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。