#!/usr/bin/env perl *TC_METHOD_FORMAT_01 ******************generic_method.tc_method************* * * Incorporating new methods in T-Coffee * Cedric Notredame 26/08/08 * ******************************************************* *This file is a method file *Copy it and adapt it to your need so that the method *you want to use can be incorporated within T-Coffee ******************************************************* * USAGE * ******************************************************* *This file is passed to t_coffee via -in: * * t_coffee -in Mgeneric_method.method * * The method is passed to the shell using the following *call: * * *Conventions: * *: no_name <=> Replaced with a space *:   <=> Replaced with a space * ******************************************************* * ALN_MODE * ******************************************************* *pairwise ->all Vs all (no self )[(n2-n)/2aln] *m_pairwise ->all Vs all (no self)[n^2-n]^2 *s_pairwise ->all Vs all (self): [n^2-n]/2 + n *multiple ->All the sequences in one go * ALN_MODE pairwise * ******************************************************* * OUT_MODE * ******************************************************* * mode for the output: *External methods: * aln -> alignmnent File (Fasta or ClustalW Format) * lib-> Lib file (TC_LIB_FORMAT_01) *Internal Methods: * fL -> Internal Function returning a List (Librairie) * fA -> Internal Function returning an Alignmnent * OUT_MODE aln ******************************************************* * SEQ_TYPE * ******************************************************* *G: Genomic, S: Sequence, P: PDB, R: Profile *Examples: *SEQTYPE S sequences against sequences (default) *SEQTYPE S_P sequence against structure *SEQTYPE P_P structure against structure *SEQTYPE PS mix of sequences and structure * SEQ_TYPE S * ******************************************************* * COMMAND LINE * *EXECUTABLE PARAM1 IN_FLAG OUT_FLAG PARAM * ******************************************************* ******************************************************* * EXECUTABLE * ******************************************************* *name of the executable *passed to the shell: executable * EXECUTABLE muscle * ******************************************************* * IN_FLAG * ******************************************************* *IN_FLAG *flag indicating the name of the in coming sequences *IN_FLAG S no_name ->no flag *IN_FLAG S &bnsp-in&bnsp -> " -in " * IN_FLAG &bnsp-in&bnsp * ******************************************************* * OUT_FLAG * ******************************************************* *OUT_FLAG *flag indicating the name of the out-coming data *same conventions as IN_FLAG *OUT_FLAG S no_name ->no flag *if you want to redirect, pass the parameters via PARAM1 *set OUT_FLAG to > * OUT_FLAG &bnsp-out&bnsp * ******************************************************* * PARAM_1 * ******************************************************* * *Parameters sent to the EXECUTABLE and specified *before* IN_FLAG *If there is more than 1 PARAM line, the lines are *concatenated *Command_line: @EP@PARAM@-gapopen%e10%s-gapext%e20 * %s white space * %e equal sign * *PARAM1 * * * ******************************************************* * PARAM_2 * ******************************************************* * *Parameters sent to the EXECUTABLE and specified *after* IN_FLAG and *before* OUT_FLAG *If there is more than 1 PARAM line, the lines are *concatenated * PARAM1 -maxiters 20 * * ******************************************************* * PARAM * ******************************************************* * *Parameters sent to the EXECUTABLE and specified *after* OUT_FLAG *If there is more than 1 PARAM line, the lines are *concatenated * *PARAM -mode=seq_msa -method=clustalw *PARAM -OUTORDER=INPUT -NEWTREE=core -align -gapopen=-15 PARAM &bnsp2>/dev/null * ******************************************************* * END * *******************************************************