ncbi_companion帮助您通过genbank使用fasta和映射文件构建参考数据库
NCBI-Companion的Python项目详细描述
ncbi_同伴
简介
ncbi_companion的目标是使用genbank entrez实用程序构造数据库、生成fasta文件和分类映射。
Biopython版权属于Biopython团队 Entrez版权归NCBI Entrez团队所有
内容
类荷载种类
This class is to used fetch species name contains in csv file, text file, excel or fasta file.
函数
| function names | parameters | Return |
|---|---|---|
| LoadSpecies | species_input, species_output, ifout | initialize |
| ReadSpeciesFile_text | None | a list (if specified, a table in local directory) |
| ReadSpeciesFile_excel | sp_col, sheetname, header, fullname | a list (or a local file) |
| ReadSpeciesFile_csv | sp_col, header, fullname | a list (or a local file ) |
| ExtractSpeciesFromFasta | ranges, delimiter | a list (or a local file) |
all those functions return a list of species names or ID list
用法
species=LoadSpecies(input_file,output_file,ifout=True)species.ReadSpeciesFile_excel(sp_col='act_sym_fullname',sheetname=0,header=0,fullname=False)
NCBIU类工具
This class implements Biopython Entrez to interact with NCBI/Genbank API to either get accession id, taxonomy id, sequences or taxonomy ranking, or converting them. Some of core functions return a tracker flag that can trace which functions have been called. This order will be used by Sqlite_Dumps class to generate fasta file and mapping file
函数
| Functions | parameters | return | database table name | Tracker Flag |
|---|---|---|---|---|
| NCBI_Tools | ncbi_key, ncbi_email, sqlite_db, ncbi_db, idtype | initialize | None | None |
| Update_API | key, email | updated key and email | None | None |
| getTracker | None | a tracker list | None | None |
| ncbi_Species2Genome | species list | accession ID list | Sp2Genome | P9 |
| ncbi_Search2Acc | search terms, howmany to quire | Search2AccIDs | Tracker | P1 |
| ncbi_Species2Acc | species list, more terms (optional) | Sp2AccIDs | Tracker | P2 |
| ncbi_GetSeqsFromAcc | table_name, column_name | Acc2Seq | Tracker | P3 |
| ncbi_GetTaxIdFromAcc | table_name, column_name | Uid2TaxIDs | Tracker | P4 |
| ncbi_eAcc2Seq | accession ID | Tracker | Acc2Seq | P5 |
| ncbi_eAcc2TaxID | accession ID | Tracker | Uid2TaxIDs | P6 |
| ncbi_Species2Taxa | species list, style, levels_n | Tracker | Sp2Taxa | P7 |
| ncbi_Id2Taxa | style, levels_n | Tracker | TaxId2Ranking | P8 |
用法
示例1：已知物种列表并搜索其trnl基因
跟踪器标志：P2--->；P3/P4--->；P4/P3--->；P8
fromNCBI_CompanionimportNCBI_Companioncompanion=NCBI_Companion.NCBI_Tools(key,email,'databasename','nuccore','acc')companion.ncbi_Species2Acc(species_list,'trnL')companion.ncbi_GetSeqsFromAcc('Sp2AccIDs','acc_id')companion.ncbi_GetTaxIdFromAcc('Sp2AccIDs','acc_id')companion.ncbi_Id2Taxa(style='qiime',levels_n=7)# 7 levels of taxonomy ranking qiime style D_0_..;
类sqlite_dumps
函数
| functions | parameters | return |
|---|---|---|
| Sqlite_Dumps | sqlite_db, output_prefix, tracker, header_type = 'acc' | initialize |
| sqlite_dump | None | a fasta and a mapping file in local |
用法
# get trackertracker=companion.getTracker()dump=Sqlite_Dumps('database constructed by NCBI_Tools','fasta and mapping file name, not extension',tracker,header_type='acc')
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