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genes_workflow.py
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'''
------------------------------------------------------------------------------------------------------------------------
This workflow is used to treat the gene sequences in order to make them ready for tree building:
This part of the workflow starts by collecting all the fasta files from the different species and sorting them into files
based on which gene they come from. This produces a set of files each with a gene name and each file contains all the
sequences from that gene.
These gene files are then aligned using mafft, and then trimmed using trimmomatic with different treshold values ranging
from 0.10 to 0.95.
The parsimony informative bases are then counted for all the genes for all the cutoff values and the best treshold value
?for each gene? Is determined using optrimal.R
The trimmed genes are then transferred to 09_manual_edit for inspection after which the trees_workflow.py can be run to
produce the trees.
------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------
Author: Oscar Wrisberg
Date: 7/12/2021
------------------------------------------------------------------------------------------------------------------------
'''
from os import O_SYNC
from gwf import Workflow, AnonymousTarget
import os.path
from inspect import getsourcefile
# import math
# import glob
gwf = Workflow()
##########################################################################################################################
# #########################################---- Retrieve Sequences ----###################################################
# ########################################################################################################################
def retrieve(path_in, file_list, output_folder, done):
"""Retrieve gene sequences from the species in the species list
and create an unaligned multifasta for each gene."""
inputs = []
outputs = [done]
options = {'cores': 10, 'memory': "20g", 'walltime': "1:00:00", 'account':"Coryphoideae"}
spec = """
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate base
cd {path_in}
# Some species are manually removed at this step due to reasons such as double sampling from same specimen or doubtful species identification on specimen
# These species are removed by editing the file_list.txt file which is found in the github folder.
# You can also create this file list yourself if you wish control over which species are included in the pipeline.
# This can be done by running the following command in the folder with the species files: ls *_trimmed.fasta > filelist.txt
# You also need to change the path of the input file_list below where this function is called.
python /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/samples2genes.py {file_list} {output_folder} > outstats.csv
touch {done}
""".format(path_in = path_in, file_list = file_list, output_folder = output_folder, done = done)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
# ########################################################################################################################
# #############################################---- MAFT ----#############################################################
# ########################################################################################################################
def mafft(gene, path_in, path_out, done):#
"""Aligning all the sequences for each gene.
Some Genes require a LOT of memory to not result in an Out Of Memory error (500g) but most will do fine with way less"""
inputs = ["/home/owrisberg/Coryphoideae/work_flow/05_blacklisting/done/retrieve_done.txt"]
outputs = [done,path_out+gene+"_aligned.fasta"]
options = {'cores': 1, 'memory': "500g", 'walltime': "50:00:00", 'account':"Coryphoideae"} # Most of the genes can run with 50g/24h but some require 500g/48h
spec = """
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate mafft_env
cd {path_in}
#Aligning using mafft localpair which should be able to handle divergent sequences flanking an alignable region.
mafft --globalpair --large --adjustdirectionaccurately --thread 1 {gene}.FNA > {path_out}{gene}_aligned.fasta
touch {done}
""".format(gene = gene, done = done, path_in = path_in, path_out=path_out)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
# ########################################################################################################################
# #############################################---- Optrimal ----#########################################################
# ########################################################################################################################
def gt_trimming(path_in,done,gene, path_out):
""" trimming all alignments for each of the GT values specified"""
inputs = [path_in+gene+"_aligned.fasta", path_in+"/done/"+gene]
outputs = [done,path_out+gene+"_aligned.fasta.old"]
options = {'cores': 10, 'memory': "20g", 'walltime': "04:00:00", 'account':"Coryphoideae"}
spec="""
#Running gaptrimming.sh
bash /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/gaptrimming.sh -g {gene}
touch {done}
""".format(path_in=path_in, done=done, gene=gene, path_out=path_out)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
def amas_preb_gt(path_in,path_out,done,cut_off):
"""Creating summary files for all the trimmed alignments for each GT value"""
inputs = [
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path_in+"done/trimal_gt/HEY1007",path_in+"done/trimal_gt/HEY1013",path_in+"done/trimal_gt/HEY1017",path_in+"done/trimal_gt/HEY1020",path_in+"done/trimal_gt/HEY1025",path_in+"done/trimal_gt/HEY1035",path_in+"done/trimal_gt/HEY1050",path_in+"done/trimal_gt/HEY1052",path_in+"done/trimal_gt/HEY1064",path_in+"done/trimal_gt/HEY110",path_in+"done/trimal_gt/HEY1119",path_in+"done/trimal_gt/HEY1168",path_in+"done/trimal_gt/HEY1171",path_in+"done/trimal_gt/HEY1197",path_in+"done/trimal_gt/HEY1201",path_in+"done/trimal_gt/HEY120",path_in+"done/trimal_gt/HEY122",path_in+"done/trimal_gt/HEY125",path_in+"done/trimal_gt/HEY12",path_in+"done/trimal_gt/HEY136",path_in+"done/trimal_gt/HEY139",path_in+"done/trimal_gt/HEY1484",path_in+"done/trimal_gt/HEY148",path_in+"done/trimal_gt/HEY1494",path_in+"done/trimal_gt/HEY14",path_in+"done/trimal_gt/HEY150",path_in+"done/trimal_gt/HEY1615",path_in+"done/trimal_gt/HEY164",path_in+"done/trimal_gt/HEY168",path_in+"done/trimal_gt/HEY17",path_in+"done/trimal_gt/HEY1801",path_in+"done/trimal_gt/HEY180",path_in+"done/trimal_gt/HEY1815",path_in+"done/trimal_gt/HEY182",path_in+"done/trimal_gt/HEY1842",path_in+"done/trimal_gt/HEY1854",path_in+"done/trimal_gt/HEY1877",path_in+"done/trimal_gt/HEY1901",path_in+"done/trimal_gt/HEY191",path_in+"done/trimal_gt/HEY194",path_in+"done/trimal_gt/HEY197",path_in+"done/trimal_gt/HEY1986",path_in+"done/trimal_gt/HEY201",path_in+"done/trimal_gt/HEY204e",path_in+"done/trimal_gt/HEY204s",path_in+"done/trimal_gt/HEY2056",path_in+"done/trimal_gt/HEY207",path_in+"done/trimal_gt/HEY215",path_in+"done/trimal_gt/HEY2164",path_in+"done/trimal_gt/HEY218",path_in+"done/trimal_gt/HEY21",path_in+"done/trimal_gt/HEY2238",path_in+"done/trimal_gt/HEY225",path_in+"done/trimal_gt/HEY226",path_in+"done/trimal_gt/HEY2291",path_in+"done/trimal_gt/HEY231",path_in+"done/trimal_gt/HEY2339",path_in+"done/trimal_gt/HEY2363",path_in+"done/trimal_gt/HEY2370",path_in+"done/trimal_gt/HEY2377",path_in+"done/trimal_gt/HEY237",path_in+"done/trimal_gt/HEY2388",path_in+"done/trimal_gt/HEY240",path_in+"done/trimal_gt/HEY2459",path_in+"done/trimal_gt/HEY245",path_in+"done/trimal_gt/HEY24",path_in+"done/trimal_gt/HEY250",path_in+"done/trimal_gt/HEY252e",path_in+"done/trimal_gt/HEY252p",path_in+"done/trimal_gt/HEY252s",path_in+"done/trimal_gt/HEY2550",path_in+"done/trimal_gt/HEY2561",path_in+"done/trimal_gt/HEY257",path_in+"done/trimal_gt/HEY267",path_in+"done/trimal_gt/HEY269",path_in+"done/trimal_gt/HEY277",path_in+"done/trimal_gt/HEY280",path_in+"done/trimal_gt/HEY281",path_in+"done/trimal_gt/HEY282",path_in+"done/trimal_gt/HEY290",path_in+"done/trimal_gt/HEY293",path_in+"done/trimal_gt/HEY296",path_in+"done/trimal_gt/HEY299",path_in+"done/trimal_gt/HEY305",path_in+"done/trimal_gt/HEY308",path_in+"done/trimal_gt/HEY310",path_in+"done/trimal_gt/HEY31",path_in+"done/trimal_gt/HEY323",path_in+"done/trimal_gt/HEY326",path_in+"done/trimal_gt/HEY32e",path_in+"done/trimal_gt/HEY32s",path_in+"done/trimal_gt/HEY332",path_in+"done/trimal_gt/HEY334",path_in+"done/trimal_gt/HEY340",path_in+"done/trimal_gt/HEY357",path_in+"done/trimal_gt/HEY360",path_in+"done/trimal_gt/HEY362",path_in+"done/trimal_gt/HEY363",path_in+"done/trimal_gt/HEY369",path_in+"done/trimal_gt/HEY378e",path_in+"done/trimal_gt/HEY378s",path_in+"done/trimal_gt/HEY38",path_in+"done/trimal_gt/HEY391",path_in+"done/trimal_gt/HEY392",path_in+"done/trimal_gt/HEY415",path_in+"done/trimal_gt/HEY417",path_in+"done/trimal_gt/HEY421",path_in+"done/trimal_gt/HEY429",path_in+"done/trimal_gt/HEY449",path_in+"done/trimal_gt/HEY464",path_in+"done/trimal_gt/HEY484",path_in+"done/trimal_gt/HEY490",path_in+"done/trimal_gt/HEY497",path_in+"done/trimal_gt/HEY4",path_in+"done/trimal_gt/HEY508",
path_in+"done/trimal_gt/HEY514",path_in+"done/trimal_gt/HEY51",path_in+"done/trimal_gt/HEY52",path_in+"done/trimal_gt/HEY556",path_in+"done/trimal_gt/HEY563",path_in+"done/trimal_gt/HEY576",path_in+"done/trimal_gt/HEY581",path_in+"done/trimal_gt/HEY587",path_in+"done/trimal_gt/HEY604",path_in+"done/trimal_gt/HEY609",path_in+"done/trimal_gt/HEY61",path_in+"done/trimal_gt/HEY629",path_in+"done/trimal_gt/HEY630",path_in+"done/trimal_gt/HEY637",path_in+"done/trimal_gt/HEY673",path_in+"done/trimal_gt/HEY680",path_in+"done/trimal_gt/HEY703",path_in+"done/trimal_gt/HEY717",path_in+"done/trimal_gt/HEY727",path_in+"done/trimal_gt/HEY728",path_in+"done/trimal_gt/HEY732",path_in+"done/trimal_gt/HEY736",path_in+"done/trimal_gt/HEY740",path_in+"done/trimal_gt/HEY743",path_in+"done/trimal_gt/HEY757",path_in+"done/trimal_gt/HEY758",path_in+"done/trimal_gt/HEY762",path_in+"done/trimal_gt/HEY763",path_in+"done/trimal_gt/HEY785",path_in+"done/trimal_gt/HEY790",path_in+"done/trimal_gt/HEY793",path_in+"done/trimal_gt/HEY7",path_in+"done/trimal_gt/HEY807",path_in+"done/trimal_gt/HEY808",path_in+"done/trimal_gt/HEY822",path_in+"done/trimal_gt/HEY825",path_in+"done/trimal_gt/HEY82",path_in+"done/trimal_gt/HEY83",path_in+"done/trimal_gt/HEY84",path_in+"done/trimal_gt/HEY855",path_in+"done/trimal_gt/HEY856",path_in+"done/trimal_gt/HEY863",path_in+"done/trimal_gt/HEY872",path_in+"done/trimal_gt/HEY874",path_in+"done/trimal_gt/HEY883e",path_in+"done/trimal_gt/HEY883n",path_in+"done/trimal_gt/HEY886",path_in+"done/trimal_gt/HEY88",path_in+"done/trimal_gt/HEY897",path_in+"done/trimal_gt/HEY89",path_in+"done/trimal_gt/HEY938",path_in+"done/trimal_gt/HEY948",path_in+"done/trimal_gt/HEY94",path_in+"done/trimal_gt/HEY950",path_in+"done/trimal_gt/HEY958",path_in+"done/trimal_gt/HEY964",path_in+"done/trimal_gt/HEY977",path_in+"done/trimal_gt/HEY982",path_in+"done/trimal_gt/HEY985",path_in+"done/trimal_gt/HEY989",
]
outputs = [path_out+"summary_"+cut_off+".txt",done]
options = {'cores': 10, 'memory': "50g", 'walltime': "00:30:00", 'account':"Coryphoideae"}
spec="""
#Activating trimal_env
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate trimal_env
#Going to folder with trimmed files
cd {path_in}/{cut_off}
#Calculating amas summary
AMAS.py summary -f fasta -d dna -i *.fasta
mv summary.txt ../summary_{cut_off}.txt
touch {done}
""".format(path_in=path_in, done=done, cut_off=cut_off)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
def amas_preb_raw(path_in,path_out,done):
"""Creating summary file for the untrimmed sequences"""
inputs = [
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path_in+"HEY514_aligned.fasta",path_in+"HEY51_aligned.fasta",path_in+"HEY52_aligned.fasta",path_in+"HEY556_aligned.fasta",path_in+"HEY563_aligned.fasta",path_in+"HEY576_aligned.fasta",path_in+"HEY581_aligned.fasta",path_in+"HEY587_aligned.fasta",path_in+"HEY604_aligned.fasta",path_in+"HEY609_aligned.fasta",path_in+"HEY61_aligned.fasta",path_in+"HEY629_aligned.fasta",path_in+"HEY630_aligned.fasta",path_in+"HEY637_aligned.fasta",path_in+"HEY673_aligned.fasta",path_in+"HEY680_aligned.fasta",path_in+"HEY703_aligned.fasta",path_in+"HEY717_aligned.fasta",path_in+"HEY727_aligned.fasta",path_in+"HEY728_aligned.fasta",path_in+"HEY732_aligned.fasta",path_in+"HEY736_aligned.fasta",path_in+"HEY740_aligned.fasta",path_in+"HEY743_aligned.fasta",path_in+"HEY757_aligned.fasta",path_in+"HEY758_aligned.fasta",path_in+"HEY762_aligned.fasta",path_in+"HEY763_aligned.fasta",path_in+"HEY785_aligned.fasta",path_in+"HEY790_aligned.fasta",path_in+"HEY793_aligned.fasta",path_in+"HEY7_aligned.fasta",path_in+"HEY807_aligned.fasta",path_in+"HEY808_aligned.fasta",path_in+"HEY822_aligned.fasta",path_in+"HEY825_aligned.fasta",path_in+"HEY82_aligned.fasta",path_in+"HEY83_aligned.fasta",path_in+"HEY84_aligned.fasta",path_in+"HEY855_aligned.fasta",path_in+"HEY856_aligned.fasta",path_in+"HEY863_aligned.fasta",path_in+"HEY872_aligned.fasta",path_in+"HEY874_aligned.fasta",path_in+"HEY883e_aligned.fasta",path_in+"HEY883n_aligned.fasta",path_in+"HEY886_aligned.fasta",path_in+"HEY88_aligned.fasta",path_in+"HEY897_aligned.fasta",path_in+"HEY89_aligned.fasta",path_in+"HEY938_aligned.fasta",path_in+"HEY948_aligned.fasta",path_in+"HEY94_aligned.fasta",path_in+"HEY950_aligned.fasta",path_in+"HEY958_aligned.fasta",path_in+"HEY964_aligned.fasta",
path_in+"HEY977_aligned.fasta",path_in+"HEY982_aligned.fasta",path_in+"HEY985_aligned.fasta",path_in+"HEY989_aligned.fasta"]
outputs = [path_out+"summary_0.txt",done]
options = {'cores': 10, 'memory': "100g", 'walltime': "04:00:00", 'account':"Coryphoideae"}
spec="""
#Activating trimal_env
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate trimal_env
#Going to folder with trimmed files
cd {path_in}
#Calculating amas summary
AMAS.py summary -f fasta -d dna -i *.fasta
mv summary.txt {path_out}summary_0.txt
touch {done}
""".format(path_in=path_in, done=done, path_out=path_out)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
def optrim(path_in,done, path_out):
""" Running the Optrimal script """
inputs = [path_in+"summary_0.txt",path_in+"summary_0.1.txt",path_in+"summary_0.15.txt",path_in+"summary_0.2.txt",path_in+"summary_0.25.txt",path_in+"summary_0.3.txt",
path_in+"summary_0.33.txt",path_in+"summary_0.4.txt",path_in+"summary_0.45.txt",path_in+"summary_0.5.txt",path_in+"summary_0.55.txt",path_in+"summary_0.6.txt",path_in+"summary_0.67.txt",
path_in+"summary_0.7.txt",path_in+"summary_0.75.txt",path_in+"summary_0.8.txt",path_in+"summary_0.85.txt",path_in+"summary_0.9.txt",path_in+"summary_0.95.txt"]
outputs = 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options = {'cores': 10, 'memory': "20g", 'walltime': "08:00:00", 'account':"Coryphoideae"}
spec="""
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate base
#Going to folder with trimmed files
cd {path_in}
echo " Starting the optrim script at:"
date
Rscript --vanilla /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/optrimal.R
mv dldp_* optrim_output/
touch {done}
cp *_aligned.fasta {path_out}
""".format(path_in=path_in, done=done, path_out=path_out)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
def no_empty(path_in,path_out,done,gene):
"""Removing empty alignments"""
inputs = []
outputs = []
options = {'cores': 10, 'memory': "20g", 'walltime': "04:00:00", 'account':"Coryphoideae"}
spec="""
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate base
#Going to folder with trimmed files
cd {path_in}
python3 /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/noempty.py {gene}
touch {done}
""".format(path_in=path_in, done=done, gene=gene)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
########################################################################################################################
####################################################---- CIALIGN ----###################################################
########################################################################################################################
def cialign(gene, path_in, path_out, done):
""" CIAlign allows the user to:
Remove sources of noise from their Multiple sequence alignment by:
Remove insertions which are not present in the majority of sequences
Remove sequences below a threshold number of bases or amino acids
Crop poorly aligned sequence ends
Remove columns containing only gaps
Remove sequences above a threshold level percentage of divergence from the majority
"""
inputs = [path_in + gene + "_aligned.fasta"]
outputs = [path_out+gene+"_cialign.fasta_cleaned.fasta", done]
options = {'cores': 8, 'memory': "100g", 'walltime': "12:00:00", 'account':"Coryphoideae"}
spec = """
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate cialign_env
cd {path_in}
CIAlign --infile {genes}_aligned.fasta --remove_divergent --outfile_stem {path_out}{genes}_cialign.fasta
touch {done}
""".format(genes = gene, done = done, path_in = path_in, path_out=path_out)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
########################################################################################################################
#####################################################---- Taper ----####################################################
########################################################################################################################
def taper(path_in, gene, path_out, done):
"""Using TAPER AFTER CIAlign to remove errors in small species-specific stretches of the multiple sequence alignments"""
inputs = [path_in+gene+"_cialign.fasta_cleaned.fasta"]
outputs = [path_out+gene+"_output_tapper.fasta", done]
options = {'cores': 1, 'memory': "40g", 'walltime': "02:00:00", 'account':"Coryphoideae"}
spec = """
cd {path_in}
#Activate the enviroment
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate cialign_env
julia /home/owrisberg/Coryphoideae/github_code/TAPER/correction_multi.jl {genes}_cialign.fasta_cleaned.fasta > {genes}_output_tapper.fasta
mv {genes}_output_tapper.fasta {path_in}TAPER
touch {done}
""".format(path_in = path_in, genes = gene, path_out = path_out, done =done)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
# ########################################################################################################################
# #############################################---- Exon Mapper ----######################################################
# ########################################################################################################################
def exon_map(path_in,path_out,done,gene):
"""This creates new alignments in `07_mapping` that contain the original alignments plus the exon sequences of the
two species that had the highest recovery success at each locus.."""
inputs = ["/home/owrisberg/Coryphoideae/work_flow/08_cialign/TAPER/done/"+gene]
outputs = [done,path_out+gene+"_output_tapper_mapped.fasta"]
options = {'cores': 4, 'memory': "20g", 'walltime': "04:00:00", 'account':"Coryphoideae"}
spec="""
#Activating conda base environment
source /home/owrisberg/miniconda3/etc/profile.d/conda.sh
conda activate base
#Going to folder with data
cd {path_in}
echo " Working directory is"
pwd
echo "listing files"
ls
# Running Wolfs Exon_mapper
python3 /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/exon_mapper.py --gene {gene} --outdir {path_out} --file_ending _output_tapper.fasta
touch {done}
""".format(path_in=path_in, done=done, gene=gene, path_out=path_out)
return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
########################################################################################################################
######################################################---- RUN ----#####################################################
########################################################################################################################
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#### Retrieve sequences and sort into files with gene names
gwf.target_from_template('Retrieve_genes', retrieve(path_in="/home/owrisberg/Coryphoideae/work_flow/04_coverage/",
file_list ="/home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/filelist.txt",
output_folder ="/home/owrisberg/Coryphoideae/work_flow/05_blacklisting/",
done = "/home/owrisberg/Coryphoideae/work_flow/05_blacklisting/done/retrieve_done.txt"
))
#Main workflow for genes
for i in range(len(genes)):
#### Running Mafft
gwf.target_from_template('Mafft_'+genes[i], mafft(gene = genes[i],
path_in = "/home/owrisberg/Coryphoideae/work_flow/05_blacklisting/",
path_out= "/home/owrisberg/Coryphoideae/work_flow/06_alignment/",
done = "/home/owrisberg/Coryphoideae/work_flow/06_alignment/done/"+genes[i]))
#### Running optrim_preb
gwf.target_from_template('gt_trimming_'+genes[i], gt_trimming(gene = genes[i],
path_in = "/home/owrisberg/Coryphoideae/work_flow/06_alignment/",
done = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/done/trimal_gt/"+genes[i],
path_out = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/"))
#### Running AMAS on the trimmed sequences for each gt value
for j in range(len(gt_values)):
gwf.target_from_template('amas_preb_gt_'+gt_values[j], amas_preb_gt(cut_off=gt_values[j],
path_in = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/",
path_out = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/",
done = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/done/amas_gt/"+gt_values[j]))
#Running AMAS on raw sequences
gwf.target_from_template('amas_raw', amas_preb_raw(path_in = "/home/owrisberg/Coryphoideae/work_flow/06_alignment/",
path_out = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/",
done = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/done/amas_raw/amaw_raw_done.txt"))
#Running optrim to find optimal trimming trimming threshold.
gwf.target_from_template('optrim', optrim(path_in = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/",
done = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/done/optrim/optrim_done.txt",
path_out = "/home/owrisberg/Coryphoideae/work_flow/08_cialign/"))
for i in range(len(genes)):
#### Running CIAlign
gwf.target_from_template('CIAlign_'+genes[i], cialign(gene = genes[i],
path_in = "/home/owrisberg/Coryphoideae/work_flow/07_optrimal/",
path_out= "/home/owrisberg/Coryphoideae/work_flow/08_cialign/",
done = "/home/owrisberg/Coryphoideae/work_flow/08_cialign/done/"+genes[i]))
#### Running TAPER
gwf.target_from_template('TAPER_'+genes[i], taper(gene = genes[i],
path_in = "/home/owrisberg/Coryphoideae/work_flow/08_cialign/",
path_out= "/home/owrisberg/Coryphoideae/work_flow/08_cialign/TAPER/",
done = "/home/owrisberg/Coryphoideae/work_flow/08_cialign/TAPER/done/"+genes[i]))
#### Running Exon_mapper
gwf.target_from_template('Exon_map_'+genes[i], exon_map(gene = genes[i],
path_in = "/home/owrisberg/Coryphoideae/work_flow/08_cialign/TAPER/",
path_out = "/home/owrisberg/Coryphoideae/work_flow/09_mapping/",
done = "/home/owrisberg/Coryphoideae/work_flow/09_mapping/done/"+genes[i]))