Skip to content

arendsee/bioinfo-utils

Repository files navigation

Bioinformatics utilities

Parsing

  • aa-code_3to1.sed - substitute 3 letter amino acid abbreviations for 1 letter abbrviations

  • parse-dssp.sh - extract secondary structure from PDB files

  • exonphaser.sh - add intron-centric phase to a GFF file

  • rebase-gff.pl - set all intervals in the GFF as offsets from the first interval

  • swap_general.sh - substitute words (with optional pre- and suffixes) using a replacement map

  • tozero.pl - replace things nearly equal to zero with zero

Job submission scripts

  • autoslurm.sh - wraps the given command in a slurm file and runs it

Weird things I don't remember writing

  • edirect-aliases.sh

Data

  • gene-code.sh - print the gene code as a human readable table

Phylogenetics and taxonomy

  • lineage2stratum.pl
  • sciname2taxid.sh
  • taxid2lineage.pl
  • taxid2sciname.pl

Blast databases

The following monstrosities should be murdered and replaced with somethig sane.

  • stratify-seqs.sh
  • phytable.sh
  • fasta2blast_taxidmap.sh

Statistics, munging, and visualization

  • round.pl
  • rplot.R
  • sumtab.R
  • summarize-gff.awk

Database access

  • entrez-tools - filters for accessing entrez data

  • rentrez-tools - access entrez tools through an R package. To complete this, just wrap some of the functionality described here, however, it is probably better to just directly use the R package.

  • retrieve_uniprot_proteomes.py - get all proteomes beneath a given common tree node

  • sra2srr.sh - given an SRA id, find the related SRR ids

Bibtex

  • sync-bib.sh - recursively extract citations from a tex (or Rnw) file

Useless scripts

  • gff2cds.pl - use bedtools or bioconductor instead
  • rename_fasta.sh - use smof instead