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CRISPRCasFinder.patch
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--- CRISPRCasFinder.ori.pl 2019-08-01 23:28:19.071094519 +0200
+++ CRISPRCasFinder.pl 2019-08-01 23:29:15.454585619 +0200
@@ -14,7 +14,7 @@
######################################################################################
# CPAN modules
-## insert perlib ##
+use lib "/usr/local/libexec/crisprcas/lib/perl5";
use strict;
use Class::Struct; #charge le module qui construit les struct
use warnings;
@@ -62,7 +62,7 @@
my $launchCasFinder = 0; # boolean variable indicating if we use casfinder or not (default value=0)
-my $casfinder = "CasFinder-2.0.3"; # repository containing new CasFinder (default 'CasFinder-2.0.3')
+my $casfinder = "/usr/local/share/macsyfinder/CasFinder-2.0.3"; # repository containing new CasFinder (default '/usr/local/share/macsyfinder/CasFinder-2.0.3')
my $kingdom = "Bacteria"; # allow to choose analysis between Archaea and Bacteria (default 'Bacteria')
@@ -70,13 +70,13 @@
my $writeFullReport = 0; # boolean variable indicating if we write crispr-cas_vicinity_report or not (default value=0)
-my $so = "./sel392v2.so"; # path to shared object (.so) file (former name: $pathSoFile)
+my $so = "/usr/local/lib/sel392v2.so"; # path to shared object (.so) file (former name: $pathSoFile)
-my $crisprdb = ""; # path to all CRISPR candidates contained in CRISPRdb (from last update)
+my $crisprdb = "/usr/local/share/CRISPRCasFinder/CRISPR_crisprdb.csv"; # path to all CRISPR candidates contained in CRISPRdb (from last update)
-my $repeats = ""; # path to file containing repeat sequences, IDs, and Nb in CRISPRdb (last update)
+my $repeats = "/usr/local/share/CRISPRCasFinder/Repeat_List.csv"; # path to file containing repeat sequences, IDs, and Nb in CRISPRdb (last update)
-my $dirRepeat = ""; # path to file containing repeat IDs and Orientation according to CRISPRDirection
+my $dirRepeat = "/usr/local/share/CRISPRCasFinder/repeatDirection.tsv"; # path to file containing repeat IDs and Orientation according to CRISPRDirection
my $html = 0; # boolean variable indicating if we use html visualization or not (default value=0)
@@ -110,7 +110,7 @@
my $gscf = 0; # option allowing to get summary file of Cas-finder and copy it to TSV repository (default value=0)
-my $cssFile = ""; # option allowing to copy CSS file (crispr.css) to get the same design as CRISPRdb when using option -HTML (default value='')
+my $cssFile = "/usr/local/share/CRISPRCasFinder/crispr.css"; # option allowing to copy CSS file (crispr.css) to get the same design as CRISPRdb when using option -HTML (default value='/usr/local/share/CRISPRCasFinder/crispr.css')
my $genCode = 11; # option allowing to modify the genetic code (translation table) for CDS annotation (default value=11)
@@ -5246,11 +5246,11 @@
-spSim or -s [XXX] Maximal allowed percentage of similarity between Spacers (default: $SpSim)
- -DBcrispr or -dbc [XXX] Option allowing to use a CSV file of all CRISPR candidates contained in CRISPRdb (from last update) (default: 'supplementary_files/CRISPR_crisprdb.csv')
+ -DBcrispr or -dbc [XXX] Option allowing to use a CSV file of all CRISPR candidates contained in CRISPRdb (from last update) (default: $crisprdb)
- -repeats or -rpts [XXX] Option allowing to use a consensus repeats list generated by CRISPRdb (default: 'supplementary_files/Repeat_List.csv')
+ -repeats or -rpts [XXX] Option allowing to use a consensus repeats list generated by CRISPRdb (default: $repeats)
- -DIRrepeat or -drpt [XXX] Option allowing to use a file containing repeat IDs and orientation according to CRISPRDirection (default: 'supplementary_files/repeatDirection.tsv')
+ -DIRrepeat or -drpt [XXX] Option allowing to use a file containing repeat IDs and orientation according to CRISPRDirection (default: $dirRepeat)
-flank or -fl [XXX] Option allowing to set size of flanking regions in base pairs (bp) for each analyzed CRISPR array (default: $flankingRegion)
@@ -5288,7 +5288,7 @@
-rcfowce Option allowing to run Casfinder only when any CRISPR exists (default: $rcfowce) (set if -cas is set)
- -definition or -def [XXX] Option allowing to specify CasFinder definition (if option -cas is set) to be more or less stringent (default: '$definition')
+ -definition or -def [XXX] Option allowing to specify CasFinder definition (if option -cas is set) to be more or less stringent (allowed values: 'General', 'Typing' or 'SubTyping'; default: '$definition')
-gffAnnot or -gff [XXX] Option allowing user to provide an annotation GFF file (if options -cas and -faa are set) (default: '$userGFF')
@@ -5329,16 +5329,16 @@
- the ID will be used for output.
Examples:
-(1): perl $0 test.fasta
+(1): CRISPRCasFinder test.fasta
In this example, your result folder will be in the directory named: "Result_test"
-(2): perl $0 -in test.fasta -md 20 -t 33.3 -mr 23 -xr 55 -ms 25 -xs 60 -pm 0.6 -px 2.5 -s 60
+(2): CRISPRCasFinder -i test.fasta -md 20 -t 33.3 -mr 23 -xr 55 -ms 25 -xs 60 -pm 0.6 -px 2.5 -s 60
-(3): perl $0 -in genomes100.fna -drpt supplementary_files/repeatDirection.tsv -rpts supplementary_files/Repeat_List.csv -cs -ccvr -dbc supplementary_files/CRISPR_crisprdb.csv -cf CasFinder-2.0.3 -html
+(3): CRISPRCasFinder -in genomes100.fna -drpt my_repeatDirection.tsv -rpts my_Repeat_List.csv -cs -fr -dbc CRISPR_crisprdb.csv -cf my_CasFinder -html
-(4): perl $0 -in sequence.fasta -cas -log -out RES_Sequence -ccc 20000 -ccvRep -keep -html -rcfowce -def S -cpuM 4 -copyCSS supplementary_files/crispr.css -cf CasFinder-2.0.3
+(4): CRISPRCasFinder -in sequence.fasta -cas -log -out RES_Sequence -ccc 20000 -ccvRep -keep -html -rcfowce -def SubTyping -cpuM 4 -copyCSS my_crispr.css
-(5): perl $0 -in sequence.fasta -cas -log -out RES_Sequence -cf CasFinder-2.0.3 -def G -force -so path/to/sel392v2.so
+(5): CRISPRCasFinder -in sequence.fasta -cas -log -out RES_Sequence -cf my_CasFinder -def G -force -so path/to/sel392v2.so
HEREDOC
}