<commit_before>DelGet - freeze v4.6 (version used to generate the data in Kapusta, Suh and Feschotte)
=====
See publication: http://biorxiv.org/content/early/2016/10/16/081307
Get micro and medium deletions specific to 2 closely related species after their split.
All options and paths are set in the file DelGet--0--CONFIG.pl (simple text file)

	Usage     : perl DelGet.pl <config_file>
	Typically : perl DelGet.pl DelGet--0--CONFIG_manipname.pl

	========================================================
	
	REQUIREMENTS:
	   (already in Lib) Perl Array::Unique = https://metacpan.org/source/SZABGAB/Array-Unique-0.08/lib/Array/Unique.pm
	   (already in Lib) Perl Array::Transpose::Ragged = https://metacpan.org/pod/Array::Transpose::Ragged
	   Blat = http://genome.ucsc.edu/FAQ/FAQblat.htmlblat3
	   Muscle = http://www.drive5.com/muscle/downloads.htm
	   Kalign = http://msa.sbc.su.se/cgi-bin/msa.cgi?mode=downloads

	========================================================   
	 	
	PURPOSE : 
	   General question = get medium size deletion rates
	   Written for 3 species (referred as 1, 2 and 3)
		  1) From a \"reference\" genome (=1), get random regions as: [anchor1]=====Genome1.region=====[anchor2]
		  2) Blat anchor1 and anchor2 sequences agains genome2 and genome3
		  3) Get length between anchors: [anchor1]=====Genome2.region=====[anchor2] and [anchor1]=====Genome3.region=====[anchor2]
<commit_msg>DelGet freeze of v4.6 readme<commit_after>DelGet - freeze v4.6 (version used to generate the data in Kapusta, Suh and Feschotte)
=====
See publication: http://biorxiv.org/content/early/2016/10/16/081307

Get micro and medium deletions specific to 2 closely related species after their split.
All options and paths are set in the file DelGet--0--CONFIG.pl (simple text file)

	Usage     : perl DelGet.pl <config_file>
	Typically : perl DelGet.pl DelGet--0--CONFIG_manipname.pl

	========================================================
	
	REQUIREMENTS:
	   (already in Lib) Perl Array::Unique = https://metacpan.org/source/SZABGAB/Array-Unique-0.08/lib/Array/Unique.pm
	   (already in Lib) Perl Array::Transpose::Ragged = https://metacpan.org/pod/Array::Transpose::Ragged
	   Blat = http://genome.ucsc.edu/FAQ/FAQblat.htmlblat3
	   Muscle = http://www.drive5.com/muscle/downloads.htm
	   Kalign = http://msa.sbc.su.se/cgi-bin/msa.cgi?mode=downloads

	========================================================   
	 	
	PURPOSE : 
	   General question = get medium size deletion rates
	   Written for 3 species (referred as 1, 2 and 3)
		  1) From a \"reference\" genome (=1), get random regions as: [anchor1]=====Genome1.region=====[anchor2]
		  2) Blat anchor1 and anchor2 sequences agains genome2 and genome3
		  3) Get length between anchors: [anchor1]=====Genome2.region=====[anchor2] and [anchor1]=====Genome3.region=====[anchor2]

{'fraction_non_alphanumeric': 0.2011938202247191, 'fraction_numerical': 0.032303370786516857, 'mean_word_length': 4.325233644859813, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '863675', 'n_tokens_mistral': 1007, 'n_tokens_neox': 878, 'n_words': 240}