LICENSE, README, example script

Author: subwaystation

LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2021 Simon Heumos
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -0,0 +1,68 @@
+# pgge
+
+## the pangenome graph evaluator
+
+This pangenome graph evaluation pipeline measures the reconstruction accuracy of a pangenome graph (in the variation graph model).
+Its goal is to give guidance in finding the best pangenome graph construction tool for a given input data and task.
+
+It has two phases:
+
+1. _[GraphAligner](https://github.com/maickrau/GraphAligner)_: (*alignment*) -- SHORT DESCRIPTION. TODO.
+
+2. _[peanut](https://github.com/subwaystation/rs-peanut)_: (*alignment evaluation*) -- SHORT DESCRIPTION. TODO.
+
+## general usage
+
+TODO
+
+Create our pangenome graph and consensus graphs using `pggb`:
+
+```
+pggb -i cerevisiae.pan.fa -s 50000 -p 90 -w 30000 -n 5 -t 16 -v -Y "#" -S -k 8 -B 10000000 -I 0.7 -o pggb -W -m -S
+```
+Evaluate the smoothed graph.
+```
+for f in pggb/*.smooth.gfa
+do
+	pgge -g $f -f cerevisiae.pan.fa -o $f.gaf -t 16 
+done
+```
+Evaluate the consensus graphs.
+```
+for f in pggb/*.consensus*.gfa
+do
+    pgge -g $f -f cerevisiae.pan.fa -o $f.gaf -t 16
+done
+```
+Print results to stdout:
+```
+for f in pggb/*.pgge
+do
+    echo $f | tr "\n" "\t"
+    cat $f
+done 
+```
+
+These commands can also be found in `scripts/pggb.sh`.
+### output
+
+The output is written to `input.gaf.pgge` in a tab-delimited format:
+```
+0.994424	0.9929550476154135	0.9970526308543786
+```
+The first number is the `aid`, the second number is the  [qsm](https://github.com/subwaystation/rs-peanut#query-sequence-match-qsm), and the third number is the [qsamm](https://github.com/subwaystation/rs-peanut#query-sequence-alignment-match-mismatch-qsamm).
+
+## installation
+TODO
+
+## TODOs
+- [ ] Finish README.
+- [ ] Explain `aid`.
+- [ ] Add option to directly start from GAF file.
+- [ ] The user should be able to select options for GraphAligner.
+- [ ] Add usage examples for _`minigraph`_, _`cactus`_, and _`SibeliaZ`_.
+- [ ] Add Dockerfile.
+- [ ] Add a CI building the Dockerfile and emitting evaluation metrics for all tools using `HLA-Zoo` data.
+- [ ] Should _`pgge`_ accept several files as input and output the results in one file?
+- [ ] Add output-folder option.
+- [ ] Integrate into nf-core/pangenome pipeline.

pgge

@@ -14,7 +14,7 @@ then
 fi
 
 ## TODO add options for GraphAligner
-## TODO add output-folder option?
+## TODO add output-folder option
 
 # read the options
 cmd=$0" "$@
@@ -92,15 +92,17 @@ $timer -f "$fmt" GraphAligner \
     -a $output_gaf \
     -x vg \
     -t $threads \
-    >/dev/null && cut -f 2,3,4,16 $output_gaf \
+    2> >(tee -a $log_file)
+
+($timer -f "$fmt" cut -f 2,3,4,16 $output_gaf \
     | sed s/id:f:// \
     | awk '{ len=$3-$2; tlen+=len; sum+=$4*len; } END { print sum / tlen }' \
-    2> >(tee -a $log_file)
+    | tr "\n" "\t" \
+    1> $output_gaf.pgge) 2> >(tee -a $log_file) 
+
 ## TODO 
 ## Directly start from GAF
 
-## TODO 
-## Emit new evaluation metric
-$timer -f "$fmt" peanut \
+($timer -f "$fmt" peanut \
     -g $output_gaf \
-    2> >(tee -a $log_file)
+    1>> $output_gaf.pgge) 2> >(tee -a $log_file)

scripts/pgge.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+pggb -i cerevisiae.pan.fa -s 50000 -p 90 -w 30000 -n 5 -t 16 -v -Y "#" -S -k 8 -B 10000000 -I 0.7 -o pggb -W -m -S
+
+for f in pggb/*.smooth.gfa
+do
+	pgge -g $f -f cerevisiae.pan.fa -o $f.gaf -t 16 
+done
+
+for f in pggb/*.consensus*.gfa
+do
+    pgge -g $f -f cerevisiae.pan.fa -o $f.gaf -t 16
+done
+
+for f in pggb/*.pgge
+do
+    echo $f | tr "\n" "\t"
+    cat $f
+done