A Python library for parsing NMR-Star files
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README.md

NMRPyStar

A library for parsing data in NMR-STAR format, used by the BMRB for NMR (Nuclear Magnetic Resonance) data archival.

This is an open source project under the MIT license; feel free to use the code in any way that helps you get some awesome science done!

Installation

The easiest way to install NMRPyStar is using pip:

$ pip install nmrpystar

If you don't have pip or easy_install, you can download the package manually from the pypi page.

Uninstallation

If it was installed with pip, it can be easily uninstalled:

$ pip uninstall nmrpystar

Quick Start

You've already got NMRPyStar installed and importable? Great! It's easy to start parsing NMR-STAR files:

import nmrpystar

myString = ...read a file/url/stdin/string...

parsed = nmrpystar.parse(myString)
if parsed.status == 'success':
    print 'it worked!!  ', parsed.value
else:
    print 'uh-oh, there was a problem with the string I gave it ... ', parsed

Python version

This library was created for use with Python2.7. Although it may work with other Python versions, I haven't tried that.

Motivation

Why is this project necessary? After all, many people have already written working NMR-STAR parsers.

However, not all parsers of the same format are identical. Here are some important characteristics of parsers:

  • what language the parser actually accepts. Some parsers are more lenient, accepting some malformed input; others may reject perfectly valid input.

    This project aims to: 1) accurately parse all valid NMR-STAR input, and 2) accurately recognize and report all invalid NMR-STAR input.

  • what the parse result is. What access does the user have to the parsed result? What information is included in the result?

    The output of this parser is a parse tree representing the structure of the input, including data blocks, save frames, loops, and key-value pairs. The parse tree is composed of Python objects, against which queries can be easily written to extract the required data.

  • error reporting: how, when, and with what context information

    Accurately reporting where and why makes it easier to locate and fix errors.

    Arguably, error reporting should be part of a format specification -- this parser does its best to report errors, but it's not always clear how an error should be reported. Suggestions welcome!

  • how the parser is used -- is it a stand-alone tool? Can it be imported as a library?

    This parser is designed to be used as a library -- simply import it, hand it your NMR-STAR input, and set it loose!

  • modularity and flexibility -- can the parser operate on stdin and stdout? Can it parse content pulled from a web page? Can it parse multiple files at once?

    This parser doesn't know anything about files, urls, or I/O streams -- any way you use to read in your data and hand it to the parser is fine. This means that it's easy to parse files from the BMRB's web interface -- just use the urllib2 library to grab a web page, and hand the contents to the parser!

  • licensing, cost, restrictions.

    This project is 100% open-source under the MIT license. This means that you may use it in any way you wish, including reading, modifying, and sharing the code.

NMR-STAR Grammar

Derived from the Spaddaccini and Hall papers describing the Star format, and with thanks to Dmitri Maziuk for his pointers.

The following grammar is used to generate a parser. Although I believe that it is correct, if you find a mistake please contact me, I am always happy to make corrections.

Tokens:

newline    :=  '\n'   |  '\r'

blank      :=  ' '    |  '\t'

space      :=  blank  |  newline

stop       :=  /stop_/i

saveclose  :=  /save_/i

loop       :=  /loop_/i

dataopen   :=  /data_/i  (not space)(+)

saveopen   :=  /save_/i  (not space)(+)

identifier :=  '_'  (not space)(+)

unquoted   :=  (not special)  (not space)(*)
  where
    special    :=  '"'  |  '#'  |  '_'  |  '\''  |  space

scstring   :=  ns  (not ns)(*)  ns
  where
    ns     :=  newline  ';'

sqstring   :=  '\''  ( nonEndingSq  |  bodyChar )(*)  '\''
  where
    nonEndingSq  :=  '\''  (not space)
    bodyChar     :=  (not ( '\''  |  newline ) )

dqstring   :=  '"'  ( nonEndingDq  |  bodyChar )(*)  '"'
  where
    nonEndingDq  :=  '"'  (not space)
    bodyChar     :=  (not ( '"'  |  newline ) )

value      :=  sqstring  |  dqstring  |  scstring  |  unquoted

comment    :=  '#'  (not newline)(*)

whitespace :=  space(+)

In addition, any amount of whitespace and comments is allowed before any token (the tokens are: stop, saveopen, saveclose, loop, dataopen, identifier, and value), except that unquoted values may not be preceded by newlines if they start with semicolons.

Also, reserved words -- stop_, save_, loop_, save_[^ \n\t\r]+, data_[^ \n\t\r]+ -- take precedence over unquoted values, meaning that stop_ cannot be an unquoted value.

Context-free grammar. Note that hierarchical rules' first letters are capitalized, while token names are all lowercase:

NMRStar  :=   Data 
    
Data     :=   dataopen  Save(*)
    
Save     :=   saveopen  Datum(*)  Loop(*)  saveclose
    
Datum    :=   identifier  value
    
Loop     :=   loop  identifier(*)  value(*)  stop

Additional constraints for STAR AST:

  • Loops
    • no duplicate keys
    • number of values must be integer multiple of the number of keys
  • Save frames
    • no duplicate keys
  • Data
    • no duplicate save frame names

Additional constraints for NMRSTAR AST:

  • Loops:
    • prefix of all keys must be identical
  • Save frames
    • prefix of all keys must be identical
    • have an _<prefix>.Sf_framecode key, value matches the save frame name
    • have an _<prefix>.Sf_category key, value is a link to the NMR-STAR data dictionary
    • no duplicate loops, based on the loop prefixes

Questionable (as in not sure if these are actually enforced) rules:

  • Save frames
    • if there's a _<prefix>.ID key, it must appear in each loop table within the save frame, under the key _<loop-prefix>.<prefix>_ID and the same value
  • General
    • _<prefix>.Entry_ID must appear in every Save frame and every loop, with the same value

Reference

Parser Combinators: a Practical Application for Generating Parsers for NMR Data by Fenwick et al, Proceedings of the ITNG, 2013.

Contact information

Found a bug? Need help figuring something out? Want a new feature? Feel free to report anything using the github issue tracker, or email me directly at mfenwick100 at gmail dot com