Results for "6"
Bio-Scripts
Genetic Algorithms demonstration with word DNA in Perl
...ual->{dna}; my $new_dna = 0; foreach my $byte (1 .. $dna_byte_length) { vec($new_dna, $byte-1, 8) &= int(rand(256)); vec($new_dna, $byte-1, 8) |= int(rand(256)); } $individual->{dna}...2420 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/To...2380 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2313 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2311 days ago
Plot custom gene density with R
library(karyoploteR) pp2298 days ago
Perl script to count the number of files in a directory with regex
...4-28_","_Hprim34_","_Hprim53_","_HPRIM1_","_HPRIM21_","_HPRIM22_","_HPRIM36_","_A110_","_A12_","_A11_","_...","_A15_","_A18_","_A19_","_C29_","_Hprim18_","_D22_","_D23_","_D21_","_A16_","_A17_","_B24_","_A3B1_","_...2286 days ago
- zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc
2258 days ago
- ...result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference...s refgenome | awk '{ FS = "\t" } ; BEGIN{L=0}; {L=L+$3}; END{print L}' 45678
2258 days ago
Perl script to find coding regions in DNA sequences
...on frequencies divided # by the random probability (uniform), that is, 1/64. After this, # the log must...($i < scalar(@codons)) { $r = $r + log($pcodons{$codons[$i]}) - log(1/64); $i = $i + 1; } prin...2204 days ago
- ...ing './compile' configure.ac:6: installing './config.guess'...ecking build system type... x86_64-pc-linux-gnu checking hos...ecking build system type... x86_64-pc-linux-gnu checking hos...ter' /usr/bin/install -c -m 644 README.md '/home/urbe/Tools...
2200 days ago
