@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/pysam/references/sequence_files.md

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+# Working with Sequence Files (FASTA/FASTQ)
+
+## FASTA Files
+
+### Overview
+
+Pysam provides the `FastaFile` class for indexed, random access to FASTA reference sequences. FASTA files must be indexed with `samtools faidx` before use.
+
+### Opening FASTA Files
+
+```python
+import pysam
+
+# Open indexed FASTA file
+fasta = pysam.FastaFile("reference.fasta")
+
+# Automatically looks for reference.fasta.fai index
+```
+
+### Creating FASTA Index
+
+```python
+# Create index using pysam
+pysam.faidx("reference.fasta")
+
+# Or using samtools command
+pysam.samtools.faidx("reference.fasta")
+```
+
+This creates a `.fai` index file required for random access.
+
+### FastaFile Properties
+
+```python
+fasta = pysam.FastaFile("reference.fasta")
+
+# List of reference sequences
+references = fasta.references
+print(f"References: {references}")
+
+# Get lengths
+lengths = fasta.lengths
+print(f"Lengths: {lengths}")
+
+# Get specific sequence length
+chr1_length = fasta.get_reference_length("chr1")
+```
+
+### Fetching Sequences
+
+#### Fetch by Region
+
+Uses **0-based, half-open** coordinates:
+
+```python
+# Fetch specific region
+sequence = fasta.fetch("chr1", 1000, 2000)
+print(f"Sequence: {sequence}")  # Returns 1000 bases
+
+# Fetch entire chromosome
+chr1_seq = fasta.fetch("chr1")
+
+# Fetch using region string (1-based)
+sequence = fasta.fetch(region="chr1:1001-2000")
+```
+
+**Important:** Numeric arguments use 0-based coordinates, region strings use 1-based coordinates (samtools convention).
+
+#### Common Use Cases
+
+```python
+# Get sequence at variant position
+def get_variant_context(fasta, chrom, pos, window=10):
+    """Get sequence context around a variant position (1-based)."""
+    start = max(0, pos - window - 1)  # Convert to 0-based
+    end = pos + window
+    return fasta.fetch(chrom, start, end)
+
+# Get sequence for gene coordinates
+def get_gene_sequence(fasta, chrom, start, end, strand):
+    """Get gene sequence with strand awareness."""
+    seq = fasta.fetch(chrom, start, end)
+
+    if strand == "-":
+        # Reverse complement
+        complement = str.maketrans("ATGCatgc", "TACGtacg")
+        seq = seq.translate(complement)[::-1]
+
+    return seq
+
+# Check reference allele
+def check_ref_allele(fasta, chrom, pos, expected_ref):
+    """Verify reference allele at position (1-based pos)."""
+    actual = fasta.fetch(chrom, pos-1, pos)  # Convert to 0-based
+    return actual.upper() == expected_ref.upper()
+```
+
+### Extracting Multiple Regions
+
+```python
+# Extract multiple regions efficiently
+regions = [
+    ("chr1", 1000, 2000),
+    ("chr1", 5000, 6000),
+    ("chr2", 10000, 11000)
+]
+
+sequences = {}
+for chrom, start, end in regions:
+    seq_id = f"{chrom}:{start}-{end}"
+    sequences[seq_id] = fasta.fetch(chrom, start, end)
+```
+
+### Working with Ambiguous Bases
+
+FASTA files may contain IUPAC ambiguity codes:
+
+- N = any base
+- R = A or G (purine)
+- Y = C or T (pyrimidine)
+- S = G or C (strong)
+- W = A or T (weak)
+- K = G or T (keto)
+- M = A or C (amino)
+- B = C, G, or T (not A)
+- D = A, G, or T (not C)
+- H = A, C, or T (not G)
+- V = A, C, or G (not T)
+
+```python
+# Handle ambiguous bases
+def count_ambiguous(sequence):
+    """Count non-ATGC bases."""
+    return sum(1 for base in sequence.upper() if base not in "ATGC")
+
+# Remove regions with too many Ns
+def has_quality_sequence(fasta, chrom, start, end, max_n_frac=0.1):
+    """Check if region has acceptable N content."""
+    seq = fasta.fetch(chrom, start, end)
+    n_count = seq.upper().count('N')
+    return (n_count / len(seq)) <= max_n_frac
+```
+
+## FASTQ Files
+
+### Overview
+
+Pysam provides `FastxFile` (or `FastqFile`) for reading FASTQ files containing raw sequencing reads with quality scores. FASTQ files do not support random access—only sequential reading.
+
+### Opening FASTQ Files
+
+```python
+import pysam
+
+# Open FASTQ file
+fastq = pysam.FastxFile("reads.fastq")
+
+# Works with compressed files
+fastq_gz = pysam.FastxFile("reads.fastq.gz")
+```
+
+### Reading FASTQ Records
+
+```python
+fastq = pysam.FastxFile("reads.fastq")
+
+for read in fastq:
+    print(f"Name: {read.name}")
+    print(f"Sequence: {read.sequence}")
+    print(f"Quality: {read.quality}")
+    print(f"Comment: {read.comment}")  # Optional header comment
+```
+
+**FastqProxy attributes:**
+- `name` - Read identifier (without @ prefix)
+- `sequence` - DNA/RNA sequence
+- `quality` - ASCII-encoded quality string
+- `comment` - Optional comment from header line
+- `get_quality_array()` - Convert quality string to numeric array
+
+### Quality Score Conversion
+
+```python
+# Convert quality string to numeric values
+for read in fastq:
+    qual_array = read.get_quality_array()
+    mean_quality = sum(qual_array) / len(qual_array)
+    print(f"{read.name}: mean Q = {mean_quality:.1f}")
+```
+
+Quality scores are Phred-scaled (typically Phred+33 encoding):
+- Q = -10 * log10(P_error)
+- ASCII 33 ('!') = Q0
+- ASCII 43 ('+') = Q10
+- ASCII 63 ('?') = Q30
+
+### Common FASTQ Processing Workflows
+
+#### Quality Filtering
+
+```python
+def filter_by_quality(input_fastq, output_fastq, min_mean_quality=20):
+    """Filter reads by mean quality score."""
+    with pysam.FastxFile(input_fastq) as infile:
+        with open(output_fastq, 'w') as outfile:
+            for read in infile:
+                qual_array = read.get_quality_array()
+                mean_q = sum(qual_array) / len(qual_array)
+
+                if mean_q >= min_mean_quality:
+                    # Write in FASTQ format
+                    outfile.write(f"@{read.name}\n")
+                    outfile.write(f"{read.sequence}\n")
+                    outfile.write("+\n")
+                    outfile.write(f"{read.quality}\n")
+```
+
+#### Length Filtering
+
+```python
+def filter_by_length(input_fastq, output_fastq, min_length=50):
+    """Filter reads by minimum length."""
+    with pysam.FastxFile(input_fastq) as infile:
+        with open(output_fastq, 'w') as outfile:
+            kept = 0
+            for read in infile:
+                if len(read.sequence) >= min_length:
+                    outfile.write(f"@{read.name}\n")
+                    outfile.write(f"{read.sequence}\n")
+                    outfile.write("+\n")
+                    outfile.write(f"{read.quality}\n")
+                    kept += 1
+    print(f"Kept {kept} reads")
+```
+
+#### Calculate Quality Statistics
+
+```python
+def calculate_fastq_stats(fastq_file):
+    """Calculate basic statistics for FASTQ file."""
+    total_reads = 0
+    total_bases = 0
+    quality_sum = 0
+
+    with pysam.FastxFile(fastq_file) as fastq:
+        for read in fastq:
+            total_reads += 1
+            read_length = len(read.sequence)
+            total_bases += read_length
+
+            qual_array = read.get_quality_array()
+            quality_sum += sum(qual_array)
+
+    return {
+        "total_reads": total_reads,
+        "total_bases": total_bases,
+        "mean_read_length": total_bases / total_reads if total_reads > 0 else 0,
+        "mean_quality": quality_sum / total_bases if total_bases > 0 else 0
+    }
+```
+
+#### Extract Reads by Name
+
+```python
+def extract_reads_by_name(fastq_file, read_names, output_file):
+    """Extract specific reads by name."""
+    read_set = set(read_names)
+
+    with pysam.FastxFile(fastq_file) as infile:
+        with open(output_file, 'w') as outfile:
+            for read in infile:
+                if read.name in read_set:
+                    outfile.write(f"@{read.name}\n")
+                    outfile.write(f"{read.sequence}\n")
+                    outfile.write("+\n")
+                    outfile.write(f"{read.quality}\n")
+```
+
+#### Convert FASTQ to FASTA
+
+```python
+def fastq_to_fasta(fastq_file, fasta_file):
+    """Convert FASTQ to FASTA (discards quality scores)."""
+    with pysam.FastxFile(fastq_file) as infile:
+        with open(fasta_file, 'w') as outfile:
+            for read in infile:
+                outfile.write(f">{read.name}\n")
+                outfile.write(f"{read.sequence}\n")
+```
+
+#### Subsample FASTQ
+
+```python
+import random
+
+def subsample_fastq(input_fastq, output_fastq, fraction=0.1, seed=42):
+    """Randomly subsample reads from FASTQ file."""
+    random.seed(seed)
+
+    with pysam.FastxFile(input_fastq) as infile:
+        with open(output_fastq, 'w') as outfile:
+            for read in infile:
+                if random.random() < fraction:
+                    outfile.write(f"@{read.name}\n")
+                    outfile.write(f"{read.sequence}\n")
+                    outfile.write("+\n")
+                    outfile.write(f"{read.quality}\n")
+```
+
+## Tabix-Indexed Files
+
+### Overview
+
+Pysam provides `TabixFile` for accessing tabix-indexed genomic data files (BED, GFF, GTF, generic tab-delimited).
+
+### Opening Tabix Files
+
+```python
+import pysam
+
+# Open tabix-indexed file
+tabix = pysam.TabixFile("annotations.bed.gz")
+
+# File must be bgzip-compressed and tabix-indexed
+```
+
+### Creating Tabix Index
+
+```python
+# Index a file
+pysam.tabix_index("annotations.bed", preset="bed", force=True)
+# Creates annotations.bed.gz and annotations.bed.gz.tbi
+
+# Presets available: bed, gff, vcf
+```
+
+### Fetching Records
+
+```python
+tabix = pysam.TabixFile("annotations.bed.gz")
+
+# Fetch region
+for row in tabix.fetch("chr1", 1000000, 2000000):
+    print(row)  # Returns tab-delimited string
+
+# Parse with specific parser
+for row in tabix.fetch("chr1", 1000000, 2000000, parser=pysam.asBed()):
+    print(f"Interval: {row.contig}:{row.start}-{row.end}")
+
+# Available parsers: asBed(), asGTF(), asVCF(), asTuple()
+```
+
+### Working with BED Files
+
+```python
+bed = pysam.TabixFile("regions.bed.gz")
+
+# Access BED fields by name
+for interval in bed.fetch("chr1", 1000000, 2000000, parser=pysam.asBed()):
+    print(f"Region: {interval.contig}:{interval.start}-{interval.end}")
+    print(f"Name: {interval.name}")
+    print(f"Score: {interval.score}")
+    print(f"Strand: {interval.strand}")
+```
+
+### Working with GTF/GFF Files
+
+```python
+gtf = pysam.TabixFile("annotations.gtf.gz")
+
+# Access GTF fields
+for feature in gtf.fetch("chr1", 1000000, 2000000, parser=pysam.asGTF()):
+    print(f"Feature: {feature.feature}")
+    print(f"Gene: {feature.gene_id}")
+    print(f"Transcript: {feature.transcript_id}")
+    print(f"Coordinates: {feature.start}-{feature.end}")
+```
+
+## Performance Tips
+
+### FASTA
+1. **Always use indexed FASTA** files (create .fai with samtools faidx)
+2. **Batch fetch operations** when extracting multiple regions
+3. **Cache frequently accessed sequences** in memory
+4. **Use appropriate window sizes** to avoid loading excessive sequence data
+
+### FASTQ
+1. **Stream processing** - FASTQ files are read sequentially, process on-the-fly
+2. **Use compressed FASTQ.gz** to save disk space (pysam handles transparently)
+3. **Avoid loading entire file** into memory—process read-by-read
+4. **For large files**, consider parallel processing with file splitting
+
+### Tabix
+1. **Always bgzip and tabix-index** files before region queries
+2. **Use appropriate presets** when creating indices
+3. **Specify parser** for named field access
+4. **Batch queries** to same file to avoid re-opening
+
+## Common Pitfalls
+
+1. **FASTA coordinate system:** fetch() uses 0-based coordinates, region strings use 1-based
+2. **Missing index:** FASTA random access requires .fai index file
+3. **FASTQ sequential only:** Cannot do random access or region-based queries on FASTQ
+4. **Quality encoding:** Assume Phred+33 unless specified otherwise
+5. **Tabix compression:** Must use bgzip, not regular gzip, for tabix indexing
+6. **Parser requirement:** TabixFile needs explicit parser for named field access
+7. **Case sensitivity:** FASTA sequences preserve case—use .upper() or .lower() for consistent comparisons