bx-python

from bx.seq.twobit import TwoBitFile

from bx.align.maf import MAFWriter

from bx.intervals.io import Interval

from bx.align.fasta import Header

from bx.seq.twobit import TwoBitFile import os # This is a placeholder for a real .2bit file # In a real scenario, you'd open an existing file. # For demonstration, we'll simulate a file path. twobit_file_path = os.environ.get('BX_TWOBIT_FILE', 'example.2bit') # Create a dummy .2bit file for demonstration if it doesn't exist # This part would typically not be in a quickstart but is here for runnability. if not os.path.exists(twobit_file_path): try: # TwoBitFile constructor expects a file-like object or a path to an existing file # For a runnable example, we would need to *create* a valid .2bit file or skip this section. # Given the complexity, let's illustrate reading an assumed existing file. # This part of the quickstart is illustrative rather than fully runnable without a .2bit file. print(f"Please provide a valid .2bit file at {twobit_file_path} to run this example.") print("Example: Download one from UCSC genome browser, e.g., 'hg38.2bit'") # Example of how you would *use* it if the file exists: # with open(twobit_file_path, 'rb') as f: # tb = TwoBitFile(f) # print(f"Sequence 'chr1' length: {tb['chr1'].length}") # print(f"Sequence 'chr1' first 10 bases: {tb['chr1'].get(0, 10)}") except Exception as e: print(f"Could not create or open dummy .2bit file for quickstart: {e}") print("Skipping TwoBitFile quickstart example.") # Example of using MAF (Multiple Alignment Format) writer from bx.align.maf import MAFWriter, MAFAlignment, MAFBlock, MAFComponent import sys print("\nDemonstrating MAFWriter:") writer = MAFWriter(sys.stdout) alignment = MAFAlignment() block = MAFBlock() # Create components for a block comp1 = MAFComponent() comp1.src = 'hg38.chr1' comp1.start = 100 comp1.size = 10 comp1.strand = '+' comp1.srcSize = 248956422 comp1.text = 'ATGCATGCAT' comp2 = MAFComponent() comp2.src = 'mm10.chrX' comp2.start = 50 comp2.size = 10 comp2.strand = '-' comp2.srcSize = 171031299 comp2.text = 'ATGCATGCAT' block.components.append(comp1) block.components.append(comp2) alignment.append(block) writer.write(alignment) print("MAF example written to stdout.")