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MAGNET.sh
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MAGNET.sh
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#!/bin/sh
##########################################################################################
# __ o __ __ __ |__ __ #
# |__) | | ' (__( | ) | ) (__( #
# | #
# #
# File: MAGNET.sh ~ MAny GeNE Trees, v1.2.0 #
VERSION="v1.2.0" #
# Author: Justin C. Bagley #
# Date: Created by Justin Bagley on Mon, Aug 29 13:12:45 2016 -0700. #
# Last update: December 23, 2020 #
# Copyright (c) 2016-2020 Justin C. Bagley. All rights reserved. #
# Please report bugs to <[email protected]>. #
# #
# Description: #
# SHELL PIPELINE FOR AUTOMATING ESTIMATION OF A MAXIMUM-LIKELIHOOD (ML) GENE TREE IN #
# RAxML FOR EACH OF MANY LOCI IN A RAD-seq, UCE, OR OTHER MULTILOCUS SEQUENCE DATASET #
# #
##########################################################################################
# Short present working directory (PWD) functions
# ------------------------------------------------------
# New common functions (most scripts written/edited from
# July 2020 onwards) for echoing $PWD, but truncating
# absolute path to precisely fit the Terminal window.
# Functions for two cases: 1) Regular PWD and 2) user-
# specified PWD.
# ------------------------------------------------------
function echoShortPWD () {
MY_ABS_PATH_LENGTH="$(echo "$PWD" | wc -c | sed 's/\ //g')";
MY_ABS_PATH_ECHO_LENGTH="$(calc "$MY_ABS_PATH_LENGTH"+43)";
MY_BASH_WINDOW_COLS="$(tput cols | sed 's/\ //g')";
#
if [[ "$MY_ABS_PATH_ECHO_LENGTH" -gt "85" ]] && [[ "$MY_ABS_PATH_ECHO_LENGTH" -gt "$MY_BASH_WINDOW_COLS" ]]; then
MY_CORRECTION_LENGTH="$(calc "$MY_ABS_PATH_ECHO_LENGTH"-"$MY_BASH_WINDOW_COLS"+3)";
MY_NUM_FINAL_PWD_CHARS="$(calc "$MY_ABS_PATH_LENGTH"-"$MY_CORRECTION_LENGTH")";
SHORT_PWD="$(echo ${PWD:${#PWD}<$MY_NUM_FINAL_PWD_CHARS?0:-$MY_NUM_FINAL_PWD_CHARS})"; ## Get last $MY_NUM_FINAL_PWD_CHARS characters of $PWD
echo "INFO | $(date) | Starting input directory (using current dir): "
echo "INFO | $(date) | ...$SHORT_PWD"
else
echo "INFO | $(date) | Starting input directory (using current dir): "
echo "INFO | $(date) | $PWD"
fi
}
# Working directory function
# ------------------------------------------------------
# Common function (most scripts) for echoing and cd'ing
# into user-specified working dir. Three cases: 1) cwd,
# 2) up one dir, and 3) some other dir.
# ------------------------------------------------------
function echoCDWorkingDir () {
if [[ -s "$USER_SPEC_PATH" ]]; then
if [[ "$USER_SPEC_PATH" = "$(printf '%q\n' "$(pwd -P)")" ]] || [[ "$USER_SPEC_PATH" = "." ]]; then
MY_CWD="$(printf '%q\n' "$(pwd -P)" | sed 's/\\//g')";
echo "INFO | $(date) | Setting working directory to: "
echo "INFO | $(date) | $MY_CWD "
elif [[ "$USER_SPEC_PATH" != "$(printf '%q\n' "$(pwd)")" ]]; then
if [[ "$USER_SPEC_PATH" = ".." ]] || [[ "$USER_SPEC_PATH" = "../" ]] || [[ "$USER_SPEC_PATH" = "..;" ]] || [[ "$USER_SPEC_PATH" = "../;" ]]; then
cd ..;
MY_CWD="$(printf '%q\n' "$(pwd)" | sed 's/\\//g')";
echo "INFO | $(date) | Setting working directory to user-specified dir: "
echo "INFO | $(date) | $MY_CWD "
else
MY_CWD=$USER_SPEC_PATH
cd "$MY_CWD";
echo "INFO | $(date) | Setting working directory to user-specified dir: "
echo "INFO | $(date) | $MY_CWD "
fi
else
echo "WARNING | $(date) | Null working directory path. Quitting... "
exit 1
fi
fi
}
# Calculator
# ------------------------------------------------------
# Function to send commands to Bash's arbitrary precision
# calculator language.
#
# A calculator function, which echos input to Bash bc.
# Usage: calc <math_commands>, e.g. calc 1+2, or with
# variables, e.g. calc $VAR1+$VAR2.
# ------------------------------------------------------
function calc () {
bc -l <<< "$@" ;
}
# Check machine type
# ------------------------------------------------------
# Common function for checking machine type, setting related
# variables.
# ------------------------------------------------------
function checkMachineType () {
unameOut="$(uname -s)";
case "${unameOut}" in
Linux*) machine=Linux;;
Darwin*) machine=Mac;;
CYGWIN*) machine=Cygwin;;
MINGW*) machine=MinGw;;
*) export machine="UNKNOWN:${unameOut}"
esac;
}
# Import variables
# ------------------------------------------------------
export EP=$(printf '!')
export TAB=$(printf '\t')
export CR=$(printf '\r')
MAGNET () {
######################################## START ###########################################
##########################################################################################
echo "INFO | $(date) |----------------------------------------------------------------"
echo "INFO | $(date) | MAGNET, v1.2.0 December 2020 "
echo "INFO | $(date) | Copyright (c) 2016-2020 Justin C. Bagley. All rights reserved. "
echo "INFO | $(date) |----------------------------------------------------------------"
# Single NEXUS (or .gphocs) file run
# ------------------------------------------------------
# Run on single input NEXUS file ('.nex'; also accepts single G-PhoCS
# formatted file, with extension '.gphocs') in current working directory,
# specified with -i flag.
# ------------------------------------------------------
#######
if [[ "$STARTING_FILE_TYPE" = "1" ]] && [[ "$MY_NEXUS" != "NULL" ]]; then
echo "INFO | $(date) | Starting MAGNET pipeline... "
echo "INFO | $(date) | Running with the following options: "
echo "INFO | $(date) | - NEXUS file, <inputNEXUS> = ${MY_NEXUS} "
echo "INFO | $(date) | - Starting <fileType> = ${STARTING_FILE_TYPE} "
echo "INFO | $(date) | - RAxML <executable> = ${MY_RAXML_EXECUTABLE} "
echo "INFO | $(date) | - Bootstrap reps, <numBootstraps> = ${MY_NUM_BOOTREPS} "
echo "INFO | $(date) | - RAxML model, <raxmlModel> = ${MY_RAXML_MODEL} "
echo "INFO | $(date) | - <simpleModel> option = ${MY_SIMPLE_MODEL} "
echo "INFO | $(date) | - <gapThreshold> option = ${MY_GAP_THRESHOLD} "
echo "INFO | $(date) | - <indivMissingData> option = ${MY_INDIV_MISSING_DATA} "
echo "INFO | $(date) | - Outgroup taxon, <outgroup> = ${MY_OUTGROUP} "
echo "INFO | $(date) | - RAxML output name = ${MY_OUTPUT_NAME} "
echo "INFO | $(date) | - Resume switch (--resume) = ${MY_RESUME_SWITCH} "
# --------------------------------------------------
# -- STEP #1: SETUP.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #1: Set up workspace (e.g. functions, working directory) and check machine type. " # | tee -a "$MY_OUTPUT_FILE_SWITCH"
echo "INFO | $(date) | ----------------------------------- "
# SET WORKING DIRECTORY AND CHECK MACHINE TYPE
# --------------------------------------------------
echoShortPWD
export MY_WORKING_DIR="$(pwd)"
checkMachineType
# START DEBUG MODE, IF CALLED
# --------------------------------------------------
if [[ "$MY_DEBUG_MODE_SWITCH" != "0" ]]; then set -xv; fi
# --------------------------------------------------
# -- STEP #2: HANDLE INPUT FILE(S).
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #2: Input single NEXUS (or G-PhoCS-formatted) file, or multiple PHYLIP files. "
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | For -f 1 or -f 2, if '.gphocs' input file present, continue; else convert NEXUS file "
echo "INFO | $(date) | to G-PhoCS format using NEXUS2gphocs code. If -f 3, then run multiple PHYLIP files in "
echo "INFO | $(date) | RAxML."
shopt -s nullglob
if [[ -n $(find . -name "*.gphocs" -type f) ]]; then
echo "INFO | $(date) | Found '.gphocs' input file... "
MY_GPHOCS_DATA_FILE=./*.gphocs ; ## Assign G-PhoCS-formatted genomic/SNP data file (originally produced/output by pyRAD) in run directory to variable.
else
echo "WARNING | $(date) | No '.gphocs' input file in current working directory... "
echo "INFO | $(date) | Attempting to convert NEXUS file, if present, to GPho-CS format... "
fi
# ---------------------------------------------------------- #
# ---------------- NEXUS2gphocs.sh FUNCTION ---------------- #
# ---------------------------------------------------------- #
NEXUS2gphocs_function () {
# GET NEXUS FILE & DATA CHARACTERISTICS, CONVERT NEXUS TO FASTA FORMAT
# --------------------------------------------------
# Extract charset info from sets block at end of NEXUS file:
# --------------------------------------------------
MY_NEXUS_CHARSETS="$(egrep "charset|CHARSET" "$MY_NEXUS" | \
awk -F"=" '{print $NF}' | sed 's/\;/\,/g' | \
awk '{a[NR]=$0} END {for (i=1;i<NR;i++) print a[i];sub(/.$/,"",a[NR]);print a[NR]}' | \
sed 's/\,/\,'$CR'/g' | sed 's/^\ //g')" ;
# Count number of loci present in the NEXUS file, based on number of charsets defined.
# Also get corrected count starting from 0 for numbering loci below...
MY_NLOCI="$(echo "$MY_NEXUS_CHARSETS" | wc -l)";
MY_CORR_NLOCI="$(calc "$MY_NLOCI" - 1)";
# This is the base name of the original nexus file, so you have it. This will not work if NEXUS file name is written in all caps, ".NEX", in the file name.
MY_NEXUS_BASENAME="$(echo "$MY_NEXUS" | sed 's/\.\///g; s/\.nex//g')";
# Convert data file from NEXUS to FASTA format using bioscripts.convert v0.4 Python package:
# However, if alignment is too long (>100,000 bp), then need to convert to FASTA using my
# script and then wrap to 60 characters with fold function (as suggested at stackexchange
# post URL: https://unix.stackexchange.com/questions/25173/how-can-i-wrap-text-at-a-certain-column-size).
# If this conversion failes because the alignment is too long, then the code to follow
# will have nothing to work with. So, I am here adding a conditional quit if the FASTA
# file is not generated.
#---------TODO: ADD IF/THEN CONDITIONAL AND MY OWN NEXUS2FASTA SCRIPT HERE!!!!----------#
convbioseq fasta "$MY_NEXUS" > "$MY_NEXUS_BASENAME".fasta ;
MY_FASTA="$(echo "$MY_NEXUS_BASENAME".fasta | sed 's/\.\///g; s/\.nex//g')";
# The line above creates a file with the name basename.fasta, where basename is the base name of the original .nex file. For example, "hypostomus_str.nex" would be converted to "hypostomus_str.fasta".
# Check to make sure the FASTA was created; if so, echo info, if not, echo warning and quit:
if [[ -s "$MY_NEXUS_BASENAME".fasta ]]; then
echo "INFO | $(date) | Input NEXUS was successfully converted to FASTA format. Moving forward... "
else
echo "WARNING | $(date) | NEXUS to FASTA file conversion FAILED. Quitting... "
exit 1
fi
# PUT COMPONENTS OF ORIGINAL NEXUS FILE AND THE FASTA FILE TOGETHER TO MAKE A
# A G-PhoCS-FORMATTED DATA FILE
# --------------------------------------------------
# Make top (first line) of the G-Phocs format file, which should
# have the number of loci on the first line:
# --------------------------------------------------
echo "$MY_NLOCI" | sed 's/[\ ]*//g' > gphocs_top.txt ;
echo "$MY_GAP_THRESHOLD" > ./gap_threshold.txt ;
count=0
(
for j in $MY_NEXUS_CHARSETS; do
echo "$j"
charRange="$(echo "$j" | sed 's/\,//g')";
echo "$charRange"
export setLower="$(echo "$j" | sed 's/\-.*$//g')";
export setUpper="$(echo "$j" | sed 's/[0-9]*\-//g' | sed 's/\,//g; s/\ //g')";
**/selectSites.pl -s "$charRange" "$MY_FASTA" > ./sites.fasta ;
**/fasta2phylip.pl ./sites.fasta > ./sites.phy ;
# Need to make sure there is a space between the tip taxon name (10 characters as output
# by the fasta2phylip.pl Perl script) and the corresponding sequence, for all tips. Use
# a perl search and replace for this:
perl -p -i -e 's/^([A-Za-z0-9\-\_\ ]{10})/$1\ /g' ./sites.phy ;
# If .phy file from NEXUS charset $j has gaps in alignment, then call
# rmGapSites.R R script to remove all column positions with gaps from
# alignment and output new, gapless PHYLIP file named "./sites_nogaps.phy".
# If charset $j does not have gaps, go to next line of loop. We do the
# above by first creating a temporary file containing all lines in
# sites.phy with the gap character:
grep -n "-" ./sites.phy > ./gaptest.tmp ;
# Next, we test for nonzero testfile, indicating presence of gaps in $j,
# using UNIX test operator "-s" (returns true if file size is not zero).
# If fails, cat sites.phy into file with same name as nogaps file that
# is output by rmGapSites.R and move forward:
if [[ -s ./gaptest.tmp ]]; then
echo "Removing column sites in locus${count} with gaps. "
R CMD BATCH **/rmGapSites.R
else
echo ""
cat ./sites.phy > ./sites_nogaps.phy ;
fi
export phylip_header="$(head -n1 ./sites_nogaps.phy)";
locus_ntax="$(head -n1 ./sites_nogaps.phy | sed 's/[\ ]*[.0-9]*$//g')";
locus_nchar="$(head -n1 ./sites_nogaps.phy | sed 's/[0-9]*\ //g')";
if [[ "$MY_INDIV_MISSING_DATA" = "0" ]]; then
sed '1d' ./sites_nogaps.phy | egrep -v 'NNNNNNNNNN|nnnnnnnnnn' > ./cleanLocus.tmp ;
cleanLocus_ntax="$(cat ./cleanLocus.tmp | wc -l)";
echo locus"$((count++))" "$cleanLocus_ntax" "$locus_nchar" > ./locus_top.tmp ;
cat ./locus_top.tmp ./cleanLocus.tmp >> ./gphocs_body.txt ;
else
echo locus"$((count++))" "$locus_ntax" "$locus_nchar" > ./locus_top.tmp ;
cat ./locus_top.tmp ./sites_nogaps.phy >> ./gphocs_body.txt ;
fi
if [[ -s ./sites.fasta ]] && [[ -s ./sites.phy ]] && [[ ! -z ./*.tmp ]] && [[ -s ./sites_nogaps.phy ]]; then
rm ./sites.fasta ./sites.phy ;
if [[ "$(ls -1 ./*.tmp 2>/dev/null | wc -l | sed 's/\ //g')" != "0" ]]; then
rm ./*.tmp ;
fi
rm ./sites_nogaps.phy ;
fi
done
)
grep -v "^[0-9]*\ [0-9]*.*$" ./gphocs_body.txt > ./gphocs_body_fix.txt ;
sed 's/locus/'"$CR"'locus/g' ./gphocs_body_fix.txt > ./gphocs_body_fix2.txt ;
cat ./gphocs_top.txt ./gphocs_body_fix2.txt > "$MY_NEXUS_BASENAME".gphocs ;
# CLEANUP: REMOVE UNNECESSARY FILES
# --------------------------------------------------
# Remove temporary header, threshold and body files.
# --------------------------------------------------
if [[ -s ./gphocs_top.txt ]]; then rm ./gphocs_top.txt ; fi ;
if [[ -s ./gap_threshold.txt ]]; then rm ./gap_threshold.txt ; fi ;
if [[ ! -z ./gphocs_body* ]]; then rm ./gphocs_body* ; fi ;
}
shopt -s nullglob
if [[ -n $(find . -name "*.nex" -type f) ]]; then
# Run the function!
NEXUS2gphocs_function
else
echo "INFO | $(date) | No NEXUS files in current working directory. Continuing... "
fi
shopt -s nullglob
if [[ -n $(find . -name "*.gphocs" -type f) ]]; then
echo "INFO | $(date) | MAGNET successfully created a '.gphocs' input file from the existing NEXUS file... "
MY_GPHOCS_DATA_FILE=./*.gphocs ; ## Assign G-PhoCS-formatted genomic/SNP data file (originally produced/output by pyRAD) in run directory to variable.
else
echo "WARNING | $(date) | Failed to convert NEXUS file into G-PhoCS format... "
echo "INFO | $(date) | Quitting."
exit
fi
# ---------------------------------------------------------- #
# ------------- gphocs2multiPhylip.sh FUNCTION ------------- #
# ---------------------------------------------------------- #
gphocs2multiPhylip_function () {
MY_NLOCI="$(head -n1 "$MY_GPHOCS_DATA_FILE")";
MY_CORR_NLOCI="$(calc "$MY_NLOCI" - 1)";
# --------------------------------------------------
# -- STEP #3: MAKE ALIGNMENTS FOR EACH LOCUS FROM GPHOCS FILE, IF STARTING FROM GPHOCS FILE.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #3: Make alignments for each locus. "
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | In a single loop, using info from '.gphocs' file to split each locus block into a separate PHYLIP-formatted "
echo "INFO | $(date) | alignment file using gphocs2multiPhylip code... "
(
for (( i=0; i<=MY_CORR_NLOCI; i++ )); do
echo "$i"
MY_NTAX="$(grep -n "locus$i\ " "$MY_GPHOCS_DATA_FILE" | \
awk -F"locus$i " '{print $NF}' | sed 's/\ [0-9]*//g')";
MY_NCHAR="$(grep -n "locus$i\ " "$MY_GPHOCS_DATA_FILE" | \
awk -F"locus$i [0-9]*\ " '{print $NF}')";
awk "/locus"$i"\ / {for(j=1; j<=MY_NTAX; j++) {getline; print}}" "$MY_GPHOCS_DATA_FILE" > ./locus"$i".tmp ;
echo "$MY_NTAX $MY_NCHAR" > ./locus"$i"_header.tmp ;
cat ./locus"$i"_header.tmp ./locus"$i".tmp > ./locus"$i".phy ;
done
)
# CLEANUP: REMOVE UNNECESSARY OR TEMPORARY FILES
# --------------------------------------------------
# Remove temporary files generated during run.
# --------------------------------------------------
if [[ ! -z ./*.tmp ]]; then rm ./*.tmp ; fi
}
# Run the function!
gphocs2multiPhylip_function
# ASSIGN PHYLIP FILES TO ENVIRONMENTAL VARIABLE
# --------------------------------------------------
# Assign PHYLIP-formatted genomic/SNP data files (e.g. output by gphocs2multiPhylip.sh
# shell script) in run directory to variable.
# --------------------------------------------------
if [[ -n $(find . -name "*.phy" -type f) ]]; then
MY_PHYLIP_ALIGNMENTS=./*.phy ; ## Assign PHYLIP-formatted genomic/SNP data files (e.g. output by gphocs2multiPhylip.sh shell script) in run directory to variable.
else
echo "..."
fi
# ---------------------------------------------------------- #
# ------------- MultiRAxMLPrepper.sh FUNCTION -------------- #
# ---------------------------------------------------------- #
MultiRAxMLPrepper_function () {
# --------------------------------------------------
# -- STEP #4: MAKE RAxML RUN FOLDERS.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #4: Make and check RAxML run folders. "
echo "INFO | $(date) | ----------------------------------- "
if [[ "$MY_RESUME_SWITCH" = "0" ]]; then
MY_N_PHYLIP_FILES="$(ls -1 ./*.phy 2>/dev/null | wc -l | sed 's/\ //g')";
# MAKE RAXML RUN FOLDERS, ONE FOR EACH GENE/LOCUS
# --------------------------------------------------
# Loop through the input .phy files and do the following for each file: (A) generate one
# folder per .phy file with the same name as the file, only minus the extension, then
# (B) move input .phy file into corresponding folder.
# --------------------------------------------------
count=1
(
for i in $MY_PHYLIP_ALIGNMENTS; do
MY_BASENAME="$(basename "$i" '.phy')";
mkdir "$MY_BASENAME"/ ;
cp "$i" "$MY_BASENAME"/ ;
echo "$((count++))" >/dev/null 2>&1 ;
done
)
# CHECK RUN FOLDERS
# --------------------------------------------------
# Setup and run check on the number of run folders created by the program:
# --------------------------------------------------
export MY_TOTAL_FILECOUNT="$(find . -type f | wc -l)";
export MY_TOTAL_DIRCOUNT="$(find . -type d | wc -l)";
#MY_NUM_RUN_FOLDERS="$(ls ./*/*.phy | wc -l | perl -pe 's/\t//g; s/\ //g')";
echo "INFO | $(date) | Number of run folders created: $count "
if [[ "$count" = "$MY_N_PHYLIP_FILES" ]]; then
echo "INFO | $(date) | Folder check PASSED: number of run folders matches number of PHYLIP alignments. "
else
echo "WARNING | $(date) | Folder check FAILED: number of run folders (${count}) does NOT match the number of PHYLIP alignments (${MY_N_PHYLIP_FILES}). This may cause errors. "
fi
elif [[ "$MY_RESUME_SWITCH" = "1" ]]; then
if [[ "$count" = "$MY_N_PHYLIP_FILES" ]]; then
echo "IMPORTANT${EP}| $(date) | Resuming a previous/existing run in current working dir. Skipping MultiRAxMLPrepper, using available run folders... "
echo "INFO | $(date) | Folder check PASSED: number of run folders matches number of PHYLIP alignments. "
else
echo "WARNING | $(date) | Folder check FAILED: number of run folders does NOT match the number of PHYLIP alignments. There may be errors. "
fi
fi
}
# Run the function!
MultiRAxMLPrepper_function
# ---------------------------------------------------------- #
# ---------------- RAxMLRunner.sh FUNCTION ----------------- #
# ---------------------------------------------------------- #
RAxMLRunner_function () {
if [[ "$MY_RESUME_SWITCH" = "0" ]]; then
# --------------------------------------------------
# -- STEP #5: ESTIMATE BEST ML GENE TREES.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #5: Estimate best maximum-likelihood (ML) gene trees. "
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | Looping through and analyzing contents of each run folder in RAxML... "
# Each folder is set with the locus name corresponding to the locus' position in the
# original .gphocs alignment (which, if output by pyRAD, is simply in the order in which
# the loci were logged to file by pyRAD, no special order). Also, each folder contains
# one .phy file carrying the same basename as the folder name, e.g. "locus0.phy". So,
# all we need to do here is loop through each folder and call RAxML to run using its
# contents as the input file, as follows:
(
for i in ./*/; do
if [[ "$i" != "./archive/" ]] && [[ "$i" != "./bad_genes/" ]] && [[ "$i" != "./R/" ]] && [[ "$i" != "./shell/" ]] && [[ "$i" != "./perl/" ]] && [[ "$i" != "./orig_phylip/" ]] && [[ "$i" != "./phylip/" ]] && [[ "$i" != "./orig_fasta/" ]] && [[ "$i" != "./fasta/" ]] && [[ "$i" != "./phylip_files/" ]]; then
echo "$i"
cd "$i";
LOCUS_NAME="$(echo "$i" | sed 's/\.\///g; s/\/$//g')"; # NOTE: not currently using "$LOCUS_NAME" here, but leave for now, bc may need to use it later...
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
cd ..;
fi
done
)
# Here: adding loop code to move all .phy files remaining in the current working
# directory, after Step #3 of the pipeline, to a new folder called "phylip_files". This
# is done here because if the phylip_files folder is present at the end of Step #3,
# then RAxML will also try to estimate a gene tree for .phy file(s) in this folder during
# Step #5 of the pipeline above.
mkdir ./phylip_files/ ;
(
for i in $MY_PHYLIP_ALIGNMENTS; do
echo "$i"
mv "$i" ./phylip_files/ ;
done
)
elif [[ "$MY_RESUME_SWITCH" = "1" ]]; then
# --------------------------------------------------
# -- STEP #3 ALT: RESUME GENE TREE ESTIMATION FROM (EXPECTED) PREVIOUS RUN.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #3: Resuming gene tree estimation. "
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | Run on remaining/incomplete run folders, skip those with completed RAxML runs. "
(
for i in ./*/; do
if [[ "$i" != "./archive/" ]] && [[ "$i" != "./bad_genes/" ]] && [[ "$i" != "./R/" ]] && [[ "$i" != "./shell/" ]] && [[ "$i" != "./perl/" ]] && [[ "$i" != "./orig_phylip/" ]] && [[ "$i" != "./phylip/" ]] && [[ "$i" != "./orig_fasta/" ]] && [[ "$i" != "./fasta/" ]] && [[ "$i" != "./phylip_files/" ]]; then
cd "$i";
LOCUS_NAME="$(echo "$i" | sed 's/\.\///g; s/\/$//g')";
#
if [[ "$MY_OUTPUT_NAME" = "raxml_out" ]] && [[ ! -s ./RAxML_info.raxml_out ]]; then
echo "$i"
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
#
elif [[ "$MY_OUTPUT_NAME" != "raxml_out" ]] && [[ ! -s ./RAxML_info."$MY_OUTPUT_NAME" ]]; then
echo "$i"
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
fi
cd ..;
fi
done
)
if [[ ! -s ./phylip_files/ ]]; then
mkdir ./phylip_files/ ;
fi
(
for i in $MY_PHYLIP_ALIGNMENTS; do
echo "INFO | $(date) | ${i}"
mv "$i" ./phylip_files/ ;
done
)
fi
}
# Run the function!
RAxMLRunner_function
if [[ "$MY_RESUME_SWITCH" = "0" ]]; then
# --------------------------------------------------
# -- STEP #6: CONDUCT POST-PROCESSING OF RAxML RESULTS.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #6: RAxML post-processing analyses. "
echo "INFO | $(date) | ----------------------------------- "
elif [[ "$MY_RESUME_SWITCH" = "1" ]]; then
# --------------------------------------------------
# -- STEP #4 ALT: CONDUCT POST-PROCESSING OF RAxML RESULTS.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #4: RAxML post-processing analyses. "
echo "INFO | $(date) | ----------------------------------- "
fi
# ---------------------------------------------------------- #
# --------------- getGeneTrees.sh FUNCTION ----------------- #
# ---------------------------------------------------------- #
getGeneTrees_function () {
echo "INFO | $(date) | Organizing gene trees and making final output file containing all trees... "
echo "INFO | $(date) | Making list of ML gene trees generated by RAxML... "
ls **/RAxML_bestTree.raxml_out > geneTrees.list ;
# Assign gene tree list to variable
MY_GENE_TREE_LIST="$(cat ./geneTrees.list)";
# ORGANIZE GENE TREES INTO ONE LOCATION
# --------------------------------------------------
# Place all inferred gene trees into a single "gene_trees" folder in the current
# working directory. However, all the gene tree files have the same name. So, in order
# to do this, we have to give each gene tree a name that matches the corresponding run
# folder, i.e. locus. We can rename each file right after downloading it.
# --------------------------------------------------
mkdir ./gene_trees/ ;
echo "INFO | $(date) | Copying *ALL* ML gene trees to 'gene_trees' folder in current directory for post-processing..."
(
for j in $MY_GENE_TREE_LIST; do
echo "$j"
cp "$j" ./gene_trees/ ;
MY_LOCUS_NAME="$(echo "$j" | sed 's/\/[A-Za-z.\_\-]*//g')";
cp ./gene_trees/RAxML_bestTree.raxml_out ./gene_trees/"$MY_LOCUS_NAME"_RAxML_best.tre ;
if [[ -s ./gene_trees/RAxML_bestTree.raxml_out ]]; then rm ./gene_trees/RAxML_bestTree.raxml_out ; fi
done
)
echo "INFO | $(date) | Making final output file 'besttrees.tre' containing best ML trees from all runs/loci..."
(
for k in ./gene_trees/*; do
echo "$k"
cat "$k" >> ./besttrees.tre ;
done
)
}
# Run the function!
getGeneTrees_function
# ---------------------------------------------------------- #
# --------------- getBootTrees.sh FUNCTION ----------------- #
# ---------------------------------------------------------- #
getBootTrees_function () {
echo "INFO | $(date) | Organizing bootstrap trees and making final output file containing all trees... "
echo "INFO | $(date) | Making list of ML bootstrap trees generated by RAxML... "
ls **/RAxML_bootstrap.raxml_out > bootTrees.list ;
# Assign bootstrap tree list to variable
MY_BOOT_TREE_LIST="$(cat ./bootTrees.list)";
# ORGANIZE BOOTSTRAP TREES INTO ONE LOCATION
# --------------------------------------------------
# Place all inferred bootstrap tree files into a single "bootstrap_trees" folder in
# working directory. However, all the boot tree files have the same name. So, in order
# to do this, we have to give each boot tree file a name that matches the corresponding
# run folder, i.e. locus. We can rename each file right after downloading it.
# --------------------------------------------------
mkdir ./bootstrap_trees ;
echo "INFO | $(date) | Copying *ALL* ML bootstrap trees to 'bootstrap_trees' folder in current directory for post-processing..."
(
for l in $MY_BOOT_TREE_LIST; do
echo "$l"
cp "$l" ./bootstrap_trees/ ;
MY_LOCUS_NAME="$(echo "$l" | sed 's/\/[A-Za-z.\_\-]*//g')";
cp ./bootstrap_trees/RAxML_bootstrap.raxml_out ./bootstrap_trees/"$MY_LOCUS_NAME"_RAxML_boot.tre ;
if [[ -s ./bootstrap_trees/RAxML_bootstrap.raxml_out ]]; then rm ./bootstrap_trees/RAxML_bootstrap.raxml_out ; fi
done
)
echo "INFO | $(date) | Making final output file 'boottrees.tre' containing best ML trees from all runs/loci..."
(
for m in ./bootstrap_trees/*; do
echo "$m"
cat "$m" >> ./boottrees.tre ;
done
)
echo "INFO | $(date) | Making final list of ML bootstrap trees ('final_bootTrees.list') in bootstrap_trees directory..."
ls ./bootstrap_trees/*.tre > final_bootTrees.list ;
}
# Run the function!
getBootTrees_function
# ---------------------------------------------------------- #
# -------------- getBipartTrees.sh FUNCTION ---------------- #
# ---------------------------------------------------------- #
getBipartTrees_function () {
echo "INFO | $(date) | Organizing bipartitions trees (with bootstrap proportion labels) and making final output file containing all bipartitions trees... "
ls **/RAxML_bipartitions.raxml_out > bipartTrees.list ;
# Assign bootstrap tree list to variable
MY_BIPART_TREE_LIST="$(cat ./bipartTrees.list)";
# ORGANIZE BIPARTITIONS TREES INTO ONE LOCATION
# --------------------------------------------------
mkdir ./bipartitions_trees
echo "INFO | $(date) | Copying *ALL* RAxML bootstrap bipartitions trees to 'bipartitions_trees' folder in current directory for post-processing..."
(
for l in ${MY_BIPART_TREE_LIST}; do
echo "$l"
cp "$l" ./bipartitions_trees/ ;
MY_LOCUS_NAME="$(echo "$l" | sed 's/\/[A-Za-z.\_\-]*//g')";
cp ./bipartitions_trees/RAxML_bipartitions.raxml_out ./bipartitions_trees/"$MY_LOCUS_NAME"_RAxML_bipartitions.tre ;
if [[ -s ./bipartitions_trees/RAxML_bipartitions.raxml_out ]]; then rm ./bipartitions_trees/RAxML_bipartitions.raxml_out ; fi
done
)
echo "INFO | $(date) | Making final output file 'biparttrees.tre' containing RAxML bipartitions trees from all runs/loci..."
(
for m in ./bipartitions_trees/*; do
echo "$m"
cat "$m" >> ./biparttrees.tre ;
done
)
echo "INFO | $(date) | Making final list of RAxML bipartitions trees ('final_bipartTrees.list') in bipartitions_trees directory..."
ls ./bipartitions_trees/*.tre > final_bipartTrees.list ;
}
# Run the function!
getBipartTrees_function
fi
#######
# Multi-PHYLIP run
# ------------------------------------------------------
# Run on multiple PHYLIP files (extension '.phy') in the
# current working directory.
# ------------------------------------------------------
#######
if [[ "$STARTING_FILE_TYPE" = "2" ]]; then
echo "INFO | $(date) | Starting MAGNET pipeline... "
echo "INFO | $(date) | Running with the following options: "
echo "INFO | $(date) | - NEXUS file, <inputNEXUS> = ${MY_NEXUS} "
echo "INFO | $(date) | - Starting <fileType> = ${STARTING_FILE_TYPE} "
echo "INFO | $(date) | - RAxML <executable> = ${MY_RAXML_EXECUTABLE} "
echo "INFO | $(date) | - Bootstrap reps, <numBootstraps> = ${MY_NUM_BOOTREPS} "
echo "INFO | $(date) | - RAxML model, <raxmlModel> = ${MY_RAXML_MODEL} "
echo "INFO | $(date) | - <simpleModel> option = ${MY_SIMPLE_MODEL} "
echo "INFO | $(date) | - <gapThreshold> option = ${MY_GAP_THRESHOLD} "
echo "INFO | $(date) | - <indivMissingData> option = ${MY_INDIV_MISSING_DATA} "
echo "INFO | $(date) | - Outgroup taxon, <outgroup> = ${MY_OUTGROUP} "
echo "INFO | $(date) | - RAxML output name = ${MY_OUTPUT_NAME} "
echo "INFO | $(date) | - Resume switch (--resume) = ${MY_RESUME_SWITCH} "
# --------------------------------------------------
# -- STEP #1: SETUP.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #1: Set up workspace (e.g. functions, working directory) and check machine type. " # | tee -a "$MY_OUTPUT_FILE_SWITCH"
echo "INFO | $(date) | ----------------------------------- "
############ SET WORKING DIRECTORY AND CHECK MACHINE TYPE
USER_SPEC_PATH="$(printf '%q\n' "$(pwd)")";
echoCDWorkingDir
MY_WORKING_DIR="$(pwd)"
checkMachineType
# --------------------------------------------------
# -- STEP #2: HANDLE INPUT FILE(S).
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #2: Input single NEXUS (or G-PhoCS-formatted) file, or multiple PHYLIP files. "
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | For -f 1 or -f 2, if '.gphocs' input file present, continue; else convert NEXUS file "
echo "INFO | $(date) | to G-PhoCS format using NEXUS2gphocs code. If -f 3, then run multiple PHYLIP files in "
echo "INFO | $(date) | RAxML."
MY_PHYLIP_ALIGNMENTS=./*.phy ; ## Assign PHYLIP-formatted multilocus gene / genomic/SNP / RAD locus sequence alignment files (e.g. output by gphocs2multiPhylip.sh shell script) in run directory to variable.
# ---------------------------------------------------------- #
# ------------- MultiRAxMLPrepper.sh FUNCTION -------------- #
# ---------------------------------------------------------- #
MultiRAxMLPrepper_function () {
if [[ "$MY_RESUME_SWITCH" = "0" ]]; then
# --------------------------------------------------
# -- STEP #3: MAKE RAxML RUN FOLDERS.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #3: Make and check RAxML run folders. "
echo "INFO | $(date) | ----------------------------------- "
MY_N_PHYLIP_FILES="$(ls -1 ./*.phy 2>/dev/null | wc -l | sed 's/\ //g')";
# MAKE RAXML RUN FOLDERS, ONE FOR EACH GENE/LOCUS
# --------------------------------------------------
# Loop through the input .phy files and do the following for each file: (A) generate one
# folder per .phy file with the same name as the file, only minus the extension, then
# (B) move input .phy file into corresponding folder.
# --------------------------------------------------
count=1
(
for i in $MY_PHYLIP_ALIGNMENTS; do
MY_BASENAME="$(basename "$i" '.phy')";
mkdir "$MY_BASENAME"/ ;
cp "$i" "$MY_BASENAME"/ ;
echo "$((count++))" >/dev/null 2>&1 ;
done
)
# CHECK RUN FOLDERS
# --------------------------------------------------
# Setup and run check on the number of run folders created by the program:
# --------------------------------------------------
export MY_TOTAL_FILECOUNT="$(find . -type f | wc -l)";
export MY_TOTAL_DIRCOUNT="$(find . -type d | wc -l)";
#MY_NUM_RUN_FOLDERS="$(ls ./*/*.phy | wc -l | perl -pe 's/\t//g; s/\ //g')";
echo "INFO | $(date) | Number of run folders created: ${count} "
if [[ "$count" = "$MY_N_PHYLIP_FILES" ]]; then
echo "INFO | $(date) | Folder check PASSED: number of run folders matches number of PHYLIP alignments. "
else
echo "WARNING | $(date) | Folder check FAILED: number of run folders (${count}) does NOT match the number of PHYLIP alignments (${MY_N_PHYLIP_FILES}). This may cause errors. "
fi
elif [[ "$MY_RESUME_SWITCH" = "1" ]]; then
if [[ "$count" = "$MY_N_PHYLIP_FILES" ]]; then
echo "IMPORTANT${EP}| $(date) | Resuming a previous/existing run in current working dir. Skipping MultiRAxMLPrepper, using available run folders... "
echo "INFO | $(date) | Folder check PASSED: number of run folders matches number of PHYLIP alignments. "
else
echo "WARNING | $(date) | Folder check FAILED: number of run folders does NOT match the number of PHYLIP alignments. There may be errors. "
fi
fi
}
# Run the function!
MultiRAxMLPrepper_function
# ---------------------------------------------------------- #
# ---------------- RAxMLRunner.sh FUNCTION ----------------- #
# ---------------------------------------------------------- #
RAxMLRunner_function () {
if [[ "$MY_RESUME_SWITCH" = "0" ]]; then
# --------------------------------------------------
# -- STEP #4: ESTIMATE BEST ML GENE TREES.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #4: Estimate best maximum-likelihood (ML) gene trees. "
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | Looping through and analyzing contents of each run folder in RAxML... "
echo "INFO | $(date) | ----------------------------------- "
# Each folder is set with the locus name corresponding to the locus' position in the
# original .gphocs alignment (which, if output by pyRAD, is simply in the order in which
# the loci were logged to file by pyRAD, no special order). Also, each folder contains
# one .phy file carrying the same basename as the folder name, e.g. "locus0.phy". So,
# all we need to do here is loop through each folder and call RAxML to run using its
# contents as the input file, as follows:
(
for i in ./*/; do
if [[ "$i" != "./archive/" ]] && [[ "$i" != "./bad_genes/" ]] && [[ "$i" != "./R/" ]] && [[ "$i" != "./shell/" ]] && [[ "$i" != "./perl/" ]] && [[ "$i" != "./orig_phylip/" ]] && [[ "$i" != "./phylip/" ]] && [[ "$i" != "./orig_fasta/" ]] && [[ "$i" != "./fasta/" ]] && [[ "$i" != "./phylip_files/" ]]; then
echo "$i"
cd "$i";
LOCUS_NAME="$(echo "$i" | sed 's/\.\///g; s/\/$//g')"; # NOTE: not currently using "$LOCUS_NAME" here, but leave for now, bc may need to use it later...
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
cd ..;
fi
done
)
# Here: adding loop code to move all .phy files remaining in the current working
# directory, after Step #3 of the pipeline, to a new folder called "phylip_files". This
# is done here because if the phylip_files folder is present at the end of Step #3,
# then RAxML will also try to estimate a gene tree for .phy file(s) in this folder during
# Step #5 of the pipeline above.
mkdir ./phylip_files
(
for i in $MY_PHYLIP_ALIGNMENTS; do
echo "$i"
mv "$i" ./phylip_files/ ;
done
)
elif [[ "$MY_RESUME_SWITCH" = "1" ]]; then
echo "INFO | $(date) | Step #3: Resuming gene tree estimation. Run on remaining/incomplete run folders, skip those with completed RAxML runs. "
(
for i in ./*/; do
if [[ "$i" != "./archive/" ]] && [[ "$i" != "./bad_genes/" ]] && [[ "$i" != "./R/" ]] && [[ "$i" != "./shell/" ]] && [[ "$i" != "./perl/" ]] && [[ "$i" != "./orig_phylip/" ]] && [[ "$i" != "./phylip/" ]] && [[ "$i" != "./orig_fasta/" ]] && [[ "$i" != "./fasta/" ]] && [[ "$i" != "./phylip_files/" ]]; then
cd "$i";
LOCUS_NAME="$(echo "$i" | sed 's/\.\///g; s/\/$//g')"; # NOTE: not currently using $LOCUS_NAME here, but leave for now, bc may need to use it later...
#
if [[ ! -s ./RAxML_info.raxml_out ]]; then
echo "$i"
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" = "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" = "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -n ${MY_OUTPUT_NAME}
fi
#
if [[ "$MY_OUTGROUP" != "NULL" ]] && [[ "$MY_SIMPLE_MODEL" != "NULL" ]]; then
"$MY_RAXML_EXECUTABLE" -f a -x "$RANDOM""$RANDOM" -p "$RANDOM""$RANDOM" -# ${MY_NUM_BOOTREPS} -m ${MY_RAXML_MODEL} -s ./*.phy --${MY_SIMPLE_MODEL} -o ${MY_OUTGROUP} -n ${MY_OUTPUT_NAME}
fi
fi
cd ..;
fi
done
)
if [[ ! -s ./phylip_files/ ]]; then
mkdir ./phylip_files/ ;
fi
(
for i in $MY_PHYLIP_ALIGNMENTS; do
echo "$i"
mv "$i" ./phylip_files/ ;
done
)
fi
}
# Run the function!
RAxMLRunner_function
if [[ "$MY_RESUME_SWITCH" = "0" ]]; then
# --------------------------------------------------
# -- STEP #5: CONDUCT POST-PROCESSING OF RAxML RESULTS.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #5: RAxML post-processing analyses. "
echo "INFO | $(date) | ----------------------------------- "
elif [[ "$MY_RESUME_SWITCH" = "1" ]]; then
# --------------------------------------------------
# -- STEP #4 ALT: CONDUCT POST-PROCESSING OF RAxML RESULTS.
# --------------------------------------------------
echo "INFO | $(date) | ----------------------------------- "
echo "INFO | $(date) | # Step #4: RAxML post-processing analyses. "
echo "INFO | $(date) | ----------------------------------- "
fi
# ---------------------------------------------------------- #
# --------------- getGeneTrees.sh FUNCTION ----------------- #
# ---------------------------------------------------------- #
getGeneTrees_function () {
echo "INFO | $(date) | Organizing gene trees and making final output file containing all trees... "
echo "INFO | $(date) | Making list of ML gene trees generated by RAxML... "
ls **/RAxML_bestTree.raxml_out > geneTrees.list ;
# Assign gene tree list to variable
MY_GENE_TREE_LIST="$(cat ./geneTrees.list)";
# ORGANIZE GENE TREES INTO ONE LOCATION
# --------------------------------------------------
# Place all inferred gene trees into a single "gene_trees" folder in the current
# working directory. However, all the gene tree files have the same name. So, in order
# to do this, we have to give each gene tree a name that matches the corresponding run
# folder, i.e. locus. We can rename each file right after downloading it.
# --------------------------------------------------
mkdir ./gene_trees/ ;
echo "INFO | $(date) | Copying *ALL* ML gene trees to 'gene_trees' folder in current directory for post-processing..."
(
for j in $MY_GENE_TREE_LIST; do