readme.org

mAGPie

mAGPie is a domian specific language (DSL) and interpreter designed to help curate AGP (a golden path) files. It’s been mostly used with Hi-C contact maps to fix assembly errors.

Interpreter

Compile

git submodule update --init --recursive
make

Usage

Expected at least one and at most two positional argument
Usage: magpie [OPTION...] <SCRIPT> [<AGP>]
mAGPie -- Curate AGP files

  -s, --simplify         Simplify the agp output. If adjacent 
                         components in the agp file are contiguous,
                         then combine and remove internal gap.
  -o, --out FILE         Output file (default: stdout)
  -h, --help             Give this help list

If no AGP file is given, it's read from stdin
Report bugs to github.com/IGBB/magpie.

Language

The entire script is read into memory.

Comments are then removed. A comment starts with ‘#’ and stop at the end of the current line.

Each word is separated by any number of spaces, newlines, and/or semi-colons.

{segment} => {sequence}[ THRU {sequence|END}]
{sequence} => {contig name}:{contig start}-{contig stop}

Currently supported verbs

MOVE {segment} {BEFORE|AFTER} {sequence}

move segment before or after referenced sequence. segment and sequence do not need to be on the same scaffold

{REV|REVCOMP} {segment}

Reverse or reverse complment the segment

CREATE {scaffold} FROM {segment}

Create an new scaffold from segment

SPLIT {sequence} AT {pos}

Create two recods from the sequence: {contig name}:{contig start}-{pos} and {contig name}:{pos+1}-{contig stop}