o Rŀg?0@sdZddlmZddlmZddlmZddlmZddlm Z ddlm Z Gdd d e Z Gd d d eZ e d krEdd lmZedSdS)zBio.Align support module (not for general use). Unless you are writing a new parser or writer for Bio.Align, you should not use this module. It provides base classes to try and simplify things. )ABC)abstractmethod)Optional)StreamModeError) Alignments)AlignmentsAbstractBaseClassc@sreZdZUdZdZdZeeed<ddZ ddZ d d Z d d Z d dZ ddZddZeddZddZdS)AlignmentIteratoralBase class for building Alignment iterators. You should write a parse method that returns an Alignment generator. You may wish to redefine the __init__ method as well. Subclasses may define the following class attributes: - mode - 't' or 'b' for text or binary files, respectively - fmt - a human-readable name for the file format. tNfmtcCs||_z t|d|j|_WnBtyP|jdkr+|ddkr*t|jddn |jdkrA|ddkr@t|jd dn td |jd d||_Ynwd|_ | |jdS) aOCreate an AlignmentIterator object. Arguments: - source - input file stream, or path to input file This method MAY be overridden by any subclass. Note when subclassing: - there should be a single non-optional argument, the source. - you can add additional optional arguments. rr rz# files must be opened in text mode.Nbz% files must be opened in binary mode.zUnknown mode '') sourceopenmode_stream TypeErrorreadrr ValueError_index _read_header)selfrrH/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/interfaces.py__init__&s2       zAlignmentIterator.__init__cCsPz|j}Wn tytdw||}|dur|j|_t|jd7_|S)zReturn the next alignment.N)rAttributeError StopIteration_read_next_alignmentr_len)rstream alignmentrrr__next__Fs   zAlignmentIterator.__next__cCspz|j}W|Sty7|j}|d}|D]}|d7}q||j|kr1t||j|ks(||_Y|Sw)a@Return the number of alignments. The number of alignments is cached. If not yet calculated, the iterator is rewound to the beginning, and the number of alignments is calculated by iterating over the alignments. The iterator is then returned to its original position in the file. rr)r!rrrewindnext)rlengthindexr#rrr__len__Ss     zAlignmentIterator.__len__cCs|SNrrrrr __enter__iszAlignmentIterator.__enter__cCs:z|j}Wn tyYdSw||jur||`dSr*)rrrclose)rexc_type exc_value exc_tracebackr"rrr__exit__ls   zAlignmentIterator.__exit__cCs|tdddkr tdt|j}|j}t}|j}|d||||| ||j|_ ||j|krCt ||j|ks:|S)aReturn the alignments as an Alignments object (which inherits from list). Only an index of the form [:] (i.e., a full slice) is supported. The file stream is returned to its zero position, and the file header is read and stored in an Alignments object. Next, we iterate over the alignments and store them in the Alignments object. The iterator is then returned to its original position in the file, and the Alignments object is returned. The Alignments object contains the exact same information as the Alignment iterator self, but stores the alignments in a list instead of as an iterator, allowing indexing. Typical usage is >>> from Bio import Align >>> alignments = Align.parse("Blat/dna_rna.psl", "psl") >>> alignments.metadata {'psLayout version': '3'} As `alignments` is an iterator and not a list, we cannot retrieve an alignment by its index: >>> alignment = alignments[2] # doctest:+ELLIPSIS Traceback (most recent call last): ... KeyError: 'only [:] (a full slice) can be used as the index' So we use the iterator to create a list-like Alignments object: >>> alignments = alignments[:] While `alignments` is a list-like object, it has the same `metadata` attribute representing the information stored in the file header: >>> alignments.metadata {'psLayout version': '3'} Now we can index individual alignments: >>> len(alignments) 4 >>> alignment = alignments[2] >>> alignment.target.id, alignment.query.id ('chr3', 'NR_111921.1') Nz0only [:] (a full slice) can be used as the indexr) sliceKeyErrortyperrrrseekr%extendr!r&)rr( read_header alignmentsr"rrr __getitem__us .      zAlignmentIterator.__getitem__cCdS)z.Read the file header and store it in metadata.Nrrr"rrrrzAlignmentIterator._read_headercCr:)z2Read one Alignment from the stream, and return it.Nrr;rrrr sz&AlignmentIterator._read_next_alignmentcCs"|jd||jd|_dS)Nr)rr5rrr+rrrr%s   zAlignmentIterator.rewind)__name__ __module__ __qualname____doc__rr rstr__annotations__rr$r)r,r1r9rrr r%rrrrrs     B  rc@sjeZdZUdZdZdZeeed<ddZ ddZ d d Z d d Z d dZ ddZeZddZddZdS)AlignmentWriteraBase class for alignment writers. This class should be subclassed. It is intended for alignment file formats with an (optional) header, one or more alignments, and an (optional) footer. The user may call the write_file() method to write a complete file containing the alignments. Alternatively, users may call the write_header(), followed by multiple calls to format_alignment() and/or write_alignments(), followed finally by write_footer(). Subclasses may define the following class attributes: - mode - 'w' or 'wb' for text or binary files, respectively - fmt - a human-readable name for the file format. wNr cCs|durb|jdkr.z|dWntytddty*t||j}Yn5w|}n1|jdkrXz|dWntyFtddtyTt||j}Yn w|}ntd|j||_||_dS) aGCreate the writer object. Arguments: - target - output file stream, or path to output file This method MAY be overridden by any subclass. Note when subclassing: - there should be a single non-optional argument, the target. - you can add additional optional arguments. NrDr z!File must be opened in text mode.wbrz#File must be opened in binary mode.zUnknown mode '%s') rwriterrrr RuntimeErrorr_target)rtargetr"rrrrs4        zAlignmentWriter.__init__cCr:)z)Write the file header to the output file.Nr)rr"r8rrr write_headerr<zAlignmentWriter.write_headercCr:)z)Write the file footer to the output file.Nrr;rrr write_footerr<zAlignmentWriter.write_footercCstd)zXFormat a single alignment as a string. alignment - an Alignment object z!This method should be implemented)NotImplementedError)rr#rrrformat_alignmentsz AlignmentWriter.format_alignmentcCsHd}|D]}|dkrtd|jd||}|||d7}q|S)zWrite a single alignment to the output file, and return 1. alignments - A list or iterator returning Alignment objects stream - Output file stream. rrzAlignment files in the z, format can contain a single alignment only.)rr rMrFrr"r8countr#linerrrwrite_single_alignment s    z&AlignmentWriter.write_single_alignmentcCs.d}|D]}||}|||d7}q|S)zWrite alignments to the output file, and return the number of alignments. alignments - A list or iterator returning Alignment objects stream - Output file stream. rr)rMrFrNrrrwrite_multiple_alignments1s    z)AlignmentWriter.write_multiple_alignmentscCs&||||||}|||S)zWrite the alignments to the file strenm, and return the number of alignments. alignments - A list or iterator returning Alignment objects stream - Output file stream. )rJwrite_alignmentsrK)rr"r8rOrrr write_file@s   zAlignmentWriter.write_filecCsB|j}z|||}W||jur||S||jur |ww)zWrite a file with the alignments, and return the number of alignments. alignments - A list or iterator returning Alignment objects )rrTrHr-)rr8r"rOrrrrFKs  zAlignmentWriter.write)r=r>r?r@rr rrArBrrJrKrMrQrRrSrTrFrrrrrCs ,   rC__main__) run_doctestN)r@abcrrtypingrBior Bio.AlignrrrrCr= Bio._utilsrVrrrrs      .