Merge pull request #21 from CEGRcode/revisions

Updates responding to reviewer comments
CEGRcode · Aug 21, 2023 · 7d4b912 · 7d4b912
2 parents 73e17f5 + 0028167
commit 7d4b912
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diff --git a/.gitignore b/.gitignore
@@ -1,30 +1,12 @@
 **/.DS_Store
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.amb
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.ann
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.bwt
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.pac
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.sa
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.1.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.2.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.3.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.4.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.rev.1.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.rev.2.bt2
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.amb
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.ann
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.bwt
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.pac
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.sa
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.amb
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.ann
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.bwt
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.pac
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.sa
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.1.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.2.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.3.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.4.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.rev.1.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.rev.2.bt2
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.*
+EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa*
+EpitopeID/hg19_EpiID/FASTA_genome/genome.fa*
+EpitopeID/hg19_EpiID_v2/FASTA_genome/genome.fa*
+StrainID/hg38_VCF
+StrainID/hg38_ENCODE
+StrainID/hg38_DepMap
+StrainID/utility_scripts/header.vcf
+StrainID/utility_scripts/CL_names.txt
+StrainID/utility_scripts/CSV
+StrainID/utility_scripts/hg38_DepMap
diff --git a/DeletionID/delScripts/detect_deletion_BAM.py b/DeletionID/delScripts/detect_deletion_BAM.py
@@ -15,7 +15,7 @@
 Log2 output minimum threshold (Default -3)		-l Log2_Threshold
 Mappability threshold to consider (Default 0.25)	-M Mappability_%
 
-Example: python2 detect_deletion_BAM.py -b NGS.bam -c Interval.bed -m Mappability.tab -o NGS_deletion.tab -l -2 -M 0.25
+Example: python detect_deletion_BAM.py -b NGS.bam -c Interval.bed -m Mappability.tab -o NGS_deletion.tab -l -2 -M 0.25
 """
 
 def calculateDeletion(PASS):

diff --git a/DeletionID/utility_scripts/get_mm10_ORF_BED.sh b/DeletionID/utility_scripts/get_mm10_ORF_BED.sh
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.1.bt2 b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.1.bt2
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.2.bt2 b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.2.bt2
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.3.bt2 b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.3.bt2
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.4.bt2 b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.4.bt2
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.amb b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.amb
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.ann b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.ann
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.bwt b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.bwt
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.pac b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.pac
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.rev.1.bt2 b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.rev.1.bt2
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.rev.2.bt2 b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.rev.2.bt2
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.sa b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.sa
diff --git a/EpitopeID/epiScripts/calculate_EpitopeSignificance.py b/EpitopeID/epiScripts/calculate_EpitopeSignificance.py
@@ -6,7 +6,7 @@
 This script takes in the paired-end table containing the stats from the EpitopeID pipeine and calculates
 the Poisson p-value threshold given a minimum 2-fold enrichment over the expected tags based on the bin size.
 
-Example: python2 calculate_EpitopeSignificance.py -t PE_table.out -p 0.05 -c 10000 -s 12000000 -o PE_sig.out
+Example: python calculate_EpitopeSignificance.py -t PE_table.out -p 0.05 -c 10000 -s 12000000 -o PE_sig.out
 """
 
 # Main program which takes in input parameters

diff --git a/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.amb b/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.amb
diff --git a/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.ann b/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.ann
diff --git a/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.bwt b/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.bwt
diff --git a/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.pac b/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.pac
diff --git a/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.sa b/EpitopeID/hg19_EpiID/FASTA_tag/ALL_TAG.fa.sa
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_genome/README.txt b/EpitopeID/hg19_EpiID_v2/FASTA_genome/README.txt
@@ -0,0 +1 @@
+genome.fa goes here
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa
@@ -0,0 +1,18 @@
+>3xFLAG
+gggagcggaggaggttccggtggaggtggttctggagattacaaggatgacgacgataagggcgattacaaggatgacgacgataagg
+gagattacaaggatgacgacgataaggtttcaggaagcggagctactaacttcagcctgctgaagcaggctggagacgtggaggagaac
+cctggacctggatcgtttcgcatgattgaacaagatggattgcacgcaggttctccggccgcttgggtggagaggctattcggctatgactggg
+cacaacagacaatcggctgctctgatgccgccgtgttccggctgtcagcgcaggggcgcccggttctttttgtcaagaccgacctgtccggtg
+ccctgaatgaactgcaggacgaggcagcgcggctatcgtggctggccacgacgggcgttccttgcgcagctgtgctcgacgttgtcactga
+agcgggaagggactggctgctattgggcgaagtgccggggcaggatctcctgtcatctcaccttgctcctgccgagaaagtatccatcatgg
+ctgatgcaatgcggcggctgcatacgcttgatccggctacctgcccattcgaccaccaagcgaaacatcgcatcgagcgagcacgtactcg
+gatggaagccggtcttgtcgatcaggatgatctggacgaagagcatcaggggctcgcgccagccgaactgttcgccaggctcaaggcgcg
+catgcccgacggcgaggatctcgtcgtgacccatggcgatgcctgcttgccgaatatcatggtggaaaatggccgcttttctggattcatcgac
+tgtggccggctgggtgtggccgaccgctatcaggacatagcgttggctacccgtgatattgctgaagagcttggcggcgaatgggctgaccg
+cttcctcgtgctttacggtatcgccgctcccgattcgcagcgcatcgccttctatcgccttcttgacgagttcttctgattcgaacatc
+>FKBP12-V	F36V variant of FKBP12
+atgggagtgcaggtggaaaccatctccccaggagacgggcgcaccttccccaagcgcggccagacctgcgtggtgcactacaccgggatgcttgaagatggaaagaaagttgattcctcccgggacagaaacaagccctttaagtttatgctaggcaagcaggaggtgatccgaggctgggaagaaggggttgcccagatgagtgtgggtcagagagccaaactgactatatctccagattatgcctatggtgccactgggcacccaggcatcatcccaccacatgccactctcgtcttcgatgtggagcttctaaaactggaa
+>HaloTag
+AATGCAGAAATAGGGACAGGCTTTCCTTTTGATCCCCATTATGTAGAGGTACTAGGAGAACGTATGCATTACGTGGACGTGGGACCAAGAGATGGCACCCCAGTTCTTTTTTTACACGGAAACCCAACCAGTTCTTATGTCTGGAGGAACATCATCCCTCACGTTGCTCCAACTCACAGATGTATAGCGCCTGATCTGATTGGGATGGGTAAATCAGACAAACCCGACTTGGGCTACTTCTTCGATGACCACGTCAGATTTATGGACGCGTTCATTGAGGCACTTGGGTTGGAAGAAGTCGTCCTGGTAATACATGACTGGGGATCAGCCCTGGGATTTCATTGGGCTAAAAGGAATCCAGAGAGAGTAAAAGGGATTGCCTTCATGGAGTTTATCAGGCCCATACCCACCTGGGATGAGTGGCCCGAGTTTGCTAGAGAGACCTTCCAGGCTTTCAGGACTACCGATGTCGGCCGTAAATTGATTATTGACCAAAATGTTTTCATCGAGGGAACGTTGCCTATGGGCGTAGTCCGTCCCCTAACGGAGGTCGAAATGGATCATTACAGAGAACCGTTTTTGAACCCTGTAGACCGTGAGCCACTGTGGCGTTTTCCAAACGAATTACCGATAGCTGGCGAACCCGCTAATATCGTCGCCCTGGTAGAGGAATACATGGACTGGCTTCATCAAAGTCCTGTTCCCAAATTGTTATTTTGGGGTACACCAGGTGTATTAATTCCACCTGCCGAAGCCGCCAGGTTGGCAAAATCATTACCGAACTGCAAAGCTGTAGACATCGGCCCCGGTTTGAATCTGCTGCAGGAGGATAACCCGGATTTGATAGGGTCTGAAATCGCGCGTTGGTTGTCAACCCTGGAAATATCAGGC
+>LAP-tag
+TTACTTGTACAGCTCGTCCATGCCGAGAGTGATCCCGGCGGCGGTCACGAACTCCTTAAGGACCATGTGATCGCGCTTCTCGTTGGGGTCTTTGCTCAGGGCGGACTGGGTGCTCAGGTAGTGGTTGTCGGGCAGCAGCACGGGGCCGTCGCCGATGGGGGTGTTCTGCTGGTAGTGGTCGGCGAGCTGCACGCTGCCGTCCTCGATGTTGTGGCGGATCTTGAAGTTCACCTTGATGCCGTTCTTCTGCTTGTCGGCCATGATATAGACGTTGTGGCTGTTGTAGTTGTACTCCAGCTTGTGCCCCAGGATGTTGCCGTCCTCCTTGAAGTCGATGCCCTTCAGCTCGATGCGGTTCACCAGGGTGTCGCCCTCGAACTTCACCTCGGCGCGGGTCTTGTAGTTGCCGTCGTCCTTGAAGAAGATGGTGCGCTCCTGGACGTAGCCTTCGGGCATGGCGGACTTGAAGAAGTCGTGCTGCTTCATGTGGTCGGGGTAGCGGCTGAAGCACTGCACGCCGTAGGTCAGGGTGGTCACGAGGGTGGGCCAGGGCACGGGCAGCTTGCCGGTGGTGCAGATGAACTTCAGGGTCAGCTTGCCGTAGGTGGCATCGCCCTCGCCCTCGCCGGACACGCTGAACTTGTGGCCGTTTACGTCGCCGTCCAGCTCGACCAGGATGGGCACCACCCCGGTGAACAGCTCCTCGCCTTTGCTCACCATCGAACCCGAGGGACCGCTCGACGACAGGGGCCCCTGGAACAGAACTTCCAGGCTCGACGAACCCGAGGGACCGCTCGAACCTCCACCTCCGCTGTCCATGTGCTGGCGTTCGAATTTAGCAGCAGCGGTTTCTTTGAATTTGGCGGCGCCCTGAAAATAAAGATTCTCGCTTGCAGTAGTTGGAATATCATAATC
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.1.bt2 b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.1.bt2
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.2.bt2 b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.2.bt2
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.3.bt2 b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.3.bt2
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.4.bt2 b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.4.bt2
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.rev.1.bt2 b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.rev.1.bt2
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.rev.2.bt2 b/EpitopeID/hg19_EpiID_v2/FASTA_tag/ALL_TAG.fa.rev.2.bt2
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/3xFLAG.fa b/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/3xFLAG.fa
@@ -0,0 +1,12 @@
+>3xFLAG
+gggagcggaggaggttccggtggaggtggttctggagattacaaggatgacgacgataagggcgattacaaggatgacgacgataagg
+gagattacaaggatgacgacgataaggtttcaggaagcggagctactaacttcagcctgctgaagcaggctggagacgtggaggagaac
+cctggacctggatcgtttcgcatgattgaacaagatggattgcacgcaggttctccggccgcttgggtggagaggctattcggctatgactggg
+cacaacagacaatcggctgctctgatgccgccgtgttccggctgtcagcgcaggggcgcccggttctttttgtcaagaccgacctgtccggtg
+ccctgaatgaactgcaggacgaggcagcgcggctatcgtggctggccacgacgggcgttccttgcgcagctgtgctcgacgttgtcactga
+agcgggaagggactggctgctattgggcgaagtgccggggcaggatctcctgtcatctcaccttgctcctgccgagaaagtatccatcatgg
+ctgatgcaatgcggcggctgcatacgcttgatccggctacctgcccattcgaccaccaagcgaaacatcgcatcgagcgagcacgtactcg
+gatggaagccggtcttgtcgatcaggatgatctggacgaagagcatcaggggctcgcgccagccgaactgttcgccaggctcaaggcgcg
+catgcccgacggcgaggatctcgtcgtgacccatggcgatgcctgcttgccgaatatcatggtggaaaatggccgcttttctggattcatcgac
+tgtggccggctgggtgtggccgaccgctatcaggacatagcgttggctacccgtgatattgctgaagagcttggcggcgaatgggctgaccg
+cttcctcgtgctttacggtatcgccgctcccgattcgcagcgcatcgccttctatcgccttcttgacgagttcttctgattcgaacatc
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/FKBP12-V.fa b/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/FKBP12-V.fa
@@ -0,0 +1,2 @@
+>FKBP12-V	F36V variant of FKBP12
+atgggagtgcaggtggaaaccatctccccaggagacgggcgcaccttccccaagcgcggccagacctgcgtggtgcactacaccgggatgcttgaagatggaaagaaagttgattcctcccgggacagaaacaagccctttaagtttatgctaggcaagcaggaggtgatccgaggctgggaagaaggggttgcccagatgagtgtgggtcagagagccaaactgactatatctccagattatgcctatggtgccactgggcacccaggcatcatcccaccacatgccactctcgtcttcgatgtggagcttctaaaactggaa
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/HaloTag.fa b/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/HaloTag.fa
@@ -0,0 +1,2 @@
+>HaloTag
+AATGCAGAAATAGGGACAGGCTTTCCTTTTGATCCCCATTATGTAGAGGTACTAGGAGAACGTATGCATTACGTGGACGTGGGACCAAGAGATGGCACCCCAGTTCTTTTTTTACACGGAAACCCAACCAGTTCTTATGTCTGGAGGAACATCATCCCTCACGTTGCTCCAACTCACAGATGTATAGCGCCTGATCTGATTGGGATGGGTAAATCAGACAAACCCGACTTGGGCTACTTCTTCGATGACCACGTCAGATTTATGGACGCGTTCATTGAGGCACTTGGGTTGGAAGAAGTCGTCCTGGTAATACATGACTGGGGATCAGCCCTGGGATTTCATTGGGCTAAAAGGAATCCAGAGAGAGTAAAAGGGATTGCCTTCATGGAGTTTATCAGGCCCATACCCACCTGGGATGAGTGGCCCGAGTTTGCTAGAGAGACCTTCCAGGCTTTCAGGACTACCGATGTCGGCCGTAAATTGATTATTGACCAAAATGTTTTCATCGAGGGAACGTTGCCTATGGGCGTAGTCCGTCCCCTAACGGAGGTCGAAATGGATCATTACAGAGAACCGTTTTTGAACCCTGTAGACCGTGAGCCACTGTGGCGTTTTCCAAACGAATTACCGATAGCTGGCGAACCCGCTAATATCGTCGCCCTGGTAGAGGAATACATGGACTGGCTTCATCAAAGTCCTGTTCCCAAATTGTTATTTTGGGGTACACCAGGTGTATTAATTCCACCTGCCGAAGCCGCCAGGTTGGCAAAATCATTACCGAACTGCAAAGCTGTAGACATCGGCCCCGGTTTGAATCTGCTGCAGGAGGATAACCCGGATTTGATAGGGTCTGAAATCGCGCGTTGGTTGTCAACCCTGGAAATATCAGGC
diff --git a/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/LAP-tag.fa b/EpitopeID/hg19_EpiID_v2/FASTA_tag/Tag_DB/LAP-tag.fa
@@ -0,0 +1,2 @@
+>LAP-tag
+TTACTTGTACAGCTCGTCCATGCCGAGAGTGATCCCGGCGGCGGTCACGAACTCCTTAAGGACCATGTGATCGCGCTTCTCGTTGGGGTCTTTGCTCAGGGCGGACTGGGTGCTCAGGTAGTGGTTGTCGGGCAGCAGCACGGGGCCGTCGCCGATGGGGGTGTTCTGCTGGTAGTGGTCGGCGAGCTGCACGCTGCCGTCCTCGATGTTGTGGCGGATCTTGAAGTTCACCTTGATGCCGTTCTTCTGCTTGTCGGCCATGATATAGACGTTGTGGCTGTTGTAGTTGTACTCCAGCTTGTGCCCCAGGATGTTGCCGTCCTCCTTGAAGTCGATGCCCTTCAGCTCGATGCGGTTCACCAGGGTGTCGCCCTCGAACTTCACCTCGGCGCGGGTCTTGTAGTTGCCGTCGTCCTTGAAGAAGATGGTGCGCTCCTGGACGTAGCCTTCGGGCATGGCGGACTTGAAGAAGTCGTGCTGCTTCATGTGGTCGGGGTAGCGGCTGAAGCACTGCACGCCGTAGGTCAGGGTGGTCACGAGGGTGGGCCAGGGCACGGGCAGCTTGCCGGTGGTGCAGATGAACTTCAGGGTCAGCTTGCCGTAGGTGGCATCGCCCTCGCCCTCGCCGGACACGCTGAACTTGTGGCCGTTTACGTCGCCGTCCAGCTCGACCAGGATGGGCACCACCCCGGTGAACAGCTCCTCGCCTTTGCTCACCATCGAACCCGAGGGACCGCTCGACGACAGGGGCCCCTGGAACAGAACTTCCAGGCTCGACGAACCCGAGGGACCGCTCGAACCTCCACCTCCGCTGTCCATGTGCTGGCGTTCGAATTTAGCAGCAGCGGTTTCTTTGAATTTGGCGGCGCCCTGAAAATAAAGATTCTCGCTTGCAGTAGTTGGAATATCATAATC
diff --git a/EpitopeID/hg19_EpiID_v2/annotation/genome_annotation.gff.gz b/EpitopeID/hg19_EpiID_v2/annotation/genome_annotation.gff.gz