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graph-genome / component_segmentation

Read in ODGI Bin output and identify co-linear components
Apache License 2.0
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Zooming: separate directories: Fixes#12 and adds to #16 v11 and v12 #28

Closed mandosoft closed 4 years ago

mandosoft commented 4 years ago

Had trouble testing on list of files using the run configuration and just chaining -j <path name> -j <path_name_2> etc. I'm sure there's a better way to do this.

JSON version is now updated to 12.

josiahseaman commented 4 years ago

I think automatic detection of input files given a prefix is a must, since we may have 30 zoom levels in the end. from glob import glob is great for that.

mandosoft commented 4 years ago

Not sure how it dumped so many log files but likely due to the w1.json. I'll rework this with glob and recommit with just the .py files. Thanks!

josiahseaman commented 4 years ago

Let's close this PR since your new plan is to make a fresh branch from master and manually edit in your fixes. Remember, each zoom level should get it's own subdirectory inside the "graph_name" subdirectory and bin2file.json will be sitting in "graph_name" with an index to all the files. I'd say sequence only needs to be listed once for bin_width=1, so it can sit next to bin2file.json and only the width=1 zoom layer need reference "fasta_file" entries.