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Added Windows and Mac binaries of KaKs_Calculator
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‎AlignmentProcessor.py‎

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'''AlignmentProcessor will run the subsituion rate pipeline to produce trimmed
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axt or phylip files for use with KaKs_calculator or PhyMl.
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Copyright 2016 by Shawn Rupp
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This package is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.'''
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from datetime import datetime
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from sys import argv
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from subprocess import Popen
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from shlex import split
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from glob import glob
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import os
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def makeDir(path, outdir, axt, phylip):
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'''Makes all sub-directories used by program.'''
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os.chdir(outdir)
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for i in ["01_splitFastaFiles", "02_rmHeader", "03_checkFrame",
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"04_countBasesPercent", "05_ReplaceStopCodons"]:
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try:
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os.mkdir(i)
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except FileExistsError:
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pass
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if axt == True:
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for i in ["06_axtFiles", "KaKsOutput"]:
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try:
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os.mkdir(i)
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except FileExistsError:
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pass
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if phylip == True:
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for i in ["06_phylipFiles", "07_codeml"]:
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try:
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os.mkdir(i)
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except FileExistsError:
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pass
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os.chdir(path)
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def convertHeaders(fasta):
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'''Changes headers of UCSC CDS fasta files to includ eonly build name and
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gene ID'''
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print("Converting fasta headers...")
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ch = Popen(split("python bin/00_ConvertHeader.py " + fasta))
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ch.wait()
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# Extcact converted file name
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path = fasta.split("/")[:-1]
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outpath = ""
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for i in path:
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outpath += i + "/"
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newfasta = outpath + "newHeader." + fasta.split("/")[-1]
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if ch.returncode == 0:
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return True, newfasta
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def splitFasta(fasta, outdir):
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'''Splits fasta alignment into one file per gene.'''
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print("Splitting fasta file into separate files by gene...")
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sf = Popen(split("python bin/01_SplitFastaFiles.py " + " "
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+ fasta + " " + outdir))
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sf.wait()
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if sf.returncode == 0:
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return True
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def rmHeader(outdir):
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'''Removes header information and changes genome build to common name.'''
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print("Changing header...")
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rh = Popen(split("python bin/02_RemoveHeader.py " + outdir))
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rh.wait()
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if rh.returncode == 0:
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return True
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def checkFrame(outdir, ref):
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'''Checks nucleotide frame of secondary species against the reference
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species'''
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print("Checking nucleotide frames...")
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cf = Popen(split("python bin/03_CheckFrame.py " + " " + outdir
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+ " " + ref))
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cf.wait()
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if cf.returncode == 0:
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return True
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def countBases(outdir, percent):
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'''Checks that each species has at least 50% of it's nucleotide content.'''
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print("Checking nucleotide content...")
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cb = Popen(split("python bin/04_CountBases.py " + " " + percent +
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" " + outdir))
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cb.wait()
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if cb.returncode == 0:
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return True
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def replaceStop(outdir):
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'''Removes stop codons for downstream analysis.'''
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print("Removing stop codons...")
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rs = Popen(split("python bin/05_ReplaceStopCodons.py " + " "
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+ outdir))
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rs.wait()
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if rs.returncode == 0:
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return True
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def axtConvert(outdir, kaks, starttime):
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'''Open all input files in the directory and convert to axt script for
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use with KaKs_Calculator'''
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print("Converting fasta files into axt files...")
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ac = Popen(split("python bin/06_FASTAtoAXT.py " + outdir))
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ac.wait()
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if ac.returncode == 0:
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if kaks == True:
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return True
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elif kaks == False:
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print("Finished converting files.")
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elapsedtime = datetime.now() - starttime
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print("Total runtime: ", elapsedtime)
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def calculateKaKs(outdir):
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'''Calculates substition rates.'''
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print("Calculating Ka/Ks values...")
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ck = Popen(split("python bin/07_KaKsonDir.py " + outdir))
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ck.wait()
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if ck.returncode == 0:
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return True
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def printCSV(outdir, starttime):
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'''Prints Ka/Ks output as a single csv file.'''
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print("Printing Ka/Ks output as a single text file...")
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Popen(split("python bin/08_compileKaKs.py " + outdir))
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print("Finished calculating Ka/Ks values.")
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elapsedtime = datetime.now() - starttime
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print("Total runtime: ", elapsedtime)
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def phylipConvert(outdir, starttime, codeml):
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'''Converts fasta files to phylip format'''
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print("Converting fasta files to phylip...")
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pc = Popen(split("python bin/06_FASTAtoPhylip.py " + " " + outdir))
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pc.wait()
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if pc.returncode == 0:
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if codeml == False:
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elapsedtime = datetime.now() - starttime
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print("Total runtime: ", elapsedtime)
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return True
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def runcodeml(outdir, starttime):
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'''Runs codeml on a directory.'''
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print("Running codeml...")
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cm = Popen(split("python bin/07_CodeMLonDir.py " + outdir + "codeml.ctl "
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+ outdir))
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cm.wait()
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if cm.returncode == 0:
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elapsedtime = datetime.now() - starttime
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print("Total runtime: ", elapsedtime)
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def helplist():
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print()
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print("### AlignmentProcessor will run the subsituion rate pipeline to \
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produce trimmed axt files for use with KaKs_calculator. ###")
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print(" example usage: python AlignmentProcessor.py -% <decimal> \
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--axt/phylip --kaks/codeml -i <input fasta file> -o \
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<path to output directory> -r <reference species>")
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print(" --axt Converts files to axt for use in KaKs_Calcuator.")
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print(" --phylip Converts files to phylip for use in PhyML.")
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print(" --kaks Runs KaKs_Calcuator if --axt is also specified")
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print(" --codeml Runs codeml if --phylip is also specified")
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print(" --ucsc converts headers of CDS fasta files obtained from \
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the UCSC genome browser")
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print(" -r the name of the reference species which will be used to \
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determine the open reading frame")
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print(" -% Sets the percentage cutoff for the countBases step (50% \
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by default).")
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print(" -i path to input file containing a multifasta alignment")
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print(" -o AlignmentProcessor will use this as its working \
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directory and print output to this directory")
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print(" -v prints coyright and version information to the screen")
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print("### Please note that you must be in the substituionManager \
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directory to run the program.###")
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print()
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def main():
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starttime = datetime.now()
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# Set optional parameters to False:
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axt = False
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phylip = False
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kaks = False
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codeml = False
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conv = False
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percent = "0.5"
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# Extract values from command line:
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for i in argv:
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if i == "-h" or i == "--help":
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helplist()
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quit()
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elif i == "-v" or i == "--version":
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print("\nAlignmentProcessor Copyright 2016 by Shawn Rupp\n")
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print("This program comes with ABSOLUTELY NO WARRANTY")
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print("This is free software, and you are welcome to redistribute\
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it under certain conditions\n")
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quit()
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elif i == "-i":
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fasta = argv[argv.index(i) + 1]
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elif i == "-o":
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outdir = argv[argv.index(i) + 1]
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if outdir[-1] != "/":
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outdir = outdir + "/"
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elif i == "-r":
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ref = argv[argv.index(i) + 1]
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elif i == "-%":
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percent = argv[argv.index(i) + 1]
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elif i == "--axt":
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axt = True
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elif i == "--phylip":
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phylip = True
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elif i == "--kaks":
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kaks = True
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elif i == "--codeml":
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codeml = True
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elif i == "--ucsc":
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conv = True
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# Save working directory to variable to call other scripts:
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path = os.getcwd()
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path = path + "/"
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# Run program if the user did not ask for help:
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if "-h" not in argv and "--help" not in argv:
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# Set checkpoint variables to False:
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ch = False
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sf = False
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rh= False
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cf = False
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cb = False
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rs = False
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ac = False
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ck = False
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pc = False
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# Begin pipeline
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makeDir(path, outdir, axt, phylip)
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if conv == True:
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ch, newfasta = convertHeaders(fasta)
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if ch == True:
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sf = splitFasta(newfasta, outdir)
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else:
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sf = splitFasta(fasta, outdir)
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if sf == True:
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rh = rmHeader(outdir)
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if rh == True:
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cf = checkFrame(outdir, ref)
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if cf == True:
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cb =countBases(outdir, percent)
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if cb == True:
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rs = replaceStop(outdir)
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# Optionally covert files to axt format:
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if axt == True:
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if rs == True:
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ac = axtConvert(outdir, kaks, starttime)
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# Run KaKs_Calculator:
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if kaks == True and codeml == False:
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if ac == True:
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ck = calculateKaKs(outdir)
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if ck == True:
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printCSV(outdir, starttime)
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# Optionally covert files to phylip format:
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if phylip == True:
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if rs == True:
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pc = phylipConvert(outdir, starttime, codeml)
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# Run codeml
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if codeml == True and kaks == False:
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if pc == True:
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runcodeml(outdir, starttime)
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if __name__ == "__main__":
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main()

‎AlignmentProcessorReadMe.txt‎

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###############################################################
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# AlignmentProcessor0.6 Package
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# AlignmentProcessor0.7 Package
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#
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# Dependencies: Python 3
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# Python 3 version of Biopython
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# Perl
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# PAML (comes packaged with Linux binaries)
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###############################################################
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### Contents ###
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conda install -c https://conda.anaconda.org/anaconda biopython
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# KaKs_Calculator
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AlignmentProcessor0.7 is packaged with KaKs_Calculator2.0 binaries for Linux
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and Windows, and a KaKs_Calculator1.2 binary for Mac (there is no 2.0 binary
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available for OSX). Before using, copy or move the appropriate binary for your
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system into the AlignmentProcessor bin which contains the python scipts.
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# PAML 4.8
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AlignmentProcessor0.7 comes packaged with Linux binaries of PAML 4.8. If you
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are using Mac or Windows, you will have to replace the Linux binaries with the
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appropriate package for you system
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(http://abacus.gene.ucl.ac.uk/software/paml.html). Make sure that it is
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titled "paml".
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#-------------------------------
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# 1. Obtaining a fasta alignment
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#-------------------------------
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# Example Usage:
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python substituionManager0.3.py -% <decimal> \
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python AlignmentProcessor.py -% <decimal> \
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--axt/phylip --kaks/codeml --ucsc -i <input fasta file> \
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-o <path to output directory> -r <reference species>
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that they are unique for each file. You may also need to provide a
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tree file for codeml (see PAML manual above).
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The control file must be titled titled “codeml.ctl”, and it must be
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locatedin the output directory.
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# Invoking the Ka/Ks pipeline with a UCSC alignment:
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python AlignmentProcessor0.6.py --axt --kaks --ucsc -r green_anole \
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python AlignmentProcessor0.7.py --axt --kaks --ucsc -r green_anole \
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-i anolis_gallus.fa -o pairwiseKaKs/
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# Invoking the CodeML pipeline with a de novo alignment:
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python AlignmentProcessor0.6.py --phylip --codeml -% 0.6 \
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python AlignmentProcessor0.7.py --phylip --codeml -% 0.6 \
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-r green_anole -i anolis_gallus.fa -o codemlOutput/
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#-------------------------------
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Change directory into the AlignmentProcessor folder. Paste the followig into
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a terminal (change the output directory to the desired loaction):
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python AlignmentProcessor0.6.py --axt --kaks --ucsc -r green_anole \
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python AlignmentProcessor.py --axt --kaks --ucsc -r green_anole \
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-i test.fa -o test/
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It should procude a text file with 17 lines.

‎bin/00_ConvertHeader.py‎

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UCSC into headers which are compliant with AlignmentProcessor.
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AlignmentProcessor0.6 Copyright 2016 by Shawn Rupp
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License (GPL3.txt) for more details.'''
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Copyright 2016 by Shawn Rupp'''
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from sys import argv
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‎bin/01_SplitFastaFiles.py‎

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and create individual FASTA alignment files for each gene.
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AlignmentProcessor0.6 Copyright 2016 by Shawn Rupp
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License (GPL3.txt) for more details.'''
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Copyright 2016 by Shawn Rupp'''
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from sys import argv
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