dmitrip/biobag

A collections of miscellaneous bioinformatics-related scripts

biobag

A collections of miscellaneous bioinformatics-related scripts

Contents

annotator.py

A simple script to annotate metagenomic bins by Diamondblasting to a database. Uses a crude approach.

deduplicatesam.py

Parses a sorted SAM file and removes lines that correspond to the first pair of a read pair if both members map to the same gene. This is useful when creating mapping statistics on shorter DNA pieces.

misctools.py

A collection of useful Python functions like a function for buffered printing to a file, iterating over a FASTA file, creating directories which fail in a threadsafe way, and calculating statistics on assemblies.

misctools.ipynb

A short tutorial for some of the functionality of the misctools.

parsebins.py

Parses a directory of FASTA files representing bins. Can translate to amino acids, create a nonredundant FASTA file of all protein sequences in any bin, and/or create an easily parse-able table of which contigs/genes belong in which bins.

parsecanopy.py

Parses Canopy clustering output, creating bin files and/or nonredundant FASTA file of all protein seqs in any bin.

unifetch.py

Script for searching a local or remote database for uniprot proteins given the primary citable accession number. Also contains a function for creating a local database easily.