BioHacks

Austin G. Davis-Richardson

A collection of Python scripts I use for random bioinformatics-related tasks.

bin
├── babelfish - convert between fasta/gbk/gff or whatever BioPython supports
├── seq-eval - evaluate arbitrary Python code on records in a fasta/q file
├── fasta-to-phylip - convert FASTA alignment to Phylip format
├── fastq-to-fasta - convert FASTQ file to FASTA file
├── filter-seq - filter sequence file based on arbitrary Python lambda
├── qseq-to-fastq - convert QSEQ file to FASTQ file
├── gc-content - measure GC content along a sliding window (can measure any "motif")
├── seq-convert - arbitrarily convert between BioPython SeqIO formats
├── concatenate-annotation - concatenate scaffolds in a genbank annotation
└── sequence-statistics - calculate various stats on sequence lengths (mean, median, n50)