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

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 gsch@mail.med.upenn.edu

Module documentation for 0.5.0.1

* convert-annotation

Very early stages. Mix between =HTTP= and =req= libraries, need to fully
convert to =req= 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

Depends on 19 packages:

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:

convert-annotation