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.COMMANDS.txt
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.COMMANDS.txt
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# ROC curves
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs.fasta bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fsff fg_seqs_shape/tec1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*tec1* -cv roc -s tec1_LinearSVC_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs.fasta bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fsff fg_seqs_shape/bcr1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*bcr1* -cv roc -s bcr1_LinearSVC_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs.fasta bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fsff fg_seqs_shape/brg1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*brg1* -cv roc -s brg1_LinearSVC_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/efg1_fg_seqs.fasta bkg_seqs/efg1_all_bkg_combined.fasta efg1 -fsff fg_seqs_shape/efg1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*efg1* -cv roc -s efg1_LinearSVC_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/ndt80_fg_seqs.fasta bkg_seqs/ndt80_all_bkg_combined.fasta ndt80 -fsff fg_seqs_shape/ndt80_fg_seqs.fasta.* -bsff bkg_seqs_shape/*ndt80* -cv roc -s ndt80_LinearSVC_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/rob1_fg_seqs.fasta bkg_seqs/rob1_all_bkg_combined.fasta rob1 -fsff fg_seqs_shape/rob1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*rob1* -cv roc -s rob1_LinearSVC_ROC.pdf
# Dec 2019 update to ROC command
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs2.fasta new_bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fbf fg_seqs/bcr1_true_sites.bed -bsff new_bkg_seqs_shapes/bcr1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv roc -s dec2019_CV_plots/bcr1_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs2.fasta new_bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fbf fg_seqs/brg1_true_sites.bed -bsff new_bkg_seqs_shapes/brg1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv roc -s dec2019_CV_plots/brg1_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/efg1_fg_seqs2.fasta new_bkg_seqs/efg1_all_bkg_combined.fasta efg1 -fbf fg_seqs/efg1_true_sites.bed -bsff new_bkg_seqs_shapes/efg1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv roc -s dec2019_CV_plots/efg1_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/ndt80_fg_seqs2.fasta new_bkg_seqs/ndt80_all_bkg_combined.fasta ndt80 -fbf fg_seqs/ndt80_true_sites.bed -bsff new_bkg_seqs_shapes/ndt80_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv roc -s dec2019_CV_plots/ndt80_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/rob1_fg_seqs2.fasta new_bkg_seqs/rob1_all_bkg_combined.fasta rob1 -fbf fg_seqs/rob1_true_sites.bed -bsff new_bkg_seqs_shapes/rob1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv roc -s dec2019_CV_plots/rob1_ROC.pdf
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs2.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fbf fg_seqs/tec1_true_sites.bed -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv roc -s dec2019_CV_plots/tec1_ROC.pdf
# PRC curves
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs.fasta bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fsff fg_seqs_shape/tec1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*tec1* -cv prc -s tec1_LinearSVC_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs.fasta bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fsff fg_seqs_shape/bcr1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*bcr1* -cv prc -s bcr1_LinearSVC_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs.fasta bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fsff fg_seqs_shape/brg1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*brg1* -cv prc -s brg1_LinearSVC_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/efg1_fg_seqs.fasta bkg_seqs/efg1_all_bkg_combined.fasta efg1 -fsff fg_seqs_shape/efg1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*efg1* -cv prc -s efg1_LinearSVC_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/ndt80_fg_seqs.fasta bkg_seqs/ndt80_all_bkg_combined.fasta ndt80 -fsff fg_seqs_shape/ndt80_fg_seqs.fasta.* -bsff bkg_seqs_shape/*ndt80* -cv prc -s ndt80_LinearSVC_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/rob1_fg_seqs.fasta bkg_seqs/rob1_all_bkg_combined.fasta rob1 -fsff fg_seqs_shape/rob1_fg_seqs.fasta.* -bsff bkg_seqs_shape/*rob1* -cv prc -s rob1_LinearSVC_PRC.pdf
# Dec 2019 update to PRC command
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs2.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fbf fg_seqs/tec1_true_sites.bed -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv prc -s dec2019_CV_plots/tec1_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs2.fasta new_bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fbf fg_seqs/bcr1_true_sites.bed -bsff new_bkg_seqs_shapes/bcr1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv prc -s dec2019_CV_plots/bcr1_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs2.fasta new_bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fbf fg_seqs/brg1_true_sites.bed -bsff new_bkg_seqs_shapes/brg1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv prc -s dec2019_CV_plots/brg1_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/efg1_fg_seqs2.fasta new_bkg_seqs/efg1_all_bkg_combined.fasta efg1 -fbf fg_seqs/efg1_true_sites.bed -bsff new_bkg_seqs_shapes/efg1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv prc -s dec2019_CV_plots/efg1_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/ndt80_fg_seqs2.fasta new_bkg_seqs/ndt80_all_bkg_combined.fasta ndt80 -fbf fg_seqs/ndt80_true_sites.bed -bsff new_bkg_seqs_shapes/ndt80_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv prc -s dec2019_CV_plots/ndt80_PRC.pdf
python discover_tfbs/build_features.py fg_seqs/rob1_fg_seqs2.fasta new_bkg_seqs/rob1_all_bkg_combined.fasta rob1 -fbf fg_seqs/rob1_true_sites.bed -bsff new_bkg_seqs_shapes/rob1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv prc -s dec2019_CV_plots/rob1_PRC.pdf
###############
# Oct. 1 2019
###############
# build background features
python discover_tfbs/create_bkg_seqs.py fg_seqs/tec1_fg_seqs.fasta tec1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.29.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
10/01/19 09:23: Generating random length-matched background sequences from CDS/exonic regions
10/01/19 09:25: Generating length-matched shuffled sequences from foreground sequences
python discover_tfbs/create_bkg_seqs.py fg_seqs/bcr1_fg_seqs.fasta bcr1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.29.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
10/01/19 09:38: Generating random length-matched background sequences from CDS/exonic regions
10/01/19 09:40: Generating length-matched shuffled sequences from foreground sequences
python discover_tfbs/create_bkg_seqs.py fg_seqs/brg1_fg_seqs.fasta brg1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.29.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
10/01/19 09:41: Generating random length-matched background sequences from CDS/exonic regions
10/01/19 09:43: Generating length-matched shuffled sequences from foreground sequences
python discover_tfbs/create_bkg_seqs.py fg_seqs/efg1_fg_seqs.fasta efg1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.29.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
10/01/19 09:44: Generating random length-matched background sequences from CDS/exonic regions
10/01/19 09:46: Generating length-matched shuffled sequences from foreground sequences
python discover_tfbs/create_bkg_seqs.py fg_seqs/rob1_fg_seqs.fasta rob1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.29.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
10/01/19 09:48: Generating random length-matched background sequences from CDS/exonic regions
10/01/19 09:50: Generating length-matched shuffled sequences from foreground sequences
python discover_tfbs/create_bkg_seqs.py fg_seqs/ndt80_fg_seqs.fasta ndt80 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.29.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
10/01/19 09:54: Generating random length-matched background sequences from CDS/exonic regions
10/01/19 09:56: Generating length-matched shuffled sequences from foreground sequences
# build feature tables
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fsff fg_seqs_shape/tec1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -cv roc -s tec1_new_LinearSVC_ROC.pdf
10/01/19 11:35:02 : Processing foreground FASTA file
=====================================================
10/01/19 11:35:02 : Reading FASTA file
10/01/19 11:35:02 : Calculating GC percent
10/01/19 11:35:02 : Calculating Poisson based metrics
10/01/19 11:35:02 : Processing DNA shape data
10/01/19 11:35:02 : Creating positive training dataset
10/01/19 11:35:02 : Processing background FASTA file
====================================================
10/01/19 11:35:02 : Reading FASTA file
10/01/19 11:35:02 : Calculating GC percent
10/01/19 11:35:02 : Calculating Poisson based metrics
10/01/19 11:35:03 : Processing DNA shape data
10/01/19 11:35:03 : Creating negative training dataset
*****************************************************
10/01/19 11:35:03 : Starting 10-fold cross-validation
10/01/19 11:35:05 : Plotting and saving ROC data
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fsff fg_seqs_shape/tec1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -cv prc -s tec1_new_LinearSVC_PRC.pdf
10/01/19 11:38:25 : Processing foreground FASTA file
=====================================================
10/01/19 11:38:25 : Reading FASTA file
10/01/19 11:38:25 : Calculating GC percent
10/01/19 11:38:25 : Calculating Poisson based metrics
10/01/19 11:38:25 : Processing DNA shape data
10/01/19 11:38:25 : Creating positive training dataset
10/01/19 11:38:25 : Processing background FASTA file
====================================================
10/01/19 11:38:25 : Reading FASTA file
10/01/19 11:38:25 : Calculating GC percent
10/01/19 11:38:25 : Calculating Poisson based metrics
10/01/19 11:38:26 : Processing DNA shape data
10/01/19 11:38:26 : Creating negative training dataset
*****************************************************
10/01/19 11:38:26 : Starting 10-fold cross-validation
10/01/19 11:38:29 : Plotting and saving PRC data
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs.fasta new_bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fsff fg_seqs_shape/bcr1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/bcr1_all_bkg_combined.fasta.* -cv roc -s bcr1_new_LinearSVC_ROC.pdf
10/01/19 11:42:45 : Processing foreground FASTA file
=====================================================
10/01/19 11:42:45 : Reading FASTA file
10/01/19 11:42:45 : Calculating GC percent
10/01/19 11:42:45 : Calculating Poisson based metrics
10/01/19 11:42:45 : Processing DNA shape data
10/01/19 11:42:45 : Creating positive training dataset
10/01/19 11:42:45 : Processing background FASTA file
====================================================
10/01/19 11:42:45 : Reading FASTA file
10/01/19 11:42:45 : Calculating GC percent
10/01/19 11:42:45 : Calculating Poisson based metrics
10/01/19 11:42:46 : Processing DNA shape data
10/01/19 11:42:46 : Creating negative training dataset
*****************************************************
10/01/19 11:42:46 : Starting 10-fold cross-validation
10/01/19 11:42:51 : Plotting and saving ROC data
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs.fasta new_bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fsff fg_seqs_shape/bcr1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/bcr1_all_bkg_combined.fasta.* -cv prc -s bcr1_new_LinearSVC_PRC.pdf
10/01/19 11:43:51 : Processing foreground FASTA file
=====================================================
10/01/19 11:43:51 : Reading FASTA file
10/01/19 11:43:51 : Calculating GC percent
10/01/19 11:43:51 : Calculating Poisson based metrics
10/01/19 11:43:51 : Processing DNA shape data
10/01/19 11:43:51 : Creating positive training dataset
10/01/19 11:43:51 : Processing background FASTA file
====================================================
10/01/19 11:43:51 : Reading FASTA file
10/01/19 11:43:51 : Calculating GC percent
10/01/19 11:43:51 : Calculating Poisson based metrics
10/01/19 11:43:52 : Processing DNA shape data
10/01/19 11:43:52 : Creating negative training dataset
*****************************************************
10/01/19 11:43:52 : Starting 10-fold cross-validation
10/01/19 11:43:57 : Plotting and saving PRC data
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs.fasta new_bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fsff fg_seqs_shape/brg1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/brg1_all_bkg_combined.fasta.* -cv roc -s brg1_new_LinearSVC_ROC.pdf
10/01/19 11:45:43 : Processing foreground FASTA file
=====================================================
10/01/19 11:45:43 : Reading FASTA file
10/01/19 11:45:43 : Calculating GC percent
10/01/19 11:45:43 : Calculating Poisson based metrics
10/01/19 11:45:43 : Processing DNA shape data
10/01/19 11:45:43 : Creating positive training dataset
10/01/19 11:45:43 : Processing background FASTA file
====================================================
10/01/19 11:45:43 : Reading FASTA file
10/01/19 11:45:43 : Calculating GC percent
10/01/19 11:45:43 : Calculating Poisson based metrics
10/01/19 11:45:45 : Processing DNA shape data
10/01/19 11:45:45 : Creating negative training dataset
*****************************************************
10/01/19 11:45:45 : Starting 10-fold cross-validation
10/01/19 11:46:07 : Plotting and saving ROC data
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs.fasta new_bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fsff fg_seqs_shape/brg1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/brg1_all_bkg_combined.fasta.* -cv prc -s brg1_new_LinearSVC_PRC.pdf
10/01/19 11:48:17 : Processing foreground FASTA file
=====================================================
10/01/19 11:48:17 : Reading FASTA file
10/01/19 11:48:17 : Calculating GC percent
10/01/19 11:48:17 : Calculating Poisson based metrics
10/01/19 11:48:17 : Processing DNA shape data
10/01/19 11:48:17 : Creating positive training dataset
10/01/19 11:48:17 : Processing background FASTA file
====================================================
10/01/19 11:48:17 : Reading FASTA file
10/01/19 11:48:17 : Calculating GC percent
10/01/19 11:48:17 : Calculating Poisson based metrics
10/01/19 11:48:19 : Processing DNA shape data
10/01/19 11:48:19 : Creating negative training dataset
*****************************************************
10/01/19 11:48:19 : Starting 10-fold cross-validation
10/01/19 11:49:04 : Plotting and saving PRC data
###############
# Oct. 12 2019
###############
# Get FASTA file from BLASTn result
bedtools getfasta -fi ../genome_files/C_albicans_SC5314_A22_current_chromosomes.fasta -bed tec1_curated_motifs_CA_A22.bed -s -fo tec1_curated_motifs_blastn_matches_CA_A22.fasta
bedtools getfasta -fi ../genome_files/C_albicans_SC5314_A22_current_chromosomes.fasta -bed bcr1_curated_motifs_CA_A22.bed -s -fo bcr1_curated_motifs_blastn_matches_CA_A22.fasta
bedtools getfasta -fi ../genome_files/C_albicans_SC5314_A22_current_chromosomes.fasta -bed brg1_curated_motifs_CA_A22.bed -s -fo bcrg1_curated_motifs_blastn_matches_CA_A22.fasta
bedtools getfasta -fi ../genome_files/C_albicans_SC5314_A22_current_chromosomes.fasta -bed efg1_curated_motifs_CA_A22.bed -s -fo efg1_curated_motifs_blastn_matches_CA_A22.fasta
bedtools getfasta -fi ../genome_files/C_albicans_SC5314_A22_current_chromosomes.fasta -bed rob1_curated_motifs_CA_A22.bed -s -fo rob1_curated_motifs_blastn_matches_CA_A22.fasta
bedtools getfasta -fi ../genome_files/C_albicans_SC5314_A22_current_chromosomes.fasta -bed ndt80_curated_motifs_CA_A22.bed -s -fo ndt80_curated_motifs_blastn_matches_CA_A22.fasta
# building features for test datasets - output from blastn run
# Tec1
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fsff fg_seqs_shape/tec1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/tec1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/tec1_curated_motifs_blastn_matches_CA_A22.fasta.* -o prediction_outputs/tec1_positive_predictions.bed
10/12/19 14:33:41 : Processing foreground FASTA file
=====================================================
10/12/19 14:33:41 : Reading FASTA file
10/12/19 14:33:41 : Calculating GC percent
10/12/19 14:33:41 : Calculating Poisson based metrics
10/12/19 14:33:41 : Processing DNA shape data
10/12/19 14:33:41 : Creating positive training dataset
10/12/19 14:33:41 : Processing background FASTA file
====================================================
10/12/19 14:33:41 : Reading FASTA file
10/12/19 14:33:41 : Calculating GC percent
10/12/19 14:33:41 : Calculating Poisson based metrics
10/12/19 14:33:42 : Processing DNA shape data
10/12/19 14:33:42 : Creating negative training dataset
*****************************************************
10/12/19 14:33:42 : Starting data training
10/12/19 14:33:47 : Calculating GC percent
10/12/19 14:33:47 : Calculating Poisson based metrics
10/12/19 14:36:00 : Processing DNA shape data
10/12/19 14:36:02 : Creating prediction dataset
10/12/19 14:36:03 : Writing positive prediction results to prediction_outputs/tec1_positive_predictions.bed
# Bcr1
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs.fasta new_bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fsff fg_seqs_shape/bcr1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/bcr1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/bcr1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/bcr1_curated_motifs_blastn_matches_CA_A22.fasta.* -o prediction_outputs/bcr1_positive_predictions.bed
# Convert BLASTn output matches to BED6 tabular format
awk 'BEGIN{FS="\t"; OFS=FS} {if ($9 < $10) {print $2, $9 - 1, $10, $1, ".", "+"} else {print $2, $10 - 1, $9, $1, ".", "-"}}' blast_output/bcr1_curated_motifs_CA_A22.blout > blast_output/bcr1_curated_motifs_CA_A22.bed
awk 'BEGIN{FS="\t"; OFS=FS} {if ($9 < $10) {print $2, $9 - 1, $10, $1, ".", "+"} else {print $2, $10 - 1, $9, $1, ".", "-"}}' blast_output/brg1_curated_motifs_CA_A22.blout > blast_output/brg1_curated_motifs_CA_A22.bed
awk 'BEGIN{FS="\t"; OFS=FS} {if ($9 < $10) {print $2, $9 - 1, $10, $1, ".", "+"} else {print $2, $10 - 1, $9, $1, ".", "-"}}' blast_output/efg1_curated_motifs_CA_A22.blout > blast_output/efg1_curated_motifs_CA_A22.bed
awk 'BEGIN{FS="\t"; OFS=FS} {if ($9 < $10) {print $2, $9 - 1, $10, $1, ".", "+"} else {print $2, $10 - 1, $9, $1, ".", "-"}}' blast_output/ndt80_curated_motifs_CA_A22.blout > blast_output/ndt80_curated_motifs_CA_A22.bed
awk 'BEGIN{FS="\t"; OFS=FS} {if ($9 < $10) {print $2, $9 - 1, $10, $1, ".", "+"} else {print $2, $10 - 1, $9, $1, ".", "-"}}' blast_output/rob1_curated_motifs_CA_A22.blout > blast_output/rob1_curated_motifs_CA_A22.bed
awk 'BEGIN{FS="\t"; OFS=FS} {if ($9 < $10) {print $2, $9 - 1, $10, $1, ".", "+"} else {print $2, $10 - 1, $9, $1, ".", "-"}}' blast_output/tec1_curated_motifs_CA_A22.blout > blast_output/tec1_curated_motifs_CA_A22.bed
# Permutation testing for model assessment
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fsff fg_seqs_shape/tec1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/tec1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/tec1_curated_motifs_blastn_matches_CA_A22.fasta.* -s prediction_outputs/tec1_svm_permutation_result.pdf
python discover_tfbs/build_features.py fg_seqs/bcr1_fg_seqs.fasta new_bkg_seqs/bcr1_all_bkg_combined.fasta bcr1 -fsff fg_seqs_shape/bcr1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/bcr1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/bcr1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/bcr1_curated_motifs_blastn_matches_CA_A22.fasta.* -s prediction_outputs/bcr1_svm_permutation_result.pdf
python discover_tfbs/build_features.py fg_seqs/brg1_fg_seqs.fasta new_bkg_seqs/brg1_all_bkg_combined.fasta brg1 -fsff fg_seqs_shape/brg1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/brg1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/brg1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/brg1_curated_motifs_blastn_matches_CA_A22.fasta.* -s prediction_outputs/brg1_svm_permutation_result.pdf
python discover_tfbs/build_features.py fg_seqs/efg1_fg_seqs.fasta new_bkg_seqs/efg1_all_bkg_combined.fasta efg1 -fsff fg_seqs_shape/efg1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/efg1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/efg1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/efg1_curated_motifs_blastn_matches_CA_A22.fasta.* -s prediction_outputs/efg1_svm_permutation_result.pdf
python discover_tfbs/build_features.py fg_seqs/ndt80_fg_seqs.fasta new_bkg_seqs/ndt80_all_bkg_combined.fasta ndt80 -fsff fg_seqs_shape/ndt80_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/ndt80_all_bkg_combined.fasta.* -p genome_wide_blastn_results/ndt80_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/ndt80_curated_motifs_blastn_matches_CA_A22.fasta.* -s prediction_outputs/ndt80_svm_permutation_result.pdf
python discover_tfbs/build_features.py fg_seqs/rob1_fg_seqs.fasta new_bkg_seqs/rob1_all_bkg_combined.fasta rob1 -fsff fg_seqs_shape/rob1_fg_seqs.fasta.* -bsff new_bkg_seqs_shapes/rob1_all_bkg_combined.fasta.* -p genome_wide_blastn_results/rob1_curated_motifs_blastn_matches_CA_A22.fasta -psff genome_wide_blastn_results/rob1_curated_motifs_blastn_matches_CA_A22.fasta.* -s prediction_outputs/rob1_svm_permutation_result.pdf
# Convert multiline shape FASTA files to single line FASTA file. This is needed for Bedtools to collect shapes of blastn matches for non-tec1 proteins.
cd data/ca_biofilm/genome_files/
for f in C_albicans_SC5314_A22_current_chromosomes.fasta.[HEMPR]*; do echo -e "--> Processing $f <--"; outfnh=$(basename "$f" | cut -d. -f1); shape=$(basename "$f" | cut -d. -f3); awk '/^>/ { if(NR>1) print ""; printf("%s\n",$0); next; } { printf("%s,",$0);} END {printf("\n");}' < "$f" > "${outfnh}_oneline.fasta.${shape}"; echo -e "${outfnh}_oneline.fasta.${shape}\n"; done
--> Processing C_albicans_SC5314_A22_current_chromosomes.fasta.EP <--
C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.EP
--> Processing C_albicans_SC5314_A22_current_chromosomes.fasta.HelT <--
C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.HelT
--> Processing C_albicans_SC5314_A22_current_chromosomes.fasta.MGW <--
C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.MGW
--> Processing C_albicans_SC5314_A22_current_chromosomes.fasta.ProT <--
C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.ProT
--> Processing C_albicans_SC5314_A22_current_chromosomes.fasta.Roll <--
C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.Roll
# liftOver Assembly 21 bound sites to Assembly 22 hapA sites
liftOver Bcr1_motifs.bed ../genome_files/Assembly21_To_Assembly22_hapA.over.chain ca22_true_motifs/bcr1_true_sites.bed bcr1_unmapped_ca22_sites.txt -bedPlus=6 -tab
liftOver Brg1_motifs.bed ../genome_files/Assembly21_To_Assembly22_hapA.over.chain ca22_true_motifs/brg1_true_sites.bed brg1_unmapped_ca22_sites.txt -bedPlus=6 -tab
liftOver Efg1_motifs.bed ../genome_files/Assembly21_To_Assembly22_hapA.over.chain ca22_true_motifs/efg1_true_sites.bed efg1_unmapped_ca22_sites.txt -bedPlus=6 -tab
liftOver Rob1_motifs.bed ../genome_files/Assembly21_To_Assembly22_hapA.over.chain ca22_true_motifs/rob1_true_sites.bed rob1_unmapped_ca22_sites.txt -bedPlus=6 -tab
liftOver Tec1_motifs.bed ../genome_files/Assembly21_To_Assembly22_hapA.over.chain ca22_true_motifs/tec1_true_sites.bed tec1_unmapped_ca22_sites.txt -bedPlus=6 -tab
liftOver Ndt80_motifs.bed ../genome_files/Assembly21_To_Assembly22_hapA.over.chain ca22_true_motifs/ndt80_true_sites.bed ndt80_unmapped_ca22_sites.txt -bedPlus=6 -tab
# Using newer way to retrieve DNA shapes, predict TFBS and weights of features
python discover_tfbs/build_features.py fg_seqs/tec1_fg_seqs2.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fbf fg_seqs/tec1_true_sites.bed -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -p genome_wide_blastn_results/tec1_curated_motifs_blastn_matches_CA_A22.fasta -pbf genome_wide_blastn_results/tec1_curated_motifs_blastn_matches_CA_A22.bed -s prediction_outputs/tec1_svm_weights2.pdf -o prediction_outputs/tec1_positive_predictions2.bed
#########################################################################################
Feb. 25th 2020 commands
# in ca_biofilm/ on Romulus
# create background sequences based on CA22 liftover true sequences
# to do: brg1 has a unambiguous Y nucleotide, which is throwing error in creating bkg seqs
create_bkg_seqs.py fg_seqs/efg1_fg_seqs2.fasta efg1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.30.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
create_bkg_seqs.py fg_seqs/ndt80_fg_seqs2.fasta ndt80 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.30.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
create_bkg_seqs.py fg_seqs/rob1_fg_seqs2.fasta rob1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.30.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
create_bkg_seqs.py fg_seqs/bcr1_fg_seqs2.fasta bcr1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.30.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
create_bkg_seqs.py fg_seqs/tec1_fg_seqs2.fasta tec1 -g non_candida_genome_files/C_albicans_SC5314_A22_current_default_coding.fasta non_candida_genome_files/dmel-all-exon-r6.30.fasta non_candida_genome_files/GCF_000005845.2_ASM584v2_cds_from_genomic.fna -o new_bkg_seqs/
# combine all bkg seq FASTA files from create_bkg_seqs.py script
cat tec1_dinuc_shuffled_len_matched_bkg_seqs.fasta tec1_cds_exon_len_matched_bkg_seqs.fasta > tec1_all_bkg_combined.fasta
cat bcr1_dinuc_shuffled_len_matched_bkg_seqs.fasta bcr1_cds_exon_len_matched_bkg_seqs.fasta > bcr1_all_bkg_combined.fasta
cat efg1_dinuc_shuffled_len_matched_bkg_seqs.fasta efg1_cds_exon_len_matched_bkg_seqs.fasta > efg1_all_bkg_combined.fasta
cat rob1_dinuc_shuffled_len_matched_bkg_seqs.fasta rob1_cds_exon_len_matched_bkg_seqs.fasta > rob1_all_bkg_combined.fasta
cat ndt80_dinuc_shuffled_len_matched_bkg_seqs.fasta ndt80_cds_exon_len_matched_bkg_seqs.fasta > ndt80_all_bkg_combined.fasta
# get DNA shape for all bkg seqs created in *all_bkg_combined* FASTA files
# in R console
library(DNAshapeR)
bkg_files <- list.files(pattern="*all_bkg_combined*", path="../new_bkg_seqs/", full.names=T)
[1] "../new_bkg_seqs//bcr1_all_bkg_combined.fasta"
[2] "../new_bkg_seqs//bcr11_all_bkg_combined.fasta"
[3] "../new_bkg_seqs//brg1_all_bkg_combined.fasta"
[4] "../new_bkg_seqs//efg1_all_bkg_combined.fasta"
[5] "../new_bkg_seqs//ndt80_all_bkg_combined.fasta"
[6] "../new_bkg_seqs//rob1_all_bkg_combined.fasta"
[7] "../new_bkg_seqs//tec1_all_bkg_combined.fasta"
for (f in bkg_files) {
+ getShape(filename=f)
+ message(paste0("Processed ", f))
+ }
# build features, train SVC model and calculate PRC plots
build_features.py fg_seqs/tec1_fg_seqs2.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fbf fg_seqs/tec1_true_sites.bed -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv -s prc_plots/tec1_prc.pdf
#########################################################################################
Mar. 19th 2020 commands
# create background sequences based on CA22 liftover true sequences
cd /home/aparopkari/ca_biofilm/job_subs
find . -type f -name "*_create_bkg_seqs.sub" | xargs -I {} sbatch {}
# build features, train SVC model and calculate PRC plots
build_features.py fg_seqs/tec1_fg_seqs2.fasta new_bkg_seqs/tec1_all_bkg_combined.fasta tec1 -fbf fg_seqs/tec1_true_sites.bed -bsff new_bkg_seqs_shapes/tec1_all_bkg_combined.fasta.* -gwsf genome_files/C_albicans_SC5314_A22_current_chromosomes_oneline.fasta.* -cv -s prc_plots/tec1_prc.pdf