convert-annotation

Convert the annotation of a gene to another in a delimited file using a variety of different databases.

http://github.com/GregorySchwartz/convert-annotation#readme

Version on this page:	0.5.0.1
LTS Haskell 8.24:	0.5.0.1
Stackage Nightly 2017-02-11:	0.5.0.1
Latest on Hackage:	0.5.1.0

See all snapshots convert-annotation appears in

GPL-3.0-only licensed by Gregory W. Schwartz

Maintained by [email protected]

This version can be pinned in stack with:convert-annotation-0.5.0.1@sha256:6f0eaf0d3df6c80a612f1cfb4a5bfbd43addc74687ba0350694ec5042ee73c1f,2025

Module documentation for 0.5.0.1

Depends on 19 packages(full list with versions):

aeson, base, bytestring, cassava, containers, convert-annotation, deepseq, HTTP, inline-r, lens, lens-aeson, optparse-generic, pipes, pipes-bytestring, pipes-csv, req, safe, text, vector

Used by 1 package in lts-8.4(full list with versions):

convert-annotation

* convert-annotation

Very early stages. Mix between =HTTP= and =wreq= libraries, need to fully
convert to =wreq= in the future.

Each mode, =info= or =annotation=, has its own help.

Main usage to convert, say, some unknown annotation to Ensembl annotation in a
=csv=:

#+BEGIN_SRC sh
cat input.csv | convert-annotation annotation --database "Ensembl" --column "gene"
#+END_SRC

#+BEGIN_SRC sh :exports results :results value code
convert-annotation -h
#+END_SRC

#+RESULTS:
#+BEGIN_SRC sh
convert-annotation, Gregory W. Schwartz. Converts an unknown annotation to some
other annotation.

Usage: convert-annotation (info | annotation)

Available options:
-h,--help Show this help text

Available commands:
info
annotation
#+END_SRC