make some tidy

jdieramon · Feb 21, 2023 · 0f075cf · 0f075cf
1 parent 7a7d167
commit 0f075cf
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Showing 15 changed files with 13,657 additions and 12 deletions.
diff --git a/slim.R → GOslim.R b/slim.R → GOslim.R
diff --git a/2MW2NVF9014-Alignment-HitTable.csv → dat/2MW2NVF9014-Alignment-HitTable.csv b/2MW2NVF9014-Alignment-HitTable.csv → dat/2MW2NVF9014-Alignment-HitTable.csv
diff --git a/B1J2TDTZ01R-Alignment-HitTable.csv → dat/B1J2TDTZ01R-Alignment-HitTable.csv b/B1J2TDTZ01R-Alignment-HitTable.csv → dat/B1J2TDTZ01R-Alignment-HitTable.csv
diff --git a/df_silly.csv → dat/df_silly.csv b/df_silly.csv → dat/df_silly.csv
diff --git a/mads_box/dat/HITS_Hom_chickpea_Ilaria.csv b/mads_box/dat/HITS_Hom_chickpea_Ilaria.csv
@@ -0,0 +1,116 @@
+list
+XP_004513719.1
+XP_004485955.1
+XP_004513719.1
+XP_012572521.1
+XP_012572287.1
+XP_004485955.1
+XP_012572287.1
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+XP_004508656.1
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+XP_004490238.1
+XP_004488426.1
+XP_004490238.1
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+XP_012568382.1
+XP_004498126.1
+XP_004500961.1
+XP_004512095.1
+XP_004498359.2
+XP_004498126.
+XP_004504398.1
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+XP_004490086.1
diff --git a/mads_box/dat/YN34UYFE013-Alignment-HitTable.csv b/mads_box/dat/YN34UYFE013-Alignment-HitTable.csv
diff --git a/mads_box/dat/mads_cds.fasta b/mads_box/dat/mads_cds.fasta
@@ -0,0 +1,68 @@
+>XM_004513662.3:236-961 PREDICTED: Cicer arietinum agamous-like MADS-box protein AGL1 (LOC101493068), transcript variant X1, mRNA
+ATGGAGCTTCCAAATCATGAAGATGGAGAAGGATCTTCCCAAAAGAAAATGGGAAGAGGGAAGATTGAAA
+TCAAGAGGATCGAAAACACGACGAATAGACAAGTCACCTTTTGCAAACGACGCAACGGATTGTTGAAGAA
+AGCCTATGAATTATCTGTTCTTTGTGATGCTGAAGTTGCTCTTGTTGTCTTCTCAACTCGTGGTCGCTTG
+TATGAGTACGCAAACAACAGTGTTAGAGCAACTATTGAAAGGTACAAAAAAGCATGTTCTGCTACCACTA
+ACGCAGAATCTGTATCTGAAGCTAATACCCAGTTTTACCAGCAAGAATCATCCAAATTGAGAAGACAGAT
+TCGAGATATTCAGAATCTTAATAGACACATCCTTGGTGAAGCTCTAGGATCTTTGAGTCTCAAGGAACTA
+AAGAATCTTGAGGGTAGATTGGAGAAAGGTTTGAGCAGAGTAAGATCAAGAAAGCATGAAACGTTGTTTG
+CTGATGTGGAGTTCATGCAAAAGCGGGAAATTGATCTGCAAAACCAGAACAATTATCTGCGAGCTAAGAT
+AGCTGAATGTGAAAGAGCTCAACAACAGCAACAAAATATGATGCCAGAAACATATTCTGAGTCCTTACCT
+TCACAATCATATGACAGAAATTTCTTTCCTGTAAATCTTCTTGGATCGGATCAGCAGTATTCACGCCAAG
+ACCAAACTGCTCTCCAACTTGTCTGA
+
+
+>XM_004485898.3:164-907 PREDICTED: Cicer arietinum floral homeotic protein AGAMOUS (LOC101493118), transcript variant X6, mRNA
+ATGGATTTTCAAAATCAATCTATGTCAGATTCTCCACAGAGAAAGATAGGAAGGGGAAAGATTGAGATCA
+AAAGGATTGAGAACACAACCAATCGCCAAGTAACTTTCTGCAAACGTAGAAATGGATTGCTCAAAAAAGC
+ATATGAATTATCTGTTCTTTGTGATGCAGAAGTTGCTCTAATAGTCTTCTCTAGCCGTGGACGCCTCTAT
+GAATATGCTAATAACAGTGTCAAAGCAACTATTGAAAGGTACAAAAAAGCATGTTCAGATTCATCTGGCA
+CTGGATCTGCTTCTGAGGCTAATGCTCAGTTTTACCAGCAAGAAGCAGACAAATTGCGTGCGCAAATTAG
+TAATCTGCAGAATAACAACAGGCAAATGATGGGTGAGTCTTTGGGCTCTATGACTGCCAAGGAACTCAAA
+AACTTGGAGGGTAAATTAGAAAAGGGAATAAGTAGGATTCGTTCCAAAAAGAACCAGCTTTTATTTGCTG
+AAATTGAATACATGCAGAAGAGGGAAATAGACTTGCACAATAACAACCAACTTCTGAGAGCAAAGATAGC
+TGAAAGTGAAAGGAACCACCATAATATGAGTGTGTTACCTGGAGGCACAAGCTATGAATCTATGCAATCT
+CAGCATCAGCAGCAGCAGCAACAATATGATTCTCGTGGTTACTTTCAAGTCACTGGATTACAACCTAGTA
+GTCAGTATGCACGACAAGACCAAATGTCACTTCAATTAGTTTGA
+
+
+>XM_004498069.3:88-819 PREDICTED: Cicer arietinum protein TRANSPARENT TESTA 16 (LOC101500959), transcript variant X1, mRNA
+ATGGGGCGTGGAAAGATAGAGATAAAGAGGATTCAAAACACAACAACAAGGCAAGTTACTTTCTCAAAAA
+GAAGAACAGGACTAATCAAGAAGACTCATGAGCTTTCTGTTTTATGTGATGCACAAATTGGACTCATCAT
+ATTCTCAAGCACTGGAAAACTCTTCCAATATTCTTCTGAACCCTATAGGATGGATCAAATCATAGAAAAG
+TACCAGAGATCTACTGGGAAACGCATTATGGTGGAAAGTGATCATCACTATAGGGAAGAAATGTTCCATG
+ACATGGCAATGCTGAGGCAAGAAAGTATTCGTGTTGAATTGGGAATTCAACGATATCTTGGAAGTGATAT
+GAATGGTTTAAAGTATGATGATTTGACTAAACTTGAAGAGGAATTAGAATTCTCTCTTGCAAAAGTTCGA
+AACCGTCAGAATGAGCTATTGAGTCAACAAATGGAGAATCTGCGAAGGAAGGAAAGAATATTGGAAGATG
+AACACATCAATTTGTCGAACTGGGAGCAAAGGGCAGTGATGGAATTTCACAAGGCAGCAATAGAAGCAAA
+CAAACAACAACAAAATGGAATGGATGAGTTTGCATTCTTTGAGGATCAACCAGCTGGTACCATTCTTCAA
+CTTGCTGCCCCTGTTCTTCCACTTCACCTTCATCCTTATCTTCAGCTTGCTCAGCCAAATATTCATCAAG
+ATTCTCTCCCTTCTAGGGACCCCAAACCATAA
+
+
+>XM_004492609.2:1-747 PREDICTED: Cicer arietinum agamous-like MADS-box protein AGL6 (LOC101510444), mRNA
+ATGGGAAGAGGGAGAGTTGAGCTGAAGAGAATAGAGAACAAAATCAACCGTCAAGTAACATTCTCAAAAA
+GAAGAAATGGTTTGTTGAAGAAAGCTTATGAACTCTCAGTACTATGTGATGCTGAAATTGCCCTTATCAT
+TTTCTCTAGCCGTGGAAAACTCTCTGAATTTGGAAGTTCAACTTCAGGCATTGCCAAAACCCTGGAACGA
+TACCAAAGGTGCTCCTTTACTTCTCAAAATGATAATATTAATGAAAATGAAACTCAGAATTGGTACCAAG
+AGATGTCAAAGCTAAAGGCAAAATATGAGTCTCTTCAAAAGTCACAAAGGCAATTGCTAGGGGAAGATCT
+AGGACCACTGAACATGAAAGAGCTACAAAGTCTTGAAAAACAGCTTGAAGGAGCTTTAGCACAAGCTAGG
+CAGAGGAAGTCACAAATTATGATTGAACAAATGGAAGAGCTTAGAAGAAAGGAACGCCATCTTGGAGACA
+TAAATAAGCAACTTAGATTCAAGCTTGAATCAGAAGGATTTAATCTTAAAGCTATTGAAAACATGTGGAG
+CTCTAATTCTGCTACTGTTTCTGGAGGAAGCAGTTTTCCTTATCAGCCTTCTGAAACCAATCCTATGGAC
+TGCCAAGCTGAACCTTTCTTACAAATAGGGTACCATCAATATGTTCAAGCAGAACCATCCAATGCTCCAA
+AGAGCATGGTTGGTGAGACTAGCTTTATCCATGGATGGATCCTTTGA
+
+
+>XM_027332283.1:307-921 PREDICTED: Cicer arietinum MADS-box protein SOC1-like (LOC101510775), transcript variant X2, mRNA
+ATGGTGAGAGGAAAAACACAGTTGAAGCGTATAGAGAATGCAACAAGTAGACAAGTAACGTTTTCAAAGA
+GGCGTAACGGATTGCTGAAGAAGGCCTTTGAACTTTCTGTTCTTTGTGATGCTGAAGTTGCTCTTATCAT
+CTTTTCTCCTAGAGGAAAACTTTATGAATTTTCTAGCTCCAGCATGCAGGACACAATTGAACGCTACCGT
+AGAAATAGCAGGAGTGCTCAACCAATGCAAAAATCAGATGAACAAAATATGCAGAATTTGAGGCAAGAAA
+CAGCAAGTTTGATGAAGAAGATTGAACTTCTTGAAGCTTCAAAACGGAAACTAATGGGAGAAGGTTTGGG
+ATCATGCTCCATGGAAGAACTACAACAGATAGAACAACAGTTGGAAAAGAGTGTAAGCACTGTTCGAGCA
+AGAAAGAATCAGGTTTACAAGAATCAAATTGTGCAACTAAAAGAAAAGGAAAAAGCCCTACTTGTTGAAA
+ATGCCAGGCTCTCTAAACAGCCACAGCAAACAACAAAAGATCAAAGAGAAAATCAACCCTATGCTGAAAG
+AAGTCCAAGCTCAGATGTAGTGACTGAATTGTTCATTGGACTACACAGGTCTTAG
+
+
diff --git a/mads_box.R → mads_box/functions.R b/mads_box.R → mads_box/functions.R
@@ -32,9 +32,7 @@ best_homolog <- function(hitFile) {
 
 
 
-#library(dplyr)
-#library(refseqR)
-#library(rentrez)
+
 
 characterizeTable <- function(targets) {
 
@@ -104,13 +102,14 @@ characterizeTable <- function(targets) {
 
 TSScoordinates <- function(gr, CDSstringset, bp = 150, chr) {
 
-  inputGR = gr[seqnames(gr) == chr]
-  gr.tss = inputGR
+  CDSstringset = unique(CDSstringset)
+  gr.tss = gr[seqnames(gr) == chr]
+  bp_cut = bp
 
-  for(i in seq_along(gr.tss)) {
-    bp_cut = bp
-    text = genome[[which(seqnames(genome) == chr)]]
-    pattern = CDSstringset[[which(names(CDSstringset) == gr.tss$LOC[i])]][1:bp_cut]
+  for(i in seq_along(gr.tss)) { 
+
+    text = genome[[which(names(genome) == chr)]]
+    pattern = CDSstringset[which(names(CDSstringset) == gr.tss$LOC[i])][[1]][1:bp_cut]
 
     if(gr.tss[i] %in% gr.tss[strand(gr.tss) == "+"]) {
 
@@ -126,7 +125,9 @@ TSScoordinates <- function(gr, CDSstringset, bp = 150, chr) {
 
   }
 
-  gr.tss
+  gr.tss  
+
+
 }
 
 ## Usage
@@ -146,8 +147,8 @@ names2LOC <- function(str) {
 ## mads_cds = readDNAStringSet("mads_cds.fasta")
 ## my_names = names(mads_cds)
 ## my_names <- sapply(my_names, function(i) names2LOC(i), USE.NAMES = F)
-                   
-                   
+
+
 names2XM <- function(str) {
   # Take a vector string (header from multifasta file) 
   # Return the XM id in a tidy format