NEF-Pipelines

A set of command line (currently... there maybe a gui later!) tools for maniulating [NEF] or NMR Exchange Format files which can be used to move NMR meta data [peaks, shifts, sequences etc] between NMR data processing programs as storable and reuable workfloes. The programs provide basic tools for manipulating nef file file structures including:

• entries: renaming
• molecular chains: listing, renaming and cloning molecular chains
• save-frames [tables]: deleting, inserting, listing and pretty printing (tabulate)
• headers creation / updating NEF headers with correct UUIDs and history
• streaming: NEF files into a pipeline
• testing: self testing of NEF pipelines

The generic commands provided are

• chains - carry out operations on chains
• entry  - carry out operations on the nef file entry
• frames - carry out operations on frames in nef frames
• header - add a header to the stream
• save - save the entries in the strean to a file / files or stdout...
• stream - stream a nef file
• test - run the test suite

It also provides tools for importing and exporing non NEF files from the following programs [transcoding / translators]

• csv  - read [rdcs]
• echidna  - read echidna data [peaks]
• fasta  - read and write fasta sequences
• mars - read and write mars [shifts and sequences]
• nmrpipe  - read nmrpipe [peaks shifts & sequencess]
• nmrstar  - read NMR-STAR [sequences & shifts]
• nmrview  - read and write nmrview [peaks, sequences & shifts]
• pales  - read and write pales/dc [rdcs]
• pdbx - read pdb [sequences]
• peaks  - carry out operations on nef peaks
• rpf  - write rpf shifts
• shifty - write shifty [shifts]
• simulate - simulate data
• sink - read the current stream and don't write anything
• sparky - read sparky files [shifts]
• talos  - read and write talos files [shifts & restraints]
• xcamshift  - write xcamshift for xplor [shifts]
• xeasy  - read xeasy files [flya dialect: sequence]
• xplor  - read xplor [sequences, dihedral & distance restraints]