o Rŀg1@sXdZGdddZGdddZGdddZGdddZd d Zd d Zd dZdS)a Parse Unigene flat file format files such as the Hs.data file. Here is an overview of the flat file format that this parser deals with: Line types/qualifiers:: 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 c@*eZdZdZd ddZddZddZdS) SequenceLineaStore the information for one SEQUENCE line from a Unigene file. Initialize with the text part of the SEQUENCE line, or nothing. Attributes and descriptions (access as LOWER CASE): - 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 NcCsbd|_d|_d|_d|_d|_d|_d|_d|_d|_d|_ d|_ |dur/||_ | |dSdS)Initialize the class.FN) accnidlidpidcloneimageis_imageendmgcseqtypetracetext_init_from_textselfrrH/var/www/html/myenv/lib/python3.10/site-packages/Bio/UniGene/__init__.py__init__iszSequenceLine.__init__cCsb|d}|D]'}|d\}}|dkr&|dddkr&d|_|dd|_t|||qdS)N; =CLONEIMAGET)splitr r setattrlowerrrpartspartkeyvalrrrrzs zSequenceLine._init_from_textcC|jS)z/Return UniGene SequenceLine object as a string.rrrrr__repr__zSequenceLine.__repr__N__name__ __module__ __qualname____doc__rrr(rrrrrNs   rc@r) ProtsimLinea|Store the information for one PROTSIM line from a Unigene file. Initialize with the text part of the PROTSIM line, or nothing. Attributes and descriptions (access as LOWER CASE) ORG= Organism PROTGI= Sequence GI of protein PROTID= Sequence ID of protein PCT= Percent alignment ALN= length of aligned region (aa) NcCs>d|_d|_d|_d|_d|_|dur||_||dSdSrrN)orgprotgiprotidpctalnrrrrrrrszProtsimLine.__init__cC6|d}|D]}|d\}}t|||qdS)Nrrrrrr rrrr zProtsimLine._init_from_textcCr%)z.Return UniGene ProtsimLine object as a string.r&r'rrrr(r)zProtsimLine.__repr__r*r+rrrrr0s   r0c@r) STSLinea;Store the information for one STS line from a Unigene file. Initialize with the text part of the STS line, or nothing. Attributes and descriptions (access as LOWER CASE) ACC= GenBank/EMBL/DDBJ accession number of STS [optional field] UNISTS= identifier in NCBI's UNISTS database NcCs,d|_d|_|dur||_||dSdSr1)runistsrrrrrrrs zSTSLine.__init__cCr7)N rr8r rrrrr9zSTSLine._init_from_textcCr%)z*Return UniGene STSLine object as a string.r&r'rrrr(r)zSTSLine.__repr__r*r+rrrrr:s   r:c@s eZdZdZddZddZdS)RecordatStore a Unigene record. Here is what is stored:: 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 cCsdd|_d|_d|_d|_d|_g|_d|_d|_d|_d|_ d|_ d|_ g|_ g|_ g|_g|_dSr1)IDspeciestitlesymbolcytobandexpress restr_expr gnm_terminusgene_id locuslinkhomol chromosomeprotsimsequenceststxmapr'rrrrs  zRecord.__init__cCs&d|jjd|jd|jd|jS)z>Represent the UniGene Record object as a string for debugging. r<) __class__r,r>rAr@r'rrrr(s&zRecord.__repr__N)r,r-r.r/rr(rrrrr=s r=ccs t|}|s dS|Vq)zGRead and load a UniGene records, for files containing multiple records.TN)_read)handlerecordrrrparsesrScCs,t|}|s td|}|rtd|S)z4Read and load a UniGene record, one record per file.zNo SwissProt record foundz$More than one SwissProt record found)rP ValueErrorread)rQrR remainderrrrrU srUc Csd}d}|D]}|d|||d}}|}|dkr1t}||_|jdd|_q|dkr9||_q|dkrA||_q|dkrI||_q|dkrQ||_q|d krl|d kr]d |_ q|d kred |_ qt d ||dkr|dd|dD|_ q|dkrdd|dD|_ q|dkr||_ q|dkr||_q|dkrt|}|j|q|dkrt|}q|dkrt|}|j|q|dkrt|} |j| q|dkrt|j|krt d|t|jf|St d||rt ddS)N r>.TITLEGENEGENE_ID LOCUSLINKHOMOLYESTNOzCannot parse HOMOL line EXPRESScSg|]}|qSrstrip.0wordrrr 2z_read..| RESTR_EXPRcSrbrrcrerrrrh4ri CHROMOSOMECYTOBANDPROTSIMSCOUNTSEQUENCESTSz//zkThe number of sequences specified in the record (%d) does not agree with the number of sequences found (%d)z Unknown tag zUnexpected end of stream.)rstripr=r>rr?r@rArFrGrHrTrCrDrIrBr0rJappendintrrKr:rLlen) rQ UG_INDENTrRlinetagvaluerJscountrKrLrrrrPsl"  rPN)r/rr0r:r=rSrUrPrrrrsF;$4