def printMods(alignerArgs, indices):
printMod(indices[0], '[BRACKETED STRING STARTING WITH "#" CHARACTER] Extra command line arguments to pass to Pecan (SETTING SOME OPTIONS WILL BE INCOMPATIBLE WITH THESE SCRIPTS)')
printMod(indices[1], '[BRACKETED STRING STARTING WITH "#" CHARACTER] Extra command line arguments to pass to Ortheus (SETTING SOME OPTIONS WILL BE INCOMPATIBLE WITH THESE SCRIPTS)')
printMod(indices[2], '[BRACKETED STRING] Java string (i.e. java -server)')
printMod(indices[3], '[INTEGER] maximum number of alignment columns in chunk for Ortheus reconstruction')
printMod(indices[4], '[INTEGER] number of columns to leave between end of reconstruction chunk and final reconstruction')
return indices[5:]
def printMods(alignerArgs, indices):
printMod(indices[0], '[INTEGER] maximum number of sequences to align in nested clique, default %s ' % alignerArgs.MAX_SEQ_NO)
return indices[1:]
def printEstimateTreeMods(alignerArgs, indices):
printMod(indices[0], '[FLOAT] default distance to use for branches in initial star tree')
printMod(indices[1], '[INTEGER] number of iterations of tree estimation to run')
printMod(indices[2], '[STRING] path to Semphy executable')
printMod(indices[3], '[BRACKETED STRING STARTING WITH "#" CHARACTER] parameters to pass to Semphy for tree building')
printMod(indices[4], '[BRACKETED STRING STARTING WITH "#" CHARACTER] parameters to pass to Semphy for pairs of sequences')
printMod(indices[5], '[INTEGER] minimum number of columns to allow to allow for gapless tree estimations ')
printMod(indices[6], 'Do sub-tree estimation of the rate, default: %s' % alignerArgs.DO_SUBTREE_BRANCH_LENGTH_ESTIMATION)
printMod(indices[7], '[FLOAT] total sub tree distance to allow in subtrees used for branch length re-estimation')
printMod(indices[8], '[STRING] species tree, if provided will guess root of tree buy minimising the number of duplications')
printMod(indices[9], '[STRING]xN in order leaf species of the leaf sequences, needed if reconciliation-prediction of the root with the species tree is performed')
return indices[10:]
def printEstimateTreeMods(alignerArgs, indices):
printMod(
indices[0],
'[FLOAT] default distance to use for branches in initial star tree')
printMod(indices[1],
'[INTEGER] number of iterations of tree estimation to run')
printMod(indices[2], '[STRING] path to Semphy executable')
printMod(
indices[3],
'[BRACKETED STRING STARTING WITH "#" CHARACTER] parameters to pass to Semphy for tree building'
)
printMod(
indices[4],
'[BRACKETED STRING STARTING WITH "#" CHARACTER] parameters to pass to Semphy for pairs of sequences'
)
printMod(
indices[5],
'[INTEGER] minimum number of columns to allow to allow for gapless tree estimations '
)
printMod(
indices[6], 'Do sub-tree estimation of the rate, default: %s' %
alignerArgs.DO_SUBTREE_BRANCH_LENGTH_ESTIMATION)
printMod(
indices[7],
'[FLOAT] total sub tree distance to allow in subtrees used for branch length re-estimation'
)
printMod(
indices[8],
'[STRING] species tree, if provided will guess root of tree buy minimising the number of duplications'
)
printMod(
indices[9],
'[STRING]xN in order leaf species of the leaf sequences, needed if reconciliation-prediction of the root with the species tree is performed'
)
return indices[10:]
def printMods(alignerArgs, indices):
printMod(indices[0], '[BRACKETED STRING] set newick tree string ')
printMod(indices[1], '[STRING]xN set sequence files (this is a mandatory argument)')
printMod(indices[2], '[STRING] set output file (else output.mfa)')
printMod(indices[3], '[STRING] set output file for tree (else output.newick)')
printMod(indices[4], '[STRING] set output score file (else output.score)')
printMod(indices[5], '[FLOAT]x[ACGT] use following nucleotide frequencies (otherwise expected frequencies have a stationary GC of 40 percent -- this is passed to all the underlying relevant methods)')
printMod(indices[6], 'Empirically estimate stationary nucleotide frequencies from input sequences')
printMod(alignerArgs.MAKE_FINAL_ALIGNMENT_INDICE, 'Make alignment (i.e. don\'t just do tree estimation or whatever) default : %s' % alignerArgs.MAKE_FINAL_ALIGNMENT)
return indices[7:]
def printMods(alignerArgs, indices):
printMod(
indices[0],
'[INTEGER] maximum number of sequences to align in nested clique, default %s '
% alignerArgs.MAX_SEQ_NO)
return indices[1:]