* :c sdZ')dfdYZbdfdYZdfdYZdfdYZd efd YZd efd YZd efdYZdefdYZdefdYZ dS(sRepresent a Sequence Feature holding info about a part of a sequence. This is heavily modeled after the Biocorba SeqFeature objects, and may be pretty biased towards GenBank stuff since I'm writing it for the GenBank parser output... What's here: Base class to hold a Feature. ---------------------------- classes: o SeqFeature Hold information about a Reference. ---------------------------------- This is an attempt to create a General class to hold Reference type information. classes: o Reference Specify locations of a feature on a Sequence. --------------------------------------------- This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in much the same way as Biocorba. This has the advantages of allowing us to handle fuzzy stuff in case anyone needs it, and also be compatible with Biocorba. classes: o FeatureLocation - Specify the start and end location of a feature. o ExactPosition - Specify the position as being exact. o WithinPosition - Specify a position occuring within some range. o BetweenPosition - Specify a position occuring between a range. o BeforePosition - Specify the position as being found before some base. o AfterPosition - Specify the position as being found after some base. s SeqFeaturecs&)dZ>?dZKdZRS(sRepresent a Sequence Feature on an object. Attributes: o location - the location of the feature on the sequence o type - the specified type of the feature (ie. CDS, exon, repeat...) o ref - A reference to another sequence. This could be an accession number for some different sequence. o ref_db - A different database for the reference accession number. o qualifier - A dictionary of qualifiers on the feature. These are analagous to the qualifiers from a GenBank feature table. The keys of the dictionary are qualifier names, the values are the qualifier values. o sub_features - Additional SeqFeatures which fall under this 'parent' feature. For instance, if we having something like: CDS join(1..10,30..40,50..60) The the top level feature would be a CDS from 1 to 60, and the sub features would be of 'CDS_span' type and would be from 1 to 10, 30 to 40 and 50 to 60, respectively. cs^?ABt|_Dd|_Et|_Ft|_Gd|_Hh|_Ig|_dS(s/Initialize a SeqFeature on a Sequence. siN( sNonesselfslocationstypesrefsref_dbsstrands qualifierss sub_features(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__?s      cs KMNd|i}O|d|i7}P|d|i|if7}Q|d|i7}R|d7}S|ii}T|i Ux1|dUr$}V|d||i|f7}qWXt |i djo>Y|d7}Zx'|i dZr}[|d |7}qWn]|Sd S( s*Make it easier to debug features. s type: %s s location: %s s ref: %s:%s s strand: %s s qualifiers: is Key: %s, Value: %s s Sub-Features s%s N(sselfstypesoutslocationsrefsref_dbsstrands qualifiersskeyssqualifier_keysssortsqual_keyslens sub_featuress sub_feature(sselfsoutsqual_keysqualifier_keyss sub_feature((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__Ks"   "  (s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pys SeqFeature)s  s Referencecs&bdZpqdZzdZRS(sfRepresent a Generic Reference object. Attributes: o location - A list of Location objects specifying regions of the sequence that the references correspond to. If no locations are specified, the entire sequence is assumed. o authors - A big old string, or a list split by author, of authors for the reference. o title - The title of the reference. o journal - Journal the reference was published in. o medline_id - A medline reference for the article. o pubmed_id - A pubmed reference for the article. o comment - A place to stick any comments about the reference. cs[qrg|_sd|_td|_ud|_vd|_wd|_xd|_dS(Ns(sselfslocationsauthorsstitlesjournals medline_ids pubmed_idscomment(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__qs      csz|}d}~x'|id~r}|d|7}qW|d|i7}|d|i7}|d|i7}|d|i7}|d|i7}|d |i 7}|Sd S( s4Output an informative string for debugging. sis location: %s s authors: %s s title: %s s journal: %s smedline id: %s spubmed id: %s s comment: %s N( soutsselfslocationssingle_locationsauthorsstitlesjournals medline_ids pubmed_idscomment(sselfsoutssingle_location((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__zs  (s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pys Referencebs  sFeatureLocationcs2dZdZdZdZRS(sSpecify the location of a feature along a sequence. This attempts to deal with fuzziness of position ends, but also make it easy to get the start and end in the 'normal' case (no fuzziness). You should access the start and end attributes with your_location.start and your_location.end. If the start and end are exact, this will return the positions, if not, we'll return the approriate Fuzzy class with info about the position and fuzziness. cstt|to||_nt||_t|to||_nt||_dS(sSpecify the start and end of a sequence feature. start and end arguments specify the values where the feature begins and ends. These can either by any of the *Position objects that inherit from AbstractPosition, or can just be integers specifying the position. In the case of integers, the values are assumed to be exact and are converted in ExactPosition arguments. This is meant to make it easy to deal with non-fuzzy ends. N(s isinstancesstartsAbstractPositionsselfs_starts ExactPositionsends_end(sselfsstartsend((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__s csd|i|ifSdS(Ns(%s..%s)(sselfs_starts_end(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__scs|djo|iSn|djo|iSn|djo-t|ii|ii|iiSnQ|djo-t|ii|ii|iiSntd|dS(s#Make it easy to get non-fuzzy starts and ends. We override get_attribute here so that in non-fuzzy cases we can just return the start and end position without any hassle. To get fuzzy start and ends, just ask for item.start and item.end. To get non-fuzzy attributes (ie. the position only) ask for 'item.nofuzzy_start', 'item.nofuzzy_end'. These should return the largest range of the fuzzy position. So something like: (10.20)..(30.40) should return 10 for start, and 40 for end. sstartsends nofuzzy_starts nofuzzy_endsCannot evaluate attribute %s.N( sattrsselfs_starts_endsminspositions extensionsmaxsAttributeError(sselfsattr((s'/mit/seven/lib/python/Bio/SeqFeature.pys __getattr__s (s__doc__s__init__s__str__s __getattr__(((s'/mit/seven/lib/python/Bio/SeqFeature.pysFeatureLocations   sAbstractPositioncsdZdZRS(s1Abstract base class representing a position. cs||_||_dS(N(spositionsselfs extension(sselfspositions extension((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__s (s__doc__s__init__(((s'/mit/seven/lib/python/Bio/SeqFeature.pysAbstractPositions s ExactPositioncs)dZddZdZRS(soSpecify the specific position of a boundary. o position - The position of the boundary. o extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types. In this case, there is no fuzziness associated with the position. icsD|djotd|nti||ddS(Nis)Non-zero extension %s for exact position.(s extensionsAttributeErrorsAbstractPositions__init__sselfsposition(sselfspositions extension((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__scst|iSdS(N(sstrsselfsposition(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__s(s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pys ExactPositions sWithinPositioncs)dZddZdZRS(sSpecify the position of a boundary within some coordinates. Arguments: o position - The start position of the boundary o extension - The range to which the boundary can extend. This allows dealing with a position like ((1.4)..100). This indicates that the start of the sequence is somewhere between 1 and 4. To represent that with this class we would set position as 1 and extension as 3. icsti|||dS(N(sAbstractPositions__init__sselfspositions extension(sselfspositions extension((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__scs%d|i|i|ifSdS(Ns(%s.%s)(sselfspositions extension(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__s(s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pysWithinPositions sBetweenPositioncs)dZddZdZRS(sSpecify the position of a boundary between two coordinates. Arguments: o position - The start position of the boundary. o extension - The range to the other position of a boundary. This specifies a coordinate which is found between the two positions. So this allows us to deal with a position like ((1^2)..100). To represent that with this class we set position as 1 and the extension as 1. icsti|||dS(N(sAbstractPositions__init__sselfspositions extension(sselfspositions extension((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__scs%d|i|i|ifSdS(Ns(%s^%s)(sselfspositions extension(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__s(s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pysBetweenPositions sBeforePositioncs)dZddZdZRS(sSpecify a position where the actual location occurs before it. Arguments: o position - The upper boundary of where the location can occur. o extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types. This is used to specify positions like (<10..100) where the location occurs somewhere before position 10. icsD|djotd|nti||ddS(Nis)Non-zero extension %s for exact position.(s extensionsAttributeErrorsAbstractPositions__init__sselfsposition(sselfspositions extension((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__scsd|iSdS(Ns<%s(sselfsposition(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__s(s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pysBeforePositions s AfterPositioncs)dZ%&ddZ,dZRS(sSpecify a position where the actual location is found after it. Arguments: o position - The lower boundary of where the location can occur. o extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types. This is used to specify positions like (>10..100) where the location occurs somewhere after position 10. icsD&'|djo(td|n*ti||ddS(Nis)Non-zero extension %s for exact position.(s extensionsAttributeErrorsAbstractPositions__init__sselfsposition(sselfspositions extension((s'/mit/seven/lib/python/Bio/SeqFeature.pys__init__&scs,-d|iSdS(Ns>%s(sselfsposition(sself((s'/mit/seven/lib/python/Bio/SeqFeature.pys__str__,s(s__doc__s__init__s__str__(((s'/mit/seven/lib/python/Bio/SeqFeature.pys AfterPositions N( s__doc__s SeqFeatures ReferencesFeatureLocationsAbstractPositions ExactPositionsWithinPositionsBetweenPositionsBeforePositions AfterPosition( s SeqFeaturesBetweenPositionsAbstractPositions AfterPositionsFeatureLocations References ExactPositionsWithinPositionsBeforePosition((s'/mit/seven/lib/python/Bio/SeqFeature.pys?'s 9)<