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Cargo.toml

@@ -0,0 +1,9 @@
+[package]
+name = "pandora_lib_pod5"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+arrow = "52.1.0"
+chrono = "0.4.38"
+podders = "0.1.4"

src/lib.rs

@@ -0,0 +1,306 @@
+use std::{
+    fs::File,
+    io::{Read, Seek, SeekFrom},
+};
+
+use arrow::array::{
+    ArrayRef, Float64Array, Int32Array, StringArray, TimestampMillisecondArray, UInt16Array,
+};
+use arrow::array::{Int16Array, UInt32Array};
+use arrow::{array::RecordBatch, ipc::reader::FileReader};
+use chrono::TimeZone;
+use chrono::{DateTime, Utc};
+use podders::{root_as_footer, ContentType};
+
+#[derive(Debug, Clone)]
+struct Pod5Info {
+    acquisition_id: String,
+    acquisition_start_time: DateTime<Utc>,
+    adc_max: i16,
+    adc_min: i16,
+    experiment_name: String,
+    flow_cell_id: String,
+    flow_cell_product_code: String,
+    protocol_name: String,
+    protocol_run_id: String,
+    protocol_start_time: DateTime<Utc>,
+    sample_id: String,
+    sample_rate: u16,
+    sequencing_kit: String,
+    sequencer_position: String,
+    sequencer_position_type: String,
+    software: String,
+    system_name: String,
+    system_type: String,
+}
+
+impl Pod5Info {
+    pub fn from_pod5(file_path: &str) -> Self {
+        let mut file = File::open(file_path).unwrap();
+        let _end = file.seek(SeekFrom::End(0)).unwrap();
+        file.seek(SeekFrom::Current(-32)).unwrap(); // Signature + Section marker + 8 bytes for footer length
+        let mut buffer = [0; 8]; // Buffer for 8 bytes
+
+        file.read_exact(&mut buffer).unwrap(); // Read 8 bytes
+
+        // Convert bytes to little-endian i64
+        let value = i64::from_le_bytes(buffer);
+
+        // Seek to the footer position
+        file.seek(SeekFrom::Current(-(8 + value))).unwrap();
+
+        // Read the footer data
+        let mut buf = vec![0; value as usize];
+        file.read_exact(&mut buf).unwrap();
+
+        // Deserialize the FlatBuffer
+        let footer = root_as_footer(&buf).unwrap();
+
+        let mut acquisition_id = String::new();
+        let mut acquisition_start_time = Utc::now();
+        let mut adc_max = 0;
+        let mut adc_min = 0;
+        let mut experiment_name = String::new();
+        let mut flow_cell_id = String::new();
+        let mut flow_cell_product_code = String::new();
+        let mut protocol_name = String::new();
+        let mut protocol_run_id = String::new();
+        let mut protocol_start_time = Utc::now();
+        let mut sample_id = String::new();
+        let mut sample_rate = 0;
+        let mut sequencing_kit = String::new();
+        let mut sequencer_position = String::new();
+        let mut sequencer_position_type = String::new();
+        let mut software = String::new();
+        let mut system_name = String::new();
+        let mut system_type = String::new();
+
+        // Update variables with actual values
+        acquisition_id = "acquisition_123".to_string();
+        acquisition_start_time = Utc::now();
+        adc_max = 32767;
+        adc_min = -32768;
+        experiment_name = "Experiment XYZ".to_string();
+        flow_cell_id = "FC123456".to_string();
+        flow_cell_product_code = "FCPROD123".to_string();
+        protocol_name = "Protocol ABC".to_string();
+        protocol_run_id = "protocol_run_456".to_string();
+        protocol_start_time = Utc::now();
+        sample_id = "sample_789".to_string();
+        sample_rate = 44100;
+        sequencing_kit = "SEQKIT123".to_string();
+        sequencer_position = "Position A1".to_string();
+        sequencer_position_type = "Type B".to_string();
+        software = "Software v1.0".to_string();
+        system_name = "System Name".to_string();
+        system_type = "System Type".to_string();
+
+        if let Some(contents) = footer.contents() {
+            for content in contents.iter() {
+                match content.content_type() {
+                    ContentType::RunInfoTable => {
+                        // println!("{content:#?}");
+                        let batch = read_arrow_table(
+                            file_path,
+                            content.offset() as u64,
+                            content.length() as u64,
+                        )
+                        .unwrap();
+                        let schema = batch[0].schema();
+                        for column in 0..batch[0].num_columns() {
+                            let array: ArrayRef = batch[0].column(column).clone();
+
+                            // Print column name and values
+                            let column_name = schema.field(column).name().to_string();
+                            // println!("Column: {}", column_name);
+
+                            // Match the type of the array to extract values
+                            match array.data_type() {
+                                arrow::datatypes::DataType::Int16 => {
+                                    let int_array =
+                                        array.as_any().downcast_ref::<Int16Array>().unwrap();
+                                    for i in 0..int_array.len() {
+                                        // println!("{}: i16,", column_name);
+                                        match column_name.as_str() {
+                                            "adc_max" => adc_max = int_array.value(i),
+                                            "adc_min" => adc_min = int_array.value(i),
+                                            _ => (),
+                                        }
+
+                                        // println!("{}", int_array.value(i));
+                                    }
+                                }
+                                arrow::datatypes::DataType::UInt16 => {
+                                    let int_array =
+                                        array.as_any().downcast_ref::<UInt16Array>().unwrap();
+                                    for i in 0..int_array.len() {
+                                        // println!("{}: u16,", column_name);
+                                        match column_name.as_str() {
+                                            "sample_rate" => sample_rate = int_array.value(i),
+                                            _ => (),
+                                        }
+                                    }
+                                }
+
+                                // arrow::datatypes::DataType::Int32 => {
+                                //     let int_array =
+                                //         array.as_any().downcast_ref::<Int32Array>().unwrap();
+                                //     for i in 0..int_array.len() {
+                                //         println!("{}: i32,", column_name);
+                                //
+                                //         // println!("{}", int_array.value(i));
+                                //     }
+                                // }
+                                // arrow::datatypes::DataType::UInt32 => {
+                                //     let int_array =
+                                //         array.as_any().downcast_ref::<UInt32Array>().unwrap();
+                                //     for i in 0..int_array.len() {
+                                //         println!("{}: u32,", column_name);
+                                //
+                                //         // println!("{}", int_array.value(i));
+                                //     }
+                                // }
+                                // arrow::datatypes::DataType::Float64 => {
+                                //     let float_array =
+                                //         array.as_any().downcast_ref::<Float64Array>().unwrap();
+                                //     for i in 0..float_array.len() {
+                                //         println!("{}: f64,", column_name);
+                                //
+                                //         // println!("{}", float_array.value(i));
+                                //     }
+                                // }
+                                arrow::datatypes::DataType::Utf8 => {
+                                    let string_array =
+                                        array.as_any().downcast_ref::<StringArray>().unwrap();
+                                    let string_array: Vec<String> = string_array
+                                        .iter()
+                                        .flat_map(|v| match v {
+                                            Some(v) => vec![v.to_string()],
+                                            None => vec![],
+                                        })
+                                        .collect();
+
+                                    let value = string_array.join(" ");
+
+                                    match column_name.as_str() {
+                                        "acquisition_id" => acquisition_id = value,
+                                        "experiment_name" => experiment_name = value,
+                                        "flow_cell_id" => flow_cell_id = value,
+                                        "flow_cell_product_code" => flow_cell_product_code = value,
+                                        "protocol_name" => protocol_name = value,
+                                        "protocol_run_id" => protocol_run_id = value,
+                                        "sample_id" => sample_id = value,
+                                        "sequencing_kit" => sequencing_kit = value,
+                                        "sequencer_position" => sequencer_position = value,
+                                        "sequencer_position_type" => {
+                                            sequencer_position_type = value
+                                        }
+                                        "software" => software = value,
+                                        "system_name" => system_name = value,
+                                        "system_type" => system_type = value,
+                                        _ => (),
+                                    }
+                                    // println!("{}: String,", column_name);
+                                    // println!("{}", string_array.join(" "));
+                                }
+                                arrow::datatypes::DataType::Timestamp(
+                                    arrow::datatypes::TimeUnit::Millisecond,
+                                    Some(timezone),
+                                ) => {
+                                    if &timezone.to_string() == "UTC" {
+                                        let timestamp_array = array
+                                            .as_any()
+                                            .downcast_ref::<TimestampMillisecondArray>()
+                                            .unwrap();
+                                        for i in 0..timestamp_array.len() {
+                                            let timestamp = timestamp_array.value(i);
+                                            let datetime: DateTime<Utc> =
+                                                Utc.timestamp_millis_opt(timestamp).unwrap();
+                                            // println!("{}: DateTime<Utc>,", column_name);
+
+                                            match column_name.as_str() {
+                                                "acquisition_start_time" => {
+                                                    acquisition_start_time = datetime
+                                                }
+                                                "protocol_start_time" => {
+                                                    protocol_start_time = datetime
+                                                }
+                                                _ => (),
+                                            }
+
+                                            // println!("{}", datetime.to_rfc3339());
+                                        }
+                                    }
+                                }
+
+                                _ => {
+                                    // println!("Unsupported data type: {:?}", array.data_type());
+                                }
+                            }
+                        }
+                    }
+                    _ => (),
+                }
+            }
+        }
+        Pod5Info {
+            acquisition_id,
+            acquisition_start_time,
+            adc_max,
+            adc_min,
+            experiment_name,
+            flow_cell_id,
+            flow_cell_product_code,
+            protocol_name,
+            protocol_run_id,
+            protocol_start_time,
+            sample_id,
+            sample_rate,
+            sequencing_kit,
+            sequencer_position,
+            sequencer_position_type,
+            software,
+            system_name,
+            system_type,
+        }
+    }
+}
+
+fn read_arrow_table(
+    file_path: &str,
+    offset: u64,
+    length: u64,
+) -> arrow::error::Result<Vec<RecordBatch>> {
+    let mut file = File::open(file_path)?;
+
+    // Seek to the start of the embedded table
+    file.seek(SeekFrom::Start(offset))?;
+
+    // Read the specified length of bytes
+    let mut buffer = vec![0; length as usize];
+    file.read_exact(&mut buffer)?;
+
+    // Deserialize bytes into Arrow RecordBatch
+    let cursor = std::io::Cursor::new(buffer);
+    let reader = FileReader::try_new(cursor, None)?;
+
+    let mut batches = Vec::new();
+    for batch in reader {
+        batches.push(batch?);
+    }
+
+    Ok(batches)
+}
+
+#[cfg(test)]
+mod tests {
+
+    use super::*;
+
+    #[test]
+    fn it_works() {
+        let file_path = "/data/run_data/20240620-CL/SAU-MRD-NB12_AUB-DIAG-NB13_PAR-DIAG-NB14/20240620_1532_1D_PAW61519_8071e9f4/pod5/PAW61519_8071e9f4_709b3710_0.pod5";
+        let r = Pod5Info::from_pod5(file_path);
+        println!("{r:#?}");
+    }
+}