Bio.Unigene软件包¶
模块内容¶
解析Unigene平面文件格式文件,如Hs.data文件。
以下是此解析器处理的平面文件格式的概述:
行类型/限定符::
ID UniGene cluster ID TITLE Title for the cluster GENE Gene symbol CYTOBAND Cytological band EXPRESS Tissues of origin for ESTs in cluster RESTR_EXPR Single tissue or development stage contributes more than half the total EST frequency for this gene. GNM_TERMINUS genomic confirmation of presence of a 3' terminus; T if a non-templated polyA tail is found among a cluster's sequences; else I if templated As are found in genomic sequence or S if a canonical polyA signal is found on the genomic sequence GENE_ID Entrez gene identifier associated with at least one sequence in this cluster; to be used instead of LocusLink. LOCUSLINK LocusLink identifier associated with at least one sequence in this cluster; deprecated in favor of GENE_ID HOMOL Homology; CHROMOSOME Chromosome. For plants, CHROMOSOME refers to mapping on the arabidopsis genome. STS STS ACC= GenBank/EMBL/DDBJ accession number of STS [optional field] UNISTS= identifier in NCBI's UNISTS database TXMAP Transcript map interval MARKER= Marker found on at least one sequence in this cluster RHPANEL= Radiation Hybrid panel used to place marker PROTSIM Protein Similarity data for the sequence with highest-scoring protein similarity in this cluster ORG= Organism PROTGI= Sequence GI of protein PROTID= Sequence ID of protein PCT= Percent alignment ALN= length of aligned region (aa) SCOUNT Number of sequences in the cluster SEQUENCE Sequence ACC= GenBank/EMBL/DDBJ accession number of sequence NID= Unique nucleotide sequence identifier (gi) PID= Unique protein sequence identifier (used for non-ESTs) CLONE= Clone identifier (used for ESTs only) END= End (5'/3') of clone insert read (used for ESTs only) LID= Library ID; see Hs.lib.info for library name and tissue MGC= 5' CDS-completeness indicator; if present, the clone associated with this sequence is believed CDS-complete. A value greater than 511 is the gi of the CDS-complete mRNA matched by the EST, otherwise the value is an indicator of the reliability of the test indicating CDS completeness; higher values indicate more reliable CDS-completeness predictions. SEQTYPE= Description of the nucleotide sequence. Possible values are mRNA, EST and HTC. TRACE= The Trace ID of the EST sequence, as provided by NCBI Trace Archive
- class Bio.UniGene.SequenceLine(text=None)¶
基类:
object
存储Unigene文件中一个序列行的信息。
用序列行的文本部分初始化,否则不初始化。
- 属性和描述(访问为小写):
ACC=序列的GenBank/EMBL/DDBJ登录号
NID=唯一核苷酸序列标识符(GI)
PID=唯一的蛋白质序列标识符(用于非EST)
克隆=克隆标识符(仅用于EST)
END=克隆插入读取的END(5‘/3’)(仅用于EST)
LID=库ID;有关库名称和组织,请参阅Hs.lib.info
MGC=5‘CDS-完整性指示符;如果存在,则与该序列相关联的克隆被认为是CDS-完整的。大于511的值是与EST匹配的CDS-Complete mRNA的GI,否则该值是指示CDS完整性的测试可靠性的指示器;更高的值表示更可靠的CDS完整性预测。
SEQTYPE=核苷酸序列的描述。可能的值有mRNA、EST和HTC。
TRACE=由NCBI跟踪档案提供的EST序列的跟踪ID
- __init__(text=None)¶
初始化类。
- __repr__()¶
以字符串形式返回Unigene SequenceLine对象。
- class Bio.UniGene.ProtsimLine(text=None)¶
基类:
object
存储Unigene文件中某一PROTSIM行的信息。
使用PROTSIM行的文本部分进行初始化,或者不初始化。
属性和描述(小写访问)ORG=有机体PROTGI=蛋白质序列GI PROTID=蛋白质序列ID PCT=比对百分比ALN=比对区域长度(AA)
- __init__(text=None)¶
初始化类。
- __repr__()¶
将Unigene ProtsimLine对象作为字符串返回。
- class Bio.UniGene.STSLine(text=None)¶
基类:
object
存储Unigene文件中某一STS行的信息。
使用STS行的文本部分进行初始化,或者不初始化。
属性和描述(访问为小写)
ACC=STS的GenBank/EMBL/DDBJ登录号 [可选字段] UNISTS=NCBI的UNISTS数据库中的标识符
- __init__(text=None)¶
初始化类。
- __repr__()¶
将Unigene STSLine对象作为字符串返回。
- class Bio.UniGene.Record¶
基类:
object
存储Unigene记录。
以下是存储的内容::
self.ID = '' # ID line self.species = '' # Hs, Bt, etc. self.title = '' # TITLE line self.symbol = '' # GENE line self.cytoband = '' # CYTOBAND line self.express = [] # EXPRESS line, parsed on ';' # Will be an array of strings self.restr_expr = '' # RESTR_EXPR line self.gnm_terminus = '' # GNM_TERMINUS line self.gene_id = '' # GENE_ID line self.locuslink = '' # LOCUSLINK line self.homol = '' # HOMOL line self.chromosome = '' # CHROMOSOME line self.protsim = [] # PROTSIM entries, array of Protsims # Type ProtsimLine self.sequence = [] # SEQUENCE entries, array of Sequence entries # Type SequenceLine self.sts = [] # STS entries, array of STS entries # Type STSLine self.txmap = [] # TXMAP entries, array of TXMap entries
- __init__()¶
初始化类。
- __repr__()¶
将Unigene记录对象表示为用于调试的字符串。
- Bio.UniGene.parse(handle)¶
对于包含多条记录的文件,读取并加载Unigene记录。
- Bio.UniGene.read(handle)¶
读取并加载Unigene记录,每个文件一个记录。