OrthoTools.py

#"""Orthologs Tools"""
#import os
#from ete3 import EvolTree, Tree
#import pandas as pd
#
## Create a variable for os.rename
#rn = os.rename
#
## ETE3 Tools
#
#
#def ete3paml(gene, paml_path, workdir='data/paml-output/', model='M1'):
#    """ Use ETE3's integration with PAML"""
#
#    # Import the species tree to compare species that are present in alignment
#    # file
#    t = Tree('data/initial-data/species_tree.nw', format=1)
#    orgsfile = pd.read_csv('data/initial-data/organisms.csv', header=None)
#
#    # Create a list name/variable and use list()
#    orgs = list(orgsfile[0])
#    organismslist = formatlist(orgs)
#
#    # Import alignment file as string
#    alignment_file = open('data/clustal-output/' + gene + '_Aligned/' + gene +
#                          '_aligned_cds_nucl.fasta', 'r')
#    alignment_str = alignment_file.read()
#    alignment_file.close()
#
#    # Keep the branches in the species tree for species in the alignment file
#    # Some species may not be present in the alignment file
#    branches2keep = []
#    for organism in organismslist:
#        if organism in alignment_str:
#            # print('Yup.')
#            branches2keep.append(organism)
#        else:
#            pass
#            # print('Nope.') Make an error code in the log
#
#    # Input a list of branches to keep on the base tree
#    speciestree = t.prune(branches2keep, preserve_branch_length=True)
#
#    # Import the newick tree
#    tree = EvolTree(speciestree)
#
#    # Import the alignment
#    tree.link_to_alignment(
#        'data/clustal-output/' +
#        gene +
#        '_Aligned/' +
#        gene +
#        '_aligned_cds_nucl.fasta')
#
#    tree.workdir = workdir
#
#    # Set the binpath of the codeml binary
#    tree.execpath = paml_path
#
#    # Run the codeml model
#    tree.run_model(model + '.' + gene)