resolve missing genes

stracquadaniolab · Oct 6, 2023 · fb8626c · fb8626c
1 parent 14c2522
commit fb8626c
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Showing 16 changed files with 182,959 additions and 271,839 deletions.
diff --git a/bin/get-salmon-mapping-qc.py b/bin/get-salmon-mapping-qc.py
diff --git a/bin/modify-syn-gff.sh b/bin/modify-syn-gff.sh
@@ -0,0 +1,97 @@
+# Script used to modify gene names in synthetic Chr11 GFF3 file to distinguish 
+# from wild-type Chr11 genes.
+
+# awk -F '\t' 'BEGIN { OFS = "\t" }
+
+# # skip first 3 lines
+# NR <= 3 { print; next }
+
+# {
+#     # split attributes field into individual attributes
+#     split($9, attributes, ";")
+#     new_attributes = ""
+#     for (i = 1; i <= length(attributes); i++) {
+#     attr = attributes[i]
+
+#     # check if attribute starts with "ID=" or "Name="
+#     if (match(attr, /^ID=/) || match(attr, /^Name=/)) {
+
+#         # extract attribute name and value
+#         attr_name = substr(attr, 1, RSTART + RLENGTH - 2)
+#         attr_value = substr(attr, RLENGTH + 1)
+
+#         # check if attribute name is "ID" or "Name" and if it has a value
+#         if ((attr_name == "ID" || attr_name == "Name") && length(attr_value) > 0) {
+
+#         # check if "gene:" or "transcript:" prefix is already present
+#         if (!match(attr_value, /^(gene|transcript):/)) {
+#             attr_value = "x." attr_value
+#         } else {
+#             attr_value = substr(attr_value, 1, RLENGTH) "x." substr(attr_value, RLENGTH + 1)
+#         }
+#         }
+
+#         # reconstruct modified attribute
+#         modified_attr = attr_name "=" attr_value
+#     } else {
+#         modified_attr = attr
+#     }
+#     new_attributes = new_attributes ";" modified_attr
+#     }
+
+#     # replace attributes field with modified attributes
+#     $9 = substr(new_attributes, 2)
+#     print
+# }
+# ' tmp-syn.gff > modified_syn_chr11.gff
+
+
+awk -F '\t' 'BEGIN { OFS = "\t" }
+
+# skip first 3 lines
+NR <= 3 { print; next }
+
+{
+    # split attributes field into individual attributes
+    split($9, attributes, ";")
+    new_attributes = ""
+    for (i = 1; i <= length(attributes); i++) {
+        attr = attributes[i]
+
+        # check if attribute starts with "ID=", "Name=", or "Parent="
+        if (match(attr, /^(ID|Name|Parent)=/)) {
+
+            # extract attribute name and value
+            attr_name = substr(attr, 1, RLENGTH - 1)
+            attr_value = substr(attr, RLENGTH + 1)
+
+            # check if attribute name is "ID" or "Name" and if it has a value
+            if ((attr_name == "ID" || attr_name == "Name") && length(attr_value) > 0) {
+
+                # check if "gene:" or "transcript:" prefix is already present
+                if (!match(attr_value, /^(gene|transcript):/)) {
+                    attr_value = "x." attr_value
+                } else {
+                    attr_value = substr(attr_value, 1, RLENGTH) "x." substr(attr_value, RLENGTH + 1)
+                }
+            } else if (attr_name == "Parent") {
+                # check if "gene:" or "transcript:" prefix is already present
+                if (!match(attr_value, /^(gene|transcript):/)) {
+                    attr_value = "x." attr_value
+                } else {
+                    attr_value = substr(attr_value, 1, RLENGTH) "x." substr(attr_value, RLENGTH + 1)
+                }
+            }
+
+            # reconstruct modified attribute
+            modified_attr = attr_name "=" attr_value
+        } else {
+            modified_attr = attr
+        }
+        new_attributes = new_attributes ";" modified_attr
+    }
+
+    # replace attributes field with modified attributes
+    $9 = substr(new_attributes, 2)
+    print
+}' data/genome/modified-syn-chr11/tmp-syn.gff > chr18.gff
diff --git a/bin/modify-syn-gff3.sh b/bin/modify-syn-gff3.sh
diff --git a/conf/base.config b/conf/base.config
@@ -86,13 +86,13 @@ profiles {
 
           // source genome files
           reference_wt = "data/genome/BY4742-genome/BY4742.fasta"
-          annotation_wt = "data/genome/BY4742-genome/BY4742.gff"
+          annotation_wt = "data/genome/BY4742/annotation/*.gff"
           reference_syn = "data/genome/syn-yeast-genome/contigs/yeast_chr11_3_39.ref.fasta"
           annotation_syn = "data/genome/syn-yeast-genome/annotation/yeast_chr11_3_39.ref.gff"
 
           // combined genome files
-          genome.reference = "data/genome/new-concat-genome/concat-wt-syn-chr11-BY4742.fasta"
-          genome.annotation = "data/genome/new-concat-genome/concat-wt-syn-chr11-BY4742.gff"
+          genome.reference = "data/genome/wt-syn-chr11-genome/wt-syn-chr11-BY4742.fasta"
+          genome.annotation = "data/genome/wt-syn-chr11-genome/wt-syn-chr11-BY4742.gff"
 
           // fastp parameters
           fastp.args = ""