o Rŀg!@sZdZddlmZddlmZddlmZGdddeZedkr+ddlmZed Sd S) z@Command line wrapper for the multiple alignment program TCOFFEE.)_Option)_Switch)AbstractCommandlinec@s"eZdZdZgdZdddZdS)TCoffeeCommandlineaCommandline object for the TCoffee alignment program. http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html The T-Coffee command line tool has a lot of switches and options. This wrapper implements a VERY limited number of options - if you would like to help improve it please get in touch. Notes ----- Last checked against: Version_6.92 References ---------- T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins, Heringa, JMB,302(205-217) 2000 Examples -------- To align a FASTA file (unaligned.fasta) with the output in ClustalW format (file aligned.aln), and otherwise default settings, use: >>> from Bio.Align.Applications import TCoffeeCommandline >>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta", ... output="clustalw", ... outfile="aligned.aln") >>> print(tcoffee_cline) t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln You would typically run the command line with tcoffee_cline() or via the Python subprocess module, as described in the Biopython tutorial. )dnaprotein dna_proteint_coffeec stddgdddtddgdd d dd td d gd d ddtddgdtddgdfddddtddgdddtddgdddtddgd d!dddtd"d#gd$d%dddtd&d'gd(td)d*gd+ddg _tj|fi|d,S)-zInitialize the class.z-outputoutputzSpecify the output type. One (or more separated by a comma) of: 'clustalw_aln', 'clustalw', 'gcg', 'msf_aln', 'pir_aln', 'fasta_aln', 'phylip', 'pir_seq', 'fasta_seq' F)equatez-infileinfilezSpecify the input file.T)filename is_requiredr z-outfileoutfilez6Specify the output file. Default: .aln)r r z-convertconvertz-Specify you want to perform a file conversionz-typetypez*Specify the type of sequence being alignedcs |jvSN) SEQ_TYPESxselfS/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_TCoffee.pyU z-TCoffeeCommandline.__init__..)checker_functionr z -outorderoutorderzpSpecify the order of sequence to outputEither 'input', 'aligned' or of Fasta file with sequence orderz-matrixmatrixzKSpecify the filename of the substitution matrix to use. Default: blosum62mtz-gapopengapopenzBIndicates the penalty applied for opening a gap (negative integer)cS t|tSr isinstanceintrrrrrhrz-gapextgapextzDIndicates the penalty applied for extending a gap (negative integer)cSr rr!rrrrrnrz-quietquietzTurn off log outputz-modemodez:Specifies a special mode: genome, quickaln, dali, 3dcoffeeN)rr parametersr__init__)rcmdkwargsrrrr(3sr    CzTCoffeeCommandline.__init__N)r )__name__ __module__ __qualname____doc__rr(rrrrrs"r__main__) run_doctestN) r.Bio.Applicationrrrrr+ Bio._utilsr0rrrrs   m