Ri1jdZGddZGddZGddZGddZd Zd Zd Zy ) 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$eZdZdZddZdZdZy) SequenceLineaStore the information for one SEQUENCE line from a Unigene file. Initialize with the text part of the SEQUENCE line, or nothing. Attributes and descriptions (access as LOWER CASE): - ACC= GenBank/EMBL/DDBJ accession number of sequence - NID= Unique nucleotide sequence identifier (gi) - PID= Unique protein sequence identifier (used for non-ESTs) - CLONE= Clone identifier (used for ESTs only) - END= End (5'/3') of clone insert read (used for ESTs only) - LID= Library ID; see Hs.lib.info for library name and tissue - MGC= 5' CDS-completeness indicator; if present, the clone associated with this sequence is believed CDS-complete. A value greater than 511 is the gi of the CDS-complete mRNA matched by the EST, otherwise the value is an indicator of the reliability of the test indicating CDS completeness; higher values indicate more reliable CDS-completeness predictions. - SEQTYPE= Description of the nucleotide sequence. Possible values are mRNA, EST and HTC. - TRACE= The Trace ID of the EST sequence, as provided by NCBI Trace Archive Ncd|_d|_d|_d|_d|_d|_d|_d|_d|_d|_ d|_ |||_ |j|yy)Initialize the class.FN) accnidlidpidcloneimageis_imageendmgcseqtypetracetext_init_from_textselfrs L/home/agent/.friday_env/lib/python3.12/site-packages/Bio/UniGene/__init__.py__init__zSequenceLine.__init__iso      DI   & c|jd}|D]O}|jd\}}|dk(r|dddk(rd|_|dd|_t||j |Qy)N; =CLONEIMAGET)splitr r setattrlowerrrpartspartkeyvals rrzSequenceLine._init_from_textzsk 4  ,Dzz#HCg~r7g%$(DM!$QRDJ D#))+s +  ,rc|jS)z/Return UniGene SequenceLine object as a string.rrs r__repr__zSequenceLine.__repr__ yyrN__name__ __module__ __qualname____doc__rrr+rrrrNs4'",rrc$eZdZdZddZdZdZy) 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) Ncd|_d|_d|_d|_d|_|||_|j |yyrrN)orgprotgiprotidpctalnrrrs rrzProtsimLine.__init__sE    DI   & rc|jd}|D]1}|jd\}}t||j|3y)Nrrr r!r"r#s rrzProtsimLine._init_from_textsB 4  ,Dzz#HC D#))+s + ,rc|jS)z.Return UniGene ProtsimLine object as a string.r)r*s rr+zProtsimLine.__repr__r,rr-r.r3rrr5r5s  ',rr5c$eZdZdZddZdZdZy)STSLinea;Store the information for one STS line from a Unigene file. Initialize with the text part of the STS line, or nothing. Attributes and descriptions (access as LOWER CASE) ACC= GenBank/EMBL/DDBJ accession number of STS [optional field] UNISTS= identifier in NCBI's UNISTS database NcVd|_d|_|||_|j|yyr7)runistsrrrs rrzSTSLine.__init__s0  DI   & rc|jd}|D]1}|jd\}}t||j|3y)N rr>r#s rrzSTSLine._init_from_textsA 3 ,Dzz#HC D#))+s + ,rc|jS)z*Return UniGene STSLine object as a string.r)r*s rr+zSTSLine.__repr__r,rr-r.r3rrrArAs',rrAceZdZdZdZdZy)RecordatStore a Unigene record. Here is what is stored:: self.ID = '' # ID line self.species = '' # Hs, Bt, etc. self.title = '' # TITLE line self.symbol = '' # GENE line self.cytoband = '' # CYTOBAND line self.express = [] # EXPRESS line, parsed on ';' # Will be an array of strings self.restr_expr = '' # RESTR_EXPR line self.gnm_terminus = '' # GNM_TERMINUS line self.gene_id = '' # GENE_ID line self.locuslink = '' # LOCUSLINK line self.homol = '' # HOMOL line self.chromosome = '' # CHROMOSOME line self.protsim = [] # PROTSIM entries, array of Protsims # Type ProtsimLine self.sequence = [] # SEQUENCE entries, array of Sequence entries # Type SequenceLine self.sts = [] # STS entries, array of STS entries # Type STSLine self.txmap = [] # TXMAP entries, array of TXMap entries cd|_d|_d|_d|_d|_g|_d|_d|_d|_d|_ d|_ d|_ g|_ g|_ g|_g|_yr7)IDspeciestitlesymbolcytobandexpress restr_expr gnm_terminusgene_id locuslinkhomol chromosomeprotsimsequenceststxmapr*s rrzRecord.__init__ss          rcd|jjd|jd|jd|jS)z>Represent the UniGene Record object as a string for debugging. rE) __class__r/rJrMrLr*s rr+zRecord.__repr__s84>>**+2dggYa }Adjj\RRrN)r/r0r1r2rr+r3rrrHrHs6&SrrHc#2K t|}|sy|w)zGRead and load a UniGene records, for files containing multiple records.N)_read)handlerecords rparseras" v  scpt|}|s td|j}|r td|S)z4Read and load a UniGene record, one record per file.zNo SwissProt record foundz$More than one SwissProt record found)r^ ValueErrorread)r_r` remainders rrdrd s9 6]F 455 I?@@ Mrcd}d}|D]K}|d|j||dj}}|j}|dk(r5t}||_|jjdd|_t|dk(r||_|dk(r||_|dk(r||_|dk(r||_|d k(r(|d k(rd |_ |d k(rd |_ td ||dk(r4|jdDcgc]}|jc}|_ |dk(r4|jdDcgc]}|jc}|_ G|dk(r ||_U|dk(r ||_c|dk(r(t!|}|j"j%||dk(r t'|}|dk(r(t)|} |j*j%| |dk(r(t-|} |j.j%| |dk(r?t1|j*k7r#td|t1|j*fz|cStd||r tdycc}wcc}w)N rJ.TITLEGENEGENE_ID LOCUSLINKHOMOLYESTNOzCannot parse HOMOL line EXPRESS| RESTR_EXPR 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.)rstriprHrJr rKrLrMrRrSrTrcstriprOrPrUrNr5rVappendintrrWrArXlen) r_ UG_INDENTr`linetagvaluewordrVscountrWrXs rr^r^sUI F23*9%,,.YZ0@0G0G0IU{{} $;XFFI#YY__S1!4FN G^ FL F]!FM I "FN K $F  G^~# $#  #;D6!BCC I 7<{{37GHtdjjlHFN L :?++c:J K$ KF  L %F  J #FO I !%(G NN ! !' * H_ZF J #E*H OO " "8 , E\%.C JJ  c " D[6??#v- Rs6??345 M|C512 2e23f4559I Ks 4I$-I)N)r2rr5rArHrardr^r3rrrsHCL88v!!H>1S1Sh 76r