:>"^$@sdZddlmZddlmZddlmZddlmZddl m Z ddl m Z ddl m Z mZed d ZGd d d e Zd dZedkrddlmZedddS)a!Bio.SeqIO support for the "tab" (simple tab separated) file format. You are expected to use this module via the Bio.SeqIO functions. The "tab" format is an ad-hoc plain text file format where each sequence is on one (long) line. Each line contains the identifier/description, followed by a tab, followed by the sequence. For example, consider the following short FASTA format file:: >ID123456 possible binding site? CATCNAGATGACACTACGACTACGACTCAGACTAC >ID123457 random sequence ACACTACGACTACGACTCAGACTACAAN Apart from the descriptions, this can be represented in the simple two column tab separated format as follows:: ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC ID123457(tab)ACACTACGACTACGACTCAGACTACAAN When reading this file, "ID123456" or "ID123457" will be taken as the record's .id and .name property. There is no other information to record. Similarly, when writing to this format, Biopython will ONLY record the record's .id and .seq (and not the description or any other information) as in the example above. )print_function)single_letter_alphabet) as_handle)Seq) SeqRecord)SequentialSequenceWriter)_clean_get_seq_stringccst|d}x|D]}y|jd\}}WnJtk r|jdkr]wtdd|jd|fYnX|j}|j}tt||d|d|ddVqWWd QRXd S) a,Iterate over tab separated lines as SeqRecord objects. Each line of the file should contain one tab only, dividing the line into an identifier and the full sequence. Arguments: - handle - input file - alphabet - optional alphabet The first field is taken as the record's .id and .name (regardless of any spaces within the text) and the second field is the sequence. Any blank lines are ignored. Examples -------- >>> with open("GenBank/NC_005816.tsv") as handle: ... for record in TabIterator(handle): ... print("%s length %i" % (record.id, len(record))) gi|45478712|ref|NP_995567.1| length 340 gi|45478713|ref|NP_995568.1| length 260 gi|45478714|ref|NP_995569.1| length 64 gi|45478715|ref|NP_995570.1| length 123 gi|45478716|ref|NP_995571.1| length 145 gi|45478717|ref|NP_995572.1| length 357 gi|45478718|ref|NP_995573.1| length 138 gi|45478719|ref|NP_995574.1| length 312 gi|45478720|ref|NP_995575.1| length 99 gi|45478721|ref|NP_995576.1| length 90 rU z,Each line should have one tab separating thez. title and sequence, this line has %i tabs: %ridname descriptionN)rsplit ValueErrorstripcountrr)handleZalphabetlinetitleseqr4/tmp/pip-build-ww9dw3qa/biopython/Bio/SeqIO/TabIO.py TabIterator-s     rc@s"eZdZdZddZdS) TabWriteraLClass to write simple tab separated format files (OBSOLETE). Each line consists of "id(tab)sequence" only. Any description, name or other annotation is not recorded. This class is now obsolete. Please use the function ``as_tab`` instead, or the top level ``Bio.SeqIO.write()`` function with ``format="tab"``. cCsB|jst|j std|_|jjt|dS)z$Write a single tab line to the file.TN)Z_header_writtenAssertionErrorZ_footer_writtenZ_record_writtenrwriteas_tab)selfrecordrrr write_recordjs zTabWriter.write_recordN)__name__ __module__ __qualname____doc__r!rrrrr_s rcCst|j}t|}d|ks-td|ks?td|ksQtd|ksctd|ksutd|kstd||fS)z3Return record as tab separated (id(tab)seq) string.r   z%s %s )rr r r)r rrrrrrrs r__main__) run_doctestverboseN)r% __future__rZ Bio.AlphabetrZBio.FilerZBio.SeqrZ Bio.SeqRecordrZBio.SeqIO.Interfacesrrr rrrr"Z Bio._utilsr)rrrr!s2