Results for "B"
Bio-Scripts
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1056 days ago
- ...JitMetaENV) ➜ test_phase_assebly conda install -c bioconda bwise Collecting pack...The following packages will be downloaded: package...da/linux-64::bwise-1.0.0-h2e03b76_1 The following packages...SE will use it. Results will be stored in: /home/urbe/JitSi...
1050 days ago
Commandline for paired end reads simulation with BBMap !
...mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed....java -ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2....an Executing align2.RandomReads3 [build=1, ref=mixed.fa, out=read...delRate=0.0, max=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nR...1050 days ago
Commands to transfer files and folder in docker !
#To copy files between host machine and container (execute the commands on host, not inside container): $ docker cp FILE_OR_FOLDER_ON_HOST CONTAINER_ID:/CONTAINER_DIRECTORY #or $ docker cp CONTAINER_ID:FILE_OR_FOLDER_IN_CONTAINER HOST_DIRECTORY1045 days ago
- ...sh Reading package lists... Done Building dependency tree...e following additional packages will be installed: libjellyfish-2...nd 0 not upgraded. Need to get 418 kB of archives. After this oper....4) ... Processing triggers for doc-base (0.10.8) ... Processing 1...
1041 days ago
Print in terminal with python !
#!/usr/bin/env python import time import curses def pbar(window): height, width = window.getmaxyx() for i in range(10): window.addstr(height -1, 0, "[" + ("=" * i) + ">" + (" " * (10 - i )) + "]") window.refresh() time.sleep(0.5) curses.wrapper(pbar)1038 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam.F...1036 days ago
Tadpole is 250x faster than SPADes assembler !
...s/Vir$ tadpole.sh Written by Brian Bushnell Last modified J...howstats=t Print assembly statistics after writing co...er extension lookups. Assembly parameters: mincountseed=3....6 (em2) Alternate ratio between low-depth kmers. error...1036 days ago
- # Make sure that Java v8+ is installed: java -version # Install Nextflow curl -fsSL get.nextflow.io | bash # Add Nextflow binary to your PATH: mv nextflow ~/bin/ # OR system-wide installation: # sudo mv nextflow /usr/local/bin
1022 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D1021 days ago
