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ScriptsDir.py
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#!/usr/bin/env python
"""
Author: M. Fahad Syed ([email protected])
"""
import os
import sys
import traceback
sys.path.append("model_reconstruction_pipeline")
import NGS_Util
projectDir = os.path.dirname(os.path.realpath(__file__))
########################################################################################## Blast Toolkit ##########################################################################################
BlastDir = "Tools/ncbi-blast-2.2.28+/bin/"
BlastDBDir = "Tools/ncbi-blast-2.2.28+/db/" #Needs to be set the user#
BlastDustDir = "Tools/ncbi-blast-2.2.28+/db/" #Needs to be set the user#
########################################################################################## Blast Toolkit ##########################################################################################
IprscanDir = "Tools/iprscan/bin/"
###############################################################################################################################################################################################
#projectBinDir = NGS_Util.createDirectoryPath(projectDir,"bin")
BLASTScripts = NGS_Util.createDirectoryPath(projectDir,"Blast_scripts")
BlastScripts_blast=BLASTScripts + "blast.bash"
BlastScripts_blastp_bwdblast=BLASTScripts + "blastp_bwdblast.bash"
BlastScripts_blastp_fwdblast=BLASTScripts + "blastp_fwdblast.bash"
BlastScripts_makeblastdb_AUTO=BLASTScripts + "makeblastdb_AUTO.bash"
BlastScripts_makedustfile_AUTO=BLASTScripts + "makedustfile_AUTO.bash"
BlastScripts_buildBlastResult=BLASTScripts + "buildBlastResult.py"
BlastScripts_combineAllBlasts=BLASTScripts + "combineAllBlasts.py"
BlastScripts_getEcs=BLASTScripts + "getEcs.py"
BlastScripts_rectify_blastresult=BLASTScripts + "rectify_blastresult.py"
GTGScripts = NGS_Util.createDirectoryPath(projectDir,"GTG_scripts")
GTGScripts_reform_knn= GTGScripts + "reform_knn.py"
GTGScripts_reform= GTGScripts + "reform.py"
GTGScripts_linebuffer= GTGScripts + "linebuffer.py"
GTGScripts_gtgknn= GTGScripts + "gtgknn.py"
GTGScripts_gtg_attributes_mod= GTGScripts + "gtg_attributes_mod.py"
GTGScripts_extract_start_len_fmt11= GTGScripts + "extract_start_len_fmt11.py"
GTGScripts_extract_seq_fmt11= GTGScripts + "extract_seq_fmt11.py"
GTGScripts_extract_nids_from_uniprot= GTGScripts + "extract_nids_from_uniprot.py"
GTGScripts_extract_combine_seq_start_len_fmt11= GTGScripts + "extract_combine_seq_start_len_fmt11.py"
GTGScripts_extract_best_hit= GTGScripts + "extract_best_hit.py"
GTGScripts_buildGTGindex= GTGScripts + "buildGTGindex.py"
IPRScanScripts = NGS_Util.createDirectoryPath(projectDir,"Iprscan_scripts")
IPRScanScripts_wsbatch_original_Dispatcher_test = IPRScanScripts + "wsbatch_original_Dispatcher_test.sh"
IPRScanScripts_iprscan_suds = IPRScanScripts + "iprscan_suds.py"
IPRScanScripts_ipr2go = IPRScanScripts + "ipr2go.py"
IPRScanScripts_ipr_reform_ecs = IPRScanScripts + "ipr_reform_ecs.bash"
IPRScanScripts_ipr_bash = IPRScanScripts + "ipr_bash.bash"
IPRScanScripts_get_seq_org_list = IPRScanScripts + "get_seq_org_list.py"
IPRScanScripts_get_interpro_ecs = IPRScanScripts + "get_interpro.ecs.py"
IPRScanScripts_fsplit = IPRScanScripts + "fsplit.sh"
IPRScanScripts_combineIPRwithECs = IPRScanScripts + "combineIPRwithECs.py"
IPRScanScripts_combine_xml_out = IPRScanScripts + "combine_xml_out.bash"
ModelTrainingScripts = NGS_Util.createDirectoryPath(projectDir,"model_training_scripts")
ModelTrainingScripts_visualize_ec_scores = ModelTrainingScripts + "visualize_ec_scores.py"
ModelTrainingScripts_tree = ModelTrainingScripts + "tree.py"
ModelTrainingScripts_run_job = ModelTrainingScripts + "run_job.sh"
ModelTrainingScripts_roc = ModelTrainingScripts + "roc.py"
ModelTrainingScripts_plot_reaction_scores = ModelTrainingScripts + "plot_reaction_scores.py"
ModelTrainingScripts_plot = ModelTrainingScripts + "plot.py"
ModelTrainingScripts_merge_scores = ModelTrainingScripts + "merge_scores.py"
ModelTrainingScripts_import_data = ModelTrainingScripts + "import_data.py"
ModelTrainingScripts_fitch = ModelTrainingScripts + "fitch.py"
ModelTrainingScripts_extract_ecs_from_iprscan = ModelTrainingScripts + "extract_ecs_from_iprscan.py"
ModelTrainingScripts_estimate_mutation_probability = ModelTrainingScripts + "estimate_mutation_probability.py"
ModelTrainingScripts_estimate_cpds_wrapper = ModelTrainingScripts + "estimate_cpds_wrapper.py"
ModelTrainingScripts_estimate_cpds = ModelTrainingScripts + "estimate_cpds.py"
ModelTrainingScripts_digraph = ModelTrainingScripts + "digraph.py"
ModelTrainingScripts_computeMergedScores = ModelTrainingScripts + "computeMergedScores.py"
ModelTrainingScripts_computeECscores = ModelTrainingScripts + "computeECscores.py"
ModelTrainingScripts_computeBlastPvalues = ModelTrainingScripts + "computeBlastPvalues.py"
ModelTrainingScripts_compute_reaction_scores = ModelTrainingScripts + "compute_reaction_scores.py"
ModelTrainingScripts_common = ModelTrainingScripts + "common.py"
ModelTrainingScripts_combined_density = ModelTrainingScripts + "combined_density.py"
ModelTrainingScripts_bayesnet = ModelTrainingScripts + "bayesnet.py"
ReconstructionScripts = NGS_Util.createDirectoryPath(projectDir,"reconstruction_scripts")
ReconstructionScripts_reco_dir = ReconstructionScripts + "reco-dir"
keggParsingScripts = NGS_Util.createDirectoryPath(projectDir,"kegg-parsing")
keggParsingScripts_build_kegg_no_general = keggParsingScripts + "build_kegg_no_general.sh"