ó ²“Ic@sdZddlmZddlmZddlmZddlmZed„Z defd„ƒYZ e d krd GHdd l m Z e d ƒZ ee e ƒƒZeeƒd ks¿t‚e dƒZ y(ee e ƒƒZesòtdƒ‚Wnek rnXdGHndS(sBio.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. iÿÿÿÿ(tsingle_letter_alphabet(tSeq(t SeqRecord(tSequentialSequenceWriterccs±xª|D]¢}y|jdƒ\}}WnH|jƒdkrDqntdd|jdƒt|ƒfƒ‚nX|jƒ}|jƒ}tt||ƒd|d|ƒVqWdS(s£Iterates 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. 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. s ts,Each line should have one tab separating thes. title and sequence, this line has %i tabs: %stidtnameN(tsplittstript ValueErrortcounttreprRR(thandletalphabettlinettitletseq((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/TabIO.pyt TabIterator(s $  t TabWritercBseZdZd„ZRS(s©Class to write simple tab separated format files. Each line consists of "id(tab)sequence" only. Any description, name or other annotation is not recorded. cCsÓ|jst‚|j st‚t|_|j|jƒ}|j|ƒ}d|ks[t‚d|ksmt‚d|kst‚d|ks‘t‚d|ks£t‚d|ksµt‚|jj d||fƒdS(s$Write a single tab line to the file.s s s s%s %s N( t_header_writtentAssertionErrort_footer_writtentTruet_record_writtentcleanRt_get_seq_stringR twrite(tselftrecordRR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/TabIO.pyt write_recordKs (t__name__t __module__t__doc__R(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/TabIO.pyRDst__main__sRunning quick self test(tStringIOsAlpha AAAAAAA Beta CCCCCCC is!Alpha AAAAAAA Extra Beta CCCCCCC s(Should have reject this invalid example!tDoneN(R t Bio.AlphabetRtBio.SeqRt Bio.SeqRecordRt InterfacesRRRRR"R tlisttrecordstlenRtFalseR (((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/TabIO.pyt s&