNcbimakeblastdbCommandline.max_file_szNcbimakeblastdbCommandline.outNcbimakeblastdbCommandline.parse_seqidsNcbimakeblastdbCommandline.taxidNcbimakeblastdbCommandline.taxid_mapNcbimakeblastdbCommandline.titleNcbimakeblastdbCommandline.version
- Bio.Blast.NCBIWWW模块
- Bio.Blast.NCBIXML模块
- Bio.Blast.ParseBlastTable模块
- Bio.Blast.Record模块
模块内容¶
用于处理BLAST程序和输出的代码。