B ‰°bä:ã@s€dZddlZddddddd d d d d ddddddgZddddddd d d d d ddddgZddddddd dddddg Zddddddd dddddg Zddddd dddddd g Zddd dddd d!d"g Zdddd dddd d!d"g Zd#d$„Z d%d&„Z d'd(„Z d)d*„Z d+d,„Z d-d.„Zd/d0„Zd1d2„Zd3d4„Zd5d6„Zd7d8„Zd9d:„Zd;d<„Zefd=d>„Zefd?d@„ZdAdB„ZedCkr|ddDlmZeddEdS)Fa…Parsers for the GAF, GPA and GPI formats from UniProt-GOA. Uniprot-GOA README + GAF format description: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README Gene Association File, GAF formats: http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/ http://geneontology.org/docs/go-annotation-file-gaf-format-2.0/ Gene Product Association Data (GPA format) README: http://geneontology.org/docs/gene-product-association-data-gpad-format/ Gene Product Information (GPI format) README: http://geneontology.org/docs/gene-product-information-gpi-format/ Go Annotation files are located here: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ éNZDBÚ DB_Object_IDZDB_Object_SymbolZ QualifierZGO_IDz DB:ReferenceZEvidenceZWithZAspectZDB_Object_NameZSynonymZDB_Object_TypeZTaxon_IDZDateZ Assigned_ByZAnnotation_ExtensionZGene_Product_Form_IDz Evidence codeZInteracting_taxon_IDZ Assigned_byZ Spliceform_IDZECO_Evidence_codezAnnotation ExtensionZAnnotation_PropertiesZ DB_subsetZDB_Object_SynonymZTaxonZAnnotation_Target_SetZAnnotation_CompletedZParent_Object_IDZDB_XrefZGene_Product_Propertiesccsrxl|D]d}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<ttt|ƒƒVqWd S) z’Read GPI 1.0 format files (PRIVATE). This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.0 format. rú!Ú ú ééú|éN)ÚrstripÚsplitÚlenÚdictÚzipÚ GPI10FIELDS)ÚhandleÚinlineÚinrec©rú.lib/python3.7/site-packages/Bio/UniProt/GOA.pyÚ_gpi10iterator•s   rccs–x|D]ˆ}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <ttt|ƒƒVqWd S) z’Read GPI 1.1 format files (PRIVATE). This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.1 format. rrrrréréér N)r r r r rÚ GPI11FIELDS)rrrrrrÚ_gpi11iterator¦s   rccs–x|D]ˆ}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <ttt|ƒƒVqWd S) z’Read GPI 1.2 format files (PRIVATE). This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.2 format. rrrrrrrér é N)r r r r rÚ GPI12FIELDS)rrrrrrÚ_gpi12iterator¹s   rcCsn| ¡}| ¡dkrt|ƒS| ¡dkr0t|ƒS| ¡dkrDt|ƒS| ¡dkrZtdƒ‚ntd|›dƒ‚dS) zèRead GPI format files. This function should be called to read a gp_information.goa_uniprot file. At the moment, there is only one format, but this may change, so this function is a placeholder a future wrapper. z!gpi-version: 1.2z!gpi-version: 1.1z!gpi-version: 1.0z!gpi-version: 2.1z1Sorry, parsing GPI version 2 not implemented yet.zUnknown GPI version rN)ÚreadlineÚstriprrrÚNotImplementedErrorÚ ValueError)rrrrrÚ gpi_iteratorÌs     r#ccs–x|D]ˆ}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <ttt|ƒƒVqWd S) zÈRead GPA 1.0 format files (PRIVATE). This iterator is used to read a gp_association.* file which is in the GPA 1.0 format. Do not call directly. Rather, use the gpaiterator function. rrrrrrrréé N)r r r r rÚ GPA10FIELDS)rrrrrrÚ_gpa10iteratorås   r'ccs–x|D]ˆ}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <ttt|ƒƒVqWd S) zÑRead GPA 1.1 format files (PRIVATE). This iterator is used to read a gp_association.goa_uniprot file which is in the GPA 1.1 format. Do not call directly. Rather use the gpa_iterator function rrrrrrrrr$r%N)r r r r rÚ GPA11FIELDS)rrrrrrÚ_gpa11iteratorùs   r)cCsD| ¡}| ¡dkrt|ƒS| ¡dkr0t|ƒStd|›dƒ‚dS)zÁRead GPA format files. This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gpa 1.1 or a gpa 1.0 iterator as needed z!gpa-version: 1.1z!gpa-version: 1.0zUnknown GPA version rN)rr r)r'r")rrrrrÚ gpa_iterator s   r*ccs¨x¢|D]š}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <|d  d¡|d <ttt|ƒƒVqWdS) Nrrrrrrrrrr%é )r r r r rÚ GAF20FIELDS)rrrrrrÚ_gaf20iterators   r-ccs¨x¢|D]š}|ddkrq| d¡ d¡}t|ƒdkr6q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <|d  d¡|d <ttt|ƒƒVqWdS) Nrrrrrrrrrr%r+)r r r r rÚ GAF10FIELDS)rrrrrrÚ_gaf10iterator.s   r/ccsðd}g}xâ|D]Ú}|ddkr q| d¡ d¡}t|ƒdkr>q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <|d  d¡|d <ttt|ƒƒ}|d |krÖ|rÖt |¡}|g}|d }|Vq|d }| |¡qWdS) Nrrrrrrrrrr%r+r)r r r r rr.ÚcopyÚappend)rÚcur_idÚ id_rec_listrrÚcur_recÚret_listrrrÚ_gaf10byproteiniterator=s*    r6ccsðd}g}xâ|D]Ú}|ddkr q| d¡ d¡}t|ƒdkr>q|d d¡|d<|d d¡|d<|d  d¡|d <|d  d¡|d <|d  d¡|d <ttt|ƒƒ}|d |krÖ|rÖt |¡}|g}|d }|Vq|d }| |¡qWdS) Nrrrrrrrrrr%r+r)r r r r rr,r0r1)rr2r3rrr4r5rrrÚ_gaf20byproteiniteratorVs*    r7cCsX| ¡}| ¡dkrt|ƒS| ¡dkr0t|ƒS| ¡dkrDt|ƒStd|›dƒ‚dS)a¤Iterate over records in a gene association file. Returns a list of all consecutive records with the same DB_Object_ID This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.0 or a gaf 1.0 iterator as needed 2016-04-09: added GAF 2.1 iterator & fixed bug in iterator assignment In the meantime GAF 2.1 uses the GAF 2.0 iterator z!gaf-version: 2.0z!gaf-version: 1.0z!gaf-version: 2.1zUnknown GAF version rN)rr r7r6r")rrrrrÚgafbyproteiniteratoros    r8cCsX| ¡}| ¡dkrt|ƒS| ¡dkr0t|ƒS| ¡dkrDt|ƒStd|›dƒ‚dS)a Iterate over a GAF 1.0 or 2.0 file. This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.0 or a gaf 1.0 iterator as needed Example: open, read, interat and filter results. Original data file has been trimed to ~600 rows. Original source ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/YEAST/goa_yeast.gaf.gz >>> from Bio.UniProt.GOA import gafiterator, record_has >>> Evidence = {'Evidence': set(['ND'])} >>> Synonym = {'Synonym': set(['YA19A_YEAST', 'YAL019W-A'])} >>> Taxon_ID = {'Taxon_ID': set(['taxon:559292'])} >>> with open('UniProt/goa_yeast.gaf', 'r') as handle: ... for rec in gafiterator(handle): ... if record_has(rec, Taxon_ID) and record_has(rec, Evidence) and record_has(rec, Synonym): ... for key in ('DB_Object_Name', 'Evidence', 'Synonym', 'Taxon_ID'): ... print(rec[key]) ... Putative uncharacterized protein YAL019W-A ND ['YA19A_YEAST', 'YAL019W-A'] ['taxon:559292'] Putative uncharacterized protein YAL019W-A ND ['YA19A_YEAST', 'YAL019W-A'] ['taxon:559292'] Putative uncharacterized protein YAL019W-A ND ['YA19A_YEAST', 'YAL019W-A'] ['taxon:559292'] z!gaf-version: 2.0z!gaf-version: 2.1z!gaf-version: 1.0zUnknown GAF version rN)rr r-r/r")rrrrrÚ gafiteratorˆs%   r9cCsŠd}xb|dd…D]R}t||tƒrTx||D]}||d7}q.W|dd…d}q|||d7}qW|||dd7}| |¡dS)zÚWrite a single UniProt-GOA record to an output stream. Caller should know the format version. Default: gaf-2.0 If header has a value, then it is assumed this is the first record, a header is written. ÚNéÿÿÿÿrrr)Ú isinstanceÚlistÚwrite)ÚoutrecrÚfieldsZoutstrÚfieldZsubfieldrrrÚwriterec¼srBcCs x|D]}t|||dqWdS)aOWrite a list of GAF records to an output stream. Caller should know the format version. Default: gaf-2.0 If header has a value, then it is assumed this is the first record, a header is written. Typically the list is the one read by fafbyproteinrec, which contains all consecutive lines with the same DB_Object_ID )r@N)rB)Z outprotrecrr@r?rrrÚwritebyproteinrecÏs rCcCsNd}xD|D]<}t||tƒr(||h}n t||ƒ}|||@r d}Pq W|S)zÜAccept a record, and a dictionary of field values. The format is {'field_name': set([val1, val2])}. If any field in the record has a matching value, the function returns True. Otherwise, returns False. FT)r<ÚstrÚset)rZ fieldvalsZretvalrAZset1rrrÚ record_hasÛs    rFÚ__main__)Ú run_doctest)Úverbose)Ú__doc__r0r,r.r&r(rrrrrrr#r'r)r*r-r/r6r7r8r9rBrCrFÚ__name__Z Bio._utilsrHrrrrÚsÔ4