Results for "grep"
Bio-Scripts
Genetic Algorithms demonstration with word DNA in Perl
...have only the fitness come through my @weights = map { $_->{fitness} } grep { $_->{survived} } @$pop...rds over $max_entry_length letters, and uppercase them @dictionary = grep { length($_) > 1 && length($...2369 days ago
- ...hecking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/g...hecking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -...
2149 days ago
- ...epth $2 | perl -e '$c = 0; while(){chomp; @s = split(/\t/); if(scalar(@s) >= 3){$c++;}} print "$c\n";'` echo "num bp: "$NUM_BP NUM_SNP=`cat $1 |grep -v "#" | awk -F "\t" '{if (!m...
1602 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...-std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/g...1548 days ago
To convert just one specific read group to fastq
...$PROJECT | efetch -format runinfo > runinfo.txt # Select the first N elements. Keep only valid SRR numbers. cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt...1540 days ago
Script to extract the cluster detail !
$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic $ cat /proc/cpuinfo | grep -i 'model name' | head -n 1 model name : Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz1376 days ago
Parse the NCBI taxonomy database with Perl !
...Bio::Tree::Tree->new(); my $nam = $dbh->get_taxon(-taxonid => $lineageId); my @lineage = $tree_functions->get_lineage_nodes($nam); return 1 if ( grep { lc ($_->scientific_name) eq...1170 days ago
- ...rgenie-1.7051/kmergenie ../illumina.int.fastq \ > kmergenie-illumina-raw-reads.log 2>&1 rm ../illumina.int.fastq k=`grep "^best k:" \ kmergenie-illumina-raw-reads.log | grep -Po "\d+"` echo "best k=${k...
926 days ago
Bash script to simulate a genome !
...5.1_ASM340174v1_genomic.fna_upper.fasta.gz | \ grep -v ">"|wc -m # 140687135...SM340174v1_genomic.fna_upper.diploid.vcf.gz| \ grep -v "^#"|wc -l # 2830139 #...-reads.log 2>&1 rm ../illumina.int.fastq k=`grep "^best k:" \ kmergenie-illum...916 days ago
Split the string with underscore and store values in array with AWK !
more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}' #Other extraction more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}'> enriched_ids_list awk 'NR==FNR{tgts[$1]; next} $1 in tgts' enriched_ids_list result/GO.out > enriched_GO.out.xls892 days ago
