Skip to content

Crossover params #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
btmonier merged 3 commits into from
Dec 10, 2025
Merged

Crossover params #3

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
7cbf8ca
Improve fallbacks
btmonier Dec 10, 2025
ce05870
Fix boolean key in yaml and DownsampleGvcf
btmonier Dec 10, 2025
4e74cb9
Version bump
btmonier Dec 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion build.gradle.kts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ plugins {
}

group = "net.maizegenetics"
version = "0.2"
version = "0.2.1"

repositories {
mavenCentral()
Expand Down
16 changes: 12 additions & 4 deletions pipeline_config.example.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ downsample_gvcf:
ignore_contig: "" # Optional: Comma-separated patterns to ignore
rates: "0.01,0.05,0.1,0.15,0.2" # Optional: Comma-separated downsampling rates
seed: 42 # Optional: Random seed for reproducibility
keep_ref: true # Optional: Keep reference blocks (default: true)
keep_ref: true # Optional: Keep reference blocks (true/false, default: true)
min_ref_block_size: 20 # Optional: Minimum ref block size (default: 20)
# input: "/custom/gvcf/directory/" # Optional: Custom GVCF input directory
# output: "/custom/downsample/output/" # Optional: Custom output directory
Expand All @@ -106,11 +106,16 @@ convert_to_fasta:

# Step 5: Align Mutated Assemblies
# Realigns the mutated FASTA files from convert_to_fasta back to the reference
# Automatically uses ref_gff and ref_fasta from align_assemblies, and FASTA files from convert_to_fasta
# Auto-detects reference and query FASTAs from step 4 output based on filename matching
# This creates a circular workflow where mutated sequences are realigned for comparison
align_mutated_assemblies:
# ref_gff: "path/to/reference.gff" # Optional: Reference GFF file
# Uses align_assemblies.ref_gff if not specified
# ref_fasta: "path/to/reference.fa" # Optional: Reference FASTA from step 4 output
# Auto-detects file matching original ref name if not specified
# fasta_input: "/custom/fasta/input/" # Optional: Query FASTA input (file, directory, or text list)
# Auto-detects non-ref files from step 4 if not specified
threads: 1 # Optional: Number of threads (default: 1)
# input: "/custom/fasta/input/" # Optional: Custom FASTA input (file, directory, or text list)
# output: "/custom/alignment/output/" # Optional: Custom output directory

# ============================================================================
Expand All @@ -127,6 +132,9 @@ pick_crossovers:
# Example:
# /path/to/assembly1.fa<TAB>parent1
# /path/to/assembly2.fa<TAB>parent2
# ref_fasta: "path/to/reference.fa" # Optional: Reference FASTA file
# Uses mutated ref FASTA from step 5 if not specified
# Falls back to align_assemblies.ref_fasta if step 5 not run
# output: "/custom/crossovers/output/" # Optional: Custom output directory

# Step 7: Create Chain Files
Expand Down Expand Up @@ -186,7 +194,7 @@ format_recombined_fastas:
rope_bwt_chr_index:
index_file_prefix: "phgIndex" # Optional: Prefix for index files (default: "phgIndex")
threads: 20 # Optional: Number of threads (default: 20)
delete_fmr_index: true # Optional: Delete .fmr files after conversion (default: true)
delete_fmr_index: true # Optional: Delete .fmr files after conversion (true/false, default: true)
# input: "/custom/fasta/input/" # Optional: Custom FASTA input (file, directory, or text list)
# output: "/custom/phg_index/" # Optional: Custom output directory (default: work_dir/output/11_rope_bwt_index_results)
# keyfile: "/path/to/keyfile.txt" # Optional: Pre-made keyfile (mutually exclusive with input)
Expand Down
3 changes: 2 additions & 1 deletion src/main/kotlin/net/maizegenetics/commands/DownsampleGvcf.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import com.github.ajalt.clikt.parameters.options.default
import com.github.ajalt.clikt.parameters.options.flag
import com.github.ajalt.clikt.parameters.options.option
import com.github.ajalt.clikt.parameters.options.required
import com.github.ajalt.clikt.parameters.types.boolean
import com.github.ajalt.clikt.parameters.types.int
import com.github.ajalt.clikt.parameters.types.path
import net.maizegenetics.Constants
Expand Down Expand Up @@ -61,7 +62,7 @@ class DownsampleGvcf : CliktCommand(name = "downsample-gvcf") {
private val keepRef by option(
"--keep-ref",
help = "Keep reference blocks"
).flag(default = true)
).boolean().default(true)

private val minRefBlockSize by option(
"--min-ref-block-size",
Expand Down
122 changes: 104 additions & 18 deletions src/main/kotlin/net/maizegenetics/commands/Orchestrate.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,14 +66,17 @@ data class ConvertToFastaConfig(
)

data class AlignMutatedAssembliesConfig(
val ref_gff: String? = null, // Optional: Reference GFF (uses align_assemblies.ref_gff if not specified)
val ref_fasta: String? = null, // Optional: Reference FASTA (uses matching ref from step 4 output if not specified)
val fasta_input: String? = null, // Optional: Query FASTA input (uses non-ref files from step 4 if not specified)
val threads: Int? = null,
val input: String? = null, // Custom FASTA input file/directory
val output: String? = null // Custom output directory
val output: String? = null // Custom output directory
)

data class PickCrossoversConfig(
val assembly_list: String,
val output: String? = null // Custom output directory
val ref_fasta: String? = null, // Optional: Reference FASTA (uses align_assemblies.ref_fasta if not specified)
val output: String? = null // Custom output directory
)

data class CreateChainFilesConfig(
Expand Down Expand Up @@ -253,8 +256,10 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
val alignMutatedAssembliesMap = configMap["align_mutated_assemblies"] as? Map<String, Any>
val alignMutatedAssemblies = alignMutatedAssembliesMap?.let {
AlignMutatedAssembliesConfig(
ref_gff = it["ref_gff"] as? String,
ref_fasta = it["ref_fasta"] as? String,
fasta_input = it["fasta_input"] as? String,
threads = it["threads"] as? Int,
input = it["input"] as? String,
output = it["output"] as? String
)
}
Expand All @@ -265,6 +270,7 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
val pickCrossovers = pickCrossoversMap?.let {
PickCrossoversConfig(
assembly_list = it["assembly_list"] as? String ?: throw IllegalArgumentException("pick_crossovers.assembly_list is required"),
ref_fasta = it["ref_fasta"] as? String,
output = it["output"] as? String
)
}
Expand Down Expand Up @@ -381,6 +387,7 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
var fastaOutputDir: Path? = null
var refFasta: Path? = null
var refGff: Path? = null
var mutatedRefFasta: Path? = null // Mutated reference FASTA from step 5
var refkeyOutputDir: Path? = null
var chainOutputDir: Path? = null
var coordinatesOutputDir: Path? = null
Expand Down Expand Up @@ -682,16 +689,68 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
logger.info("STEP 5: Align Mutated Assemblies")
logger.info("=".repeat(80))

// Determine input (custom or from previous step)
val fastaInput = config.align_mutated_assemblies.input?.let { Path.of(it) } ?: fastaOutputDir
if (fastaInput == null) {
throw RuntimeException("Cannot run align-mutated-assemblies: no FASTA input available (specify 'input' in config or run convert-to-fasta first)")
// Determine ref_gff (config value or from step 1)
val step5RefGff = config.align_mutated_assemblies.ref_gff?.let { Path.of(it) } ?: refGff
if (step5RefGff == null) {
throw RuntimeException("Cannot run align-mutated-assemblies: reference GFF not available (specify 'ref_gff' in config or run align_assemblies first)")
}
if (refFasta == null) {
throw RuntimeException("Cannot run align-mutated-assemblies: reference FASTA not available")

// Determine ref_fasta and fasta_input from step 4 output
// If fastaOutputDir exists, find the reference FASTA (matching original ref name) and query FASTAs
var step5RefFasta: Path? = config.align_mutated_assemblies.ref_fasta?.let { Path.of(it) }
var step5FastaInput: Path? = config.align_mutated_assemblies.fasta_input?.let { Path.of(it) }

// If not explicitly specified, try to derive from step 4 output
if (step5RefFasta == null || step5FastaInput == null) {
if (fastaOutputDir != null && fastaOutputDir.exists()) {
// Get the reference FASTA filename (without path) to match against step 4 output
val refFastaName = refFasta?.fileName?.toString()?.replace(Regex("\\.(fa|fasta|fna)(\\.gz)?$"), "")

if (refFastaName != null) {
// Find all FASTA files in the output directory
val allFastaFiles = fastaOutputDir.toFile().listFiles { file ->
file.isFile && file.name.matches(Regex(".*\\.(fa|fasta|fna)(\\.gz)?$"))
}?.map { it.toPath() } ?: emptyList()

// Find the reference FASTA (filename contains the ref name)
val matchingRefFasta = allFastaFiles.find { path ->
path.fileName.toString().contains(refFastaName, ignoreCase = true)
}

// Get non-reference FASTAs
val queryFastas = allFastaFiles.filter { path ->
!path.fileName.toString().contains(refFastaName, ignoreCase = true)
}

if (step5RefFasta == null && matchingRefFasta != null) {
step5RefFasta = matchingRefFasta
logger.info("Auto-detected reference FASTA from step 4: $step5RefFasta")
}

if (step5FastaInput == null && queryFastas.isNotEmpty()) {
// Create a text file listing the query FASTAs
val queryListFile = fastaOutputDir.resolve("query_fastas.txt")
queryListFile.writeText(queryFastas.joinToString("\n") { it.toAbsolutePath().toString() })
step5FastaInput = queryListFile
logger.info("Auto-detected ${queryFastas.size} query FASTA files from step 4")
}
}
}

// Fall back to original behavior if auto-detection failed
if (step5RefFasta == null) {
step5RefFasta = refFasta
}
if (step5FastaInput == null) {
step5FastaInput = fastaOutputDir
}
}

if (step5FastaInput == null) {
throw RuntimeException("Cannot run align-mutated-assemblies: no FASTA input available (specify 'fasta_input' in config or run convert-to-fasta first)")
}
if (refGff == null) {
throw RuntimeException("Cannot run align-mutated-assemblies: reference GFF not available")
if (step5RefFasta == null) {
throw RuntimeException("Cannot run align-mutated-assemblies: reference FASTA not available (specify 'ref_fasta' in config or run convert-to-fasta first)")
}

// Determine output directory (custom or default)
Expand All @@ -700,9 +759,9 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
val args = buildList {
add("align-mutated-assemblies")
add("--work-dir=${workDir}")
add("--ref-gff=${refGff}")
add("--ref-fasta=${refFasta}")
add("--fasta-input=${fastaInput}")
add("--ref-gff=${step5RefGff}")
add("--ref-fasta=${step5RefFasta}")
add("--fasta-input=${step5FastaInput}")
if (config.align_mutated_assemblies.threads != null) {
add("--threads=${config.align_mutated_assemblies.threads}")
}
Expand All @@ -721,11 +780,33 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
throw RuntimeException("align-mutated-assemblies failed with exit code $exitCode")
}

// Save the mutated reference FASTA for use in step 6
mutatedRefFasta = step5RefFasta

logger.info("Step 5 completed successfully")
logger.info("")
} else {
if (config.align_mutated_assemblies != null) {
logger.info("Skipping align-mutated-assemblies (not in run_steps)")

// Try to recover mutated ref FASTA from step 5 config or step 4 output
if (config.align_mutated_assemblies.ref_fasta != null) {
mutatedRefFasta = Path.of(config.align_mutated_assemblies.ref_fasta)
logger.info("Using configured mutated reference FASTA: $mutatedRefFasta")
} else if (fastaOutputDir != null && fastaOutputDir.exists()) {
// Try to auto-detect from step 4 output
val refFastaName = refFasta?.fileName?.toString()?.replace(Regex("\\.(fa|fasta|fna)(\\.gz)?$"), "")
if (refFastaName != null) {
val matchingRefFasta = fastaOutputDir.toFile().listFiles { file ->
file.isFile && file.name.matches(Regex(".*\\.(fa|fasta|fna)(\\.gz)?$")) &&
file.name.contains(refFastaName, ignoreCase = true)
}?.firstOrNull()?.toPath()
if (matchingRefFasta != null) {
mutatedRefFasta = matchingRefFasta
logger.info("Auto-detected mutated reference FASTA: $mutatedRefFasta")
}
}
}
} else {
logger.info("Skipping align-mutated-assemblies (not configured)")
}
Expand All @@ -738,8 +819,13 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
logger.info("STEP 6: Pick Crossovers")
logger.info("=".repeat(80))

if (refFasta == null) {
throw RuntimeException("Cannot run pick-crossovers: reference FASTA not available")
// Use pick_crossovers.ref_fasta if specified, otherwise use mutated ref FASTA from step 5,
// finally fall back to original ref FASTA from step 1
val pickCrossoversRefFasta = config.pick_crossovers.ref_fasta?.let { Path.of(it) }
?: mutatedRefFasta
?: refFasta
if (pickCrossoversRefFasta == null) {
throw RuntimeException("Cannot run pick-crossovers: reference FASTA not available (specify 'ref_fasta' in pick_crossovers config, run align_mutated_assemblies, or run align_assemblies first)")
}

// Determine output directory (custom or default)
Expand All @@ -748,7 +834,7 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
val args = buildList {
add("pick-crossovers")
add("--work-dir=${workDir}")
add("--ref-fasta=${refFasta}")
add("--ref-fasta=${pickCrossoversRefFasta}")
add("--assembly-list=${config.pick_crossovers.assembly_list}")
if (customOutput != null) {
add("--output-dir=${customOutput}")
Expand Down