Sasha (Alexander) Mikheyev mikheyev

A demo of Mike Bostock’s TopoJSON using states & provinces boundaries from Natural Earth.

With simplification turned on (-s 100), this reduces the original 57MB GeoJSON file to a mere 515KB!

Papers2 Library Cleanup

For a variety of reasons, my Papers2 library folder (~/Library/Application Support/Papers2) was cluttered with many duplicate papers, generally only one of which was linked to a document in Papers2. Here is how I cleaned it up.

From a Terminal, cd ~/Library/Application\ Support.
open .
Copy the Papers2 folder to the Desktop. This is your backup.
In Papers2, cmd+,, select Library, select Add next to "Rename files in library folder as:", and select Separator -> _ then click Apply.
Back in your Terminal, find ./ -iregex ".*[^_]\.pdf" -delete

If you want to see what's going to be deleted before doing it, run find ./ -iregex ".*[^_]\.pdf"

List files tracked by git

git ls-tree --full-tree -r HEAD

Stop tracking files

git rm --cached filename_here

	ERCC-00002 ERCC exon 1 1061 0.000000 + . gene_id "ERCC-00002"; transcript_id "DQ459430";
	ERCC-00003 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00003"; transcript_id "DQ516784";
	ERCC-00004 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00004"; transcript_id "DQ516752";
	ERCC-00009 ERCC exon 1 984 0.000000 + . gene_id "ERCC-00009"; transcript_id "DQ668364";
	ERCC-00012 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00012"; transcript_id "DQ883670";
	ERCC-00013 ERCC exon 1 808 0.000000 + . gene_id "ERCC-00013"; transcript_id "EF011062";
	ERCC-00014 ERCC exon 1 1957 0.000000 + . gene_id "ERCC-00014"; transcript_id "DQ875385";
	ERCC-00016 ERCC exon 1 844 0.000000 + . gene_id "ERCC-00016"; transcript_id "DQ883664";
	ERCC-00017 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00017"; transcript_id "DQ459420";
	ERCC-00019 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00019"; transcript_id "DQ883651";

	>ERCC-00002
	TCCAGATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCG
	GCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGACTAGCGTAC
	GAGCACTATGGTCAGTAATTCCTGGAGGAATAGGTACCAAGAAAAAAACG
	AACCTTTGGGTTCCAGAGCTGTACGGTCGCACTGAACTCGGATAGGTCTC
	AGAAAAACGAAATATAGGCTTACGGTAGGTCCGAATGGCACAAAGCTTGT
	TCCGTTAGCTGGCATAAGATTCCATGCCTAGATGTGATACACGTTTCTGG
	AAACTGCCTCGTCATGCGACTGTTCCCCGGGGTCAGGGCCGCTGGTATTT
	GCTGTAAAGAGGGGCGTTGAGTCCGTCCGACTTCACTGCCCCCTTTCAGC
	CTTTTGGGTCCTGTATCCCAATTCTCAGAGGTCCCGCCGTACGCTGAGGA