TST: add tests for GraphBin

[Vini2]

Add tests for GraphBin in gbintk.

• test spades input
• test megahit input
• test flye input

GraphBin on spades

File name: test_cli_graphbin.py
Function name: test_graphbin_spades_run

Inputs: file names in the tests/data/5G_metaSPAdes directory.

• graph: assembly_graph_with_scaffolds.gfa
• contigs: contigs.fasta
• paths: contigs.paths
• binned: initial_contig_bins.csv
• outpath: tmp_dir

How to invoke:

gbintk graphbin --assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --output {outpath}

GraphBin on megahit

File name: test_cli_graphbin.py
Function name: test_graphbin_megahit_run

Inputs: file names in the tests/data/5G_MEGAHIT directory.

• graph: final.gfa
• contigs: final.contigs.fa
• binned: initial_contig_bins.csv
• outpath: tmp_dir

How to invoke:

gbintk graphbin --assembler megahit --graph {graph} --contigs {contigs} --binned {binned} --output {outpath}

GraphBin on flye

File name: test_cli_graphbin.py
Function name: test_graphbin_flye_run

Inputs: file names in the tests/data/1Y3B_Flye directory.

• graph: assembly_graph.gfa
• contigs: assembly.fasta
• paths: assembly_info.txt
• binned: initial_contig_bins.csv
• outpath: tmp_dir

How to invoke:

gbintk graphbin --assembler flye --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --output {outpath}

[KatherineCaley]

Hi @Vini2, happy to take on this issue!

Should the tests inspect the output written to the tmp dir for correctness, or just check that the command is run without failure?

[Vini2]

Hi @KatherineCaley!

Thanks for picking this issue. For now just checking that the command runs is enough. I've only checked the output for one case in MetaCoAG only.

Thanks!