feat: add support for FASTA and FASTQ formats with corresponding conv…

…erting functions

src/engine/eval/call/builtin/to_fasta.rs

@@ -0,0 +1,64 @@
+use super::*;
+use crate::engine::vm::VmSourceType;
+use std::io::Write;
+
+fn print_fasta(vm: &mut Vm) -> FilterxResult<value::Value> {
+    vm.status.printed = true;
+    let name_index = vm.source.ret_column_names.iter().position(|x| x == "name");
+    let seq_index = vm.source.ret_column_names.iter().position(|x| x == "seq");
+
+    if name_index.is_none() {
+        let h = &mut vm.hint;
+        h.white("Lost ")
+            .cyan("'name'")
+            .white(" column.")
+            .print_and_exit();
+    }
+
+    if seq_index.is_none() {
+        let h = &mut vm.hint;
+        h.white("Lost ")
+            .cyan("'seq'")
+            .white(" column.")
+            .print_and_exit();
+    }
+    let name_index = name_index.unwrap();
+    let seq_index = seq_index.unwrap();
+    let df = vm.source.lazy().collect()?;
+    let columns = df.get_columns();
+    let name_col = &columns[name_index];
+    let seq_col = &columns[seq_index];
+    if name_col.len() != seq_col.len() {
+        let h = &mut vm.hint;
+        h.white("Length of ")
+            .cyan("'name'")
+            .white(" and ")
+            .cyan("'seq'")
+            .white(" columns are different.")
+            .print_and_exit();
+    }
+    let writer = vm.writer.as_mut().unwrap().as_mut();
+    for i in 0..name_col.len() {
+        let name = name_col.get(i).unwrap();
+        let seq = seq_col.get(i).unwrap();
+        let _ = writeln!(writer, ">{}", name.get_str().unwrap_or("name"))?;
+        let _ = writeln!(writer, "{}", seq.get_str().unwrap_or("seq"))?;
+        vm.status.consume_rows += 1;
+        if vm.status.consume_rows >= vm.status.limit_rows {
+            vm.status.stop = true;
+            break;
+        }
+    }
+    Ok(value::Value::None)
+}
+
+pub fn to_fasta(vm: &mut Vm) -> FilterxResult<value::Value> {
+    if vm.source_type == VmSourceType::Fasta || vm.source_type == VmSourceType::Fastq {
+        return print_fasta(vm);
+    }
+    let h = &mut vm.hint;
+    h.white("Only ")
+        .cyan("fastq, fasta ")
+        .white("formats are supported for now.")
+        .print_and_exit();
+}

src/engine/eval/call/builtin/to_fastq.rs

@@ -0,0 +1,94 @@
+use super::*;
+use crate::engine::vm::VmSourceType;
+use std::io::Write;
+
+fn print_fastq(vm: &mut Vm) -> FilterxResult<value::Value> {
+    vm.status.printed = true;
+    let name_index = vm.source.ret_column_names.iter().position(|x| x == "name");
+    let seq_index = vm.source.ret_column_names.iter().position(|x| x == "seq");
+    let qual_index = vm.source.ret_column_names.iter().position(|x| x == "qual");
+    if name_index.is_none() {
+        let h = &mut vm.hint;
+        h.white("Lost ")
+            .cyan("'name'")
+            .white(" column.")
+            .print_and_exit();
+    }
+    if seq_index.is_none() {
+        let h = &mut vm.hint;
+        h.white("Lost ")
+            .cyan("'seq'")
+            .white(" column.")
+            .print_and_exit();
+    }
+    let name_index = name_index.unwrap();
+    let seq_index = seq_index.unwrap();
+    let df = vm.source.lazy().collect()?;
+    let columns = df.get_columns();
+    let name_col = &columns[name_index];
+    let seq_col = &columns[seq_index];
+    if name_col.len() != seq_col.len() {
+        let h = &mut vm.hint;
+        h.white("Length of ")
+            .cyan("'name'")
+            .white(" and ")
+            .cyan("'seq'")
+            .white(" columns are different.")
+            .print_and_exit();
+    }
+    let writer = vm.writer.as_mut().unwrap().as_mut();
+    if qual_index.is_some() {
+        let qual_index = qual_index.unwrap();
+        let qual_col = &columns[qual_index];
+        for i in 0..name_col.len() {
+            let name = name_col.get(i).unwrap();
+            let seq = seq_col.get(i).unwrap();
+            let q = qual_col.get(i).unwrap();
+            let _ = writeln!(writer, "@{}", name.get_str().unwrap_or("name"))?;
+            let _ = writeln!(writer, "{}", seq.get_str().unwrap_or("seq"))?;
+            let _ = writeln!(writer, "+")?;
+            let _ = writeln!(writer, "{}", q.get_str().unwrap_or("qual"))?;
+            vm.status.consume_rows += 1;
+            if vm.status.consume_rows >= vm.status.limit_rows {
+                vm.status.stop = true;
+                break;
+            }
+        }
+    } else {
+        let mut qual_buffer = String::with_capacity(512);
+        for i in 0..name_col.len() {
+            let name = name_col.get(i).unwrap();
+            let seq = seq_col.get(i).unwrap();
+            let seq = seq.get_str().unwrap_or("seq");
+            let _ = writeln!(writer, "@{}", name.get_str().unwrap_or("name"))?;
+            let _ = writeln!(writer, "{}", seq)?;
+            let _ = writeln!(writer, "+")?;
+            if qual_buffer.len() != seq.len() {
+                if qual_buffer.len() > seq.len() {
+                    qual_buffer.truncate(seq.len());
+                } else {
+                    qual_buffer.push_str(&"?".repeat(seq.len() - qual_buffer.len()))
+                }
+            }
+            let _ = writeln!(writer, "{}", &qual_buffer)?;
+            vm.status.consume_rows += 1;
+            if vm.status.consume_rows >= vm.status.limit_rows {
+                vm.status.stop = true;
+                break;
+            }
+        }
+    }
+
+    Ok(value::Value::None)
+}
+
+pub fn to_fastq(vm: &mut Vm) -> FilterxResult<value::Value> {
+    if vm.source_type == VmSourceType::Fasta || vm.source_type == VmSourceType::Fastq {
+        return print_fastq(vm);
+    }
+    let h = &mut vm.hint;
+    h.white("Only ")
+        .cyan("fastq, fasta ")
+        .white("formats are supported for now.")
+        .print_and_exit();
+}