BioX MacGuffins

A comprehensive collection of bioinformatics tools and scripts for sequence analysis, quality control, and data processing.

Requirements: Python 3.13+, BioPython 1.86+

Core Modules

Sequence Operations

• fastx.py - FASTA/FASTQ file operations (sequence-level operations)

  • Degenerate base counting
  • Sequence validation and filtering

• readsets.py - Read pair operations (R1/R2 aware)

  • Complexity filtering
  • Paired-end sequence analysis

• sambams.py - SAM/BAM file manipulation

  • CIGAR string filtering

• fastx_utils.py - Utility functions

  • Sequence complement/reverse complement (DNA, RNA, IUPAC)
  • FASTA/FASTQ parsing helpers
  • File collection utilities

Data Structures

• macguffin_classes.py - Core classes

  • Primer - Genomic primer representation (chromosome, position, coordinates)
  • RunCollection - Pipeline run organization (samples, read sets)
  • RunSet - Paired-end read set management

• configs.py - Configuration settings

Tools

Sequence Analysis

• tools/blastools.py - BLAST result manipulation

  • Self-hit removal from BLAST reports

• tools/ref_filler.py - Reference sequence expansion

  • Fills alignment gaps by extracting variants from aligned sequences
  • Generates subsequence FASTA files for missing regions

• tools/pairwise_align.py - Pairwise sequence alignment

  • Aligns sequence pairs using Biopython

• tools/ann_to_bed.py - Format conversion

  • Converts UCSC RepMask annotation format to BED format

Data Processing

• tools/clstr_splitter.py - CD-HIT cluster parser

  • Splits CD-HIT cluster output into individual cluster files

• tools/dircutadapt.py - CutAdapt wrapper

  • Batch adapter trimming for FASTQ files in a directory

• tools/subsample.py - Subsampling tool

  • Generates subsampled FASTQ files using SeqTK
  • Optional bulk processing from TSV file

• tools/extract_index_files.py - Index extraction

  • Extracts index sequences from paired-end FASTQ (generates I1/I2 from R1/R2)
  • Supports gzipped input

• tools/fasta_subseq_dl.py - Sequence download

  • Downloads FASTA subsequences from NCBI using Accession IDs and coordinates

• tools/bed_expansion.py - BED region expansion

  • Expands BED regions below a minimum length threshold symmetrically

Miscellaneous

• tools/graph_assembler.py - De Bruijn-like sequence assembly

  • Graph-based read assembly using greedy overlap matching
  • Implements Depth-First Search path finding

• tools/detect_fusions.py - Fusion read detection

  • K-mer based detection of spanning and chimeric fusion reads in paired-end FASTQ
  • Deduplicates k-mers shared between fusion partners to reduce false positives

• tools/detect_tandem_repeats.py - Tandem repeat detection

  • Identifies assembled contigs containing tandem repeats of a gene
  • Fetches exon sequences from NCBI by accession and aligns against contigs

Archive (Legacy)

The archive/ directory contains deprecated/retired tools:

• fadiff.py - FASTA difference (superseded by standard tools)
• fauniq.py - FASTA unique (superseded by standard tools)
• fqfilter.py - FASTQ filtering
• cigar_filter.py - CIGAR filtering (see sambams.py)
• map_accessiontaxid.py - Accession to TaxID mapping
• taxid_annotate.py - TaxID annotation
• snp_primer_validate.py - SNP primer validation
• read_pair_merger.py - Paired-end merging
• tabtodb.py - TAB to database conversion
• windowshopper.py - Window-based sequence analysis
• rpm_prep - RPM packaging preparation