<commit_before>#!/usr/bin/perl
# This programm find circular RNA in RNA-seq;
use strict;
use warnings;
use Getopt::Long;
use Fcntl qw(:flock);
use threads;

####################################################################################
# USAGE
#					UROBORUS.pl 2.1.1
#	circRNA identification tool in total RNA-seq data (or Ploy(A)-minus RNA-seq data)
my $USAGE =<<USAGE;
	UROBORUS.pl 2.1.1         (Oct. 1, 2019)
	usage:
	UROBORUS.pl -index /path/genome -gtf /path/genes.gtf -fasta /path/ unmapped.sam accepted_hits.bam
	-index:	genome index(use bowtie index);
	-gtf:	gene anotation file(*.gtf file);
	-fasta:	path for genome sequence in fasta file (*.fa) in separate chromosome;
	-p:	threads (Integer,default = 6);
	-temp:	keeping the temperary file;
	-help:	usage help;
USAGE
#contact: <EMAIL>
####################################################################################

	my ( $opt_index, $opt_gtf, $opt_fasta,$opt_p,$opt_help,$opt_temp);
	$opt_p = 6;
	$opt_help = 0;
	$opt_temp = 0;

	GetOptions(
		'index=s' => \$opt_index,
		'gtf=s' => \$opt_gtf,
		'fasta=s' => \$opt_fasta,
		'p=i' => \$opt_p,
		'help' => \$opt_help,
		'temp' => \$opt_temp,
	);
	
	if ($opt_help) { print "$USAGE\n"; exit 0; }
	<commit_msg>Changes to make it more robust for the input files<commit_after>#!/usr/bin/perl
# This programm find circular RNA in RNA-seq;
use strict;
use warnings;
use Getopt::Long;
use Fcntl qw(:flock);
use threads;

####################################################################################
# USAGE
#					UROBORUS.pl 2.1.1
#	circRNA identification tool in total RNA-seq data (or Ploy(A)-minus RNA-seq data)
my $USAGE =<<USAGE;
	UROBORUS.pl 2.1.1         (Oct. 1, 2019)
	usage:
		UROBORUS.pl -index /path/genome -gtf /path/genes.gtf -fasta /path/ unmapped.sam accepted_hits.bam
		-index:	genome index(use bowtie index);
		-gtf:	gene anotation file(*.gtf file);
		-fasta:	path for genome sequence in fasta file (*.fa) in separate chromosome;
		-p:	threads (Integer,default = 6);
		-temp:	keeping the temperary file;
		-help:	usage help;
USAGE
#contact: <EMAIL>
####################################################################################

	my ( $opt_index, $opt_gtf, $opt_fasta,$opt_p,$opt_help,$opt_temp);
	$opt_p = 6;
	$opt_help = 0;
	$opt_temp = 0;

	GetOptions(
		'index=s' => \$opt_index,
		'gtf=s' => \$opt_gtf,
		'fasta=s' => \$opt_fasta,
		'p=i' => \$opt_p,
		'help' => \$opt_help,
		'temp' => \$opt_temp,
	);
	
	if ($opt_help) { print "$USAGE\n"; exit 0; }
	
{'fraction_non_alphanumeric': 0.2773780975219824, 'fraction_numerical': 0.012789768185451638, 'mean_word_length': 4.359743040685225, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 17, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7008417', 'n_tokens_mistral': 1043, 'n_tokens_neox': 928, 'n_words': 243}