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updating header in guidance.py

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Auden Cote-L'Heureux 2025-01-19 11:07:25 -05:00 committed by GitHub
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1 changed files with 4 additions and 4 deletions
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PTL2/Scripts/guidance.py
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@ -2,11 +2,11 @@
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero # Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
# This script runs Guidance in an iterative fashion for more both MSA construction # This script runs Guidance in an iterative fashion for more both MSA construction
# and more rigorous homology assessment than what is offered in PhyloToL 6 part 1. # and more rigorous homology assessment than what is offered in EukPhylo part 1.
# Guidance runs until the input number of iterations (--guidance_iters, default = 5) # Guidance runs until the input number of iterations (--guidance_iters, default = 5)
# has been reached, or until there are no sequences below the sequence score cutoff. # has been reached, or until there are no sequences below the sequence score cutoff.
# All sequences below the score cutoff (--seq_cutoff, default = 0.3) are removed at # All sequences below the score cutoff (--seq_cutoff, default = 0.3) are removed at
# each iteration. By default, PhyloToL does not remove residues that fall below the # each iteration. By default, EukPhylo does not remove residues that fall below the
# given residue cutoff (--res_cutoff) and columns that fall below the given column # given residue cutoff (--res_cutoff) and columns that fall below the given column
# cutoff (--col_cutoff, defaults are 0), though this can be turned on by adjusting # cutoff (--col_cutoff, defaults are 0), though this can be turned on by adjusting
# these parameters. Outputs at this point are found in the “Guidance_NotGapTrimmed” # these parameters. Outputs at this point are found in the “Guidance_NotGapTrimmed”
@ -16,7 +16,7 @@
# This step is either intended to be run starting with --start = unaligned (but not raw) # This step is either intended to be run starting with --start = unaligned (but not raw)
# inputs, meaning one amino acid alignment per OG. It can also be run directly after the # inputs, meaning one amino acid alignment per OG. It can also be run directly after the
# preguidance step. The run() function is called in two places: in phylotol.py generally, # preguidance step. The run() function is called in two places: in eukphylo.py generally,
# and in contamination.py if the contamination loop is using Guidance as the re-alignment # and in contamination.py if the contamination loop is using Guidance as the re-alignment
# method. # method.
@ -24,7 +24,7 @@
import os, sys, re import os, sys, re
from Bio import SeqIO from Bio import SeqIO
#Called in phylotol.py and contamination.py #Called in eukphylo.py and contamination.py
def run(params): def run(params):
if params.start == 'raw' or params.start == 'unaligned': if params.start == 'raw' or params.start == 'unaligned':