Results for "C"
Bio-Scripts
Perl script to find coding regions in DNA sequences
...age showing the error if (scalar(@ARGV) < 2) { print "dnaloglkh.pl codontable DNAsequence\n"; e...open the first file: table of codon usage frequencies if (...nce my @seql = ; # load the complete sequence into an array...Extremely different values of coding potential should be obta...2168 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to b...ttps://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for....fasta --threads N where N is an integer specifying how many threads BWA-me...2137 days ago
- ➜ Tools git:(master) ✗ git clone git://github.com/bcgsc/bloomfilter.git Clon...lib checking for g++... g++ checking whether the C++ compil...s/Unit make[2]: Entering directory '/home/urbe/Tools/bloomfi...filter' make[2]: Leaving directory '/home/urbe/Tools/bloomfi...
2164 days ago
- # To follow these instructions, we'll assume your system a...libexpat1-dev libssl-dev libmysqlclient-dev libxml2-dev # RHEL/CentOS system admins should run...wherever you want to maintain such software: export PERL_BASE=...ake install # Install dependencies for Ensembl API, VEP, Onco...
2157 days ago
Perl script to count number of Ns in a multifasta file !
...perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta >...8 28079 0.00326994712582024 scaffold5_size7253348 7253348 0...6 132882 0.0808326956276302 scaffold18_size1445477 1445477 5...25 25709 0.0910646226214596 scaffold47_size306566 306566 162...2157 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2157 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage:...$tmpFile="tmpOutfile"; foreach my $chr (@$SeqIds) { my $c...qid = $1; $sequences{$seqid}{desc} = $2; p...2153 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl...ATSUMA analysis # User need to set the reference multifasta file name here m...amedAdinetaV2.fa"; #Ur target file my $satsumaLoc="/home/urbe/Tools/SATSUMA/sat...2153 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Se...# Flush output my $outfile_cds = Bio::SeqIO->new( -format...'fasta', -file => ">$ARGV[2].cds.fasta" ); my $outfile_pep...'fasta', -file => ">$ARGV[2].cdna.fasta" ); my $outfile_gen...) # cdna - transcribed sequence (devoid of introns, but cont...2152 days ago
- ...ustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts export AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/au...longMIRA_canuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30 -l metaz...
2150 days ago
