chore: add muc1 examples

vinzenzmay · holtgrewe · commit ffc5281db1c8 · 2025-11-03T20:38:59.000+01:00
Co-Authored-With: Manuel Holtgrewe &lt;zyklenfrei@gmail.com&gt;
diff --git a/.gitattributes b/.gitattributes
@@ -1,2 +1,10 @@
 # SCM syntax highlighting & preventing 3-way merges
 pixi.lock merge=binary linguist-language=YAML linguist-generated=true
+examples/*.bam filter=lfs diff=lfs merge=lfs -text
+examples/*.bam.bai filter=lfs diff=lfs merge=lfs -text
+examples/*.fa filter=lfs diff=lfs merge=lfs -text
+examples/*.bed filter=lfs diff=lfs merge=lfs -text
+examples/**/*.bam filter=lfs diff=lfs merge=lfs -text
+examples/**/*.bam.bai filter=lfs diff=lfs merge=lfs -text
+examples/**/*.fa filter=lfs diff=lfs merge=lfs -text
+examples/**/*.bed filter=lfs diff=lfs merge=lfs -text
diff --git a/examples/muc1/data/muc1.bam b/examples/muc1/data/muc1.bam
@@ -0,0 +1,3 @@
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+size 7473755
diff --git a/examples/muc1/data/muc1.bam.bai b/examples/muc1/data/muc1.bam.bai
@@ -0,0 +1,3 @@
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diff --git a/examples/muc1/data/muc1.fa b/examples/muc1/data/muc1.fa
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+size 305447
diff --git a/examples/muc1/data/muc1.fa.fai b/examples/muc1/data/muc1.fa.fai
@@ -0,0 +1 @@
+1	300436	3	60	61
diff --git a/examples/muc1/data/muc1.mononucleotides.lt6.bed b/examples/muc1/data/muc1.mononucleotides.lt6.bed
@@ -0,0 +1,3 @@
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+size 17985
diff --git a/examples/muc1/data/muc1.trf.bed b/examples/muc1/data/muc1.trf.bed
@@ -0,0 +1,3 @@
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diff --git a/examples/muc1/data/muc1.unique.bed b/examples/muc1/data/muc1.unique.bed
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diff --git a/examples/muc1/muc1.bed b/examples/muc1/muc1.bed
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diff --git a/examples/muc1/muc1.mononucleotides.lt6.bed b/examples/muc1/muc1.mononucleotides.lt6.bed
@@ -0,0 +1,3 @@
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diff --git a/examples/muc1/muc1.trf.bed b/examples/muc1/muc1.trf.bed
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 932
diff --git a/examples/muc1/muc1.unique.bed b/examples/muc1/muc1.unique.bed
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 1361
diff --git a/examples/muc1/transform.sh b/examples/muc1/transform.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+# in the files trf, unique, mononucleotides,
+# the coordinates are still absolute. However, We have created a small sub-genome (muc1.fa) whose location is defined in muc1.bed.
+# This script transforms all coordinates to be relative to the start of muc1.fa (i.e. the start of the first region in muc1.bed is position 1).
+
+# Get the offset (start position) from muc1.bed
+OFFSET=$(head -n 1 muc1.bed | cut -f 2)
+
+echo "Offset from muc1.bed: $OFFSET"
+
+# Create data directory if it doesn't exist
+mkdir -p data
+
+# Transform coordinates in each file
+for file in muc1.trf.bed muc1.unique.bed muc1.mononucleotides.lt6.bed; do
+    if [ -f "$file" ]; then
+        echo "Transforming coordinates in $file..."
+
+        # Create backup in data directory
+        cp "$file" "data/${file}"
+
+        # Transform coordinates (subtract offset from columns 2 and 3)
+        # Assuming BED-like format: chr start end ...
+        awk -v offset="$OFFSET" 'BEGIN {OFS="\t"} {
+            if (NF >= 3) {
+                $2 = $2 - offset;
+                $3 = $3 - offset;
+            }
+            print
+        }' "data/${file}" >"$file"
+
+        echo "Done with $file"
+    else
+        echo "Warning: $file not found, skipping..."
+    fi
+done
+
+echo "Coordinate transformation complete!"
diff --git a/pixi.lock b/pixi.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -173,14 +173,15 @@ svirlpool = { path = ".", editable = true }
 [tool.pixi.dependencies]
 python = ">=3.12"
 hatch = ">=1.14.0"
+go-shfmt = "*"
 
 [tool.pixi.environments]
 default = { solve-group = "default" }
 dev = { features = ["dev"], solve-group = "default" }
 
 [tool.pixi.tasks]
-check = "black --check --diff --preview src tests && ruff check src tests"
-format = "black --preview src tests && ruff check --fix src tests"
+check = "black --check --diff --preview src tests && ruff check src tests && shfmt -i 4 -d **/*.sh"
+format = "black --preview src tests && ruff check --fix src tests && shfmt -i 4 -w **/*.sh"
 typecheck = "pyright src/ tests/"
 test = "pytest --cov=svirlpool --cov-report=term-missing tests/ --durations 0 -s"
 test-snapshot = "pytest --cov=svirlpool tests/ --snapshot-update"

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