Results for "r"
Bio-Scripts
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt1060 days ago
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.fa1060 days ago
- ...ollecting package metadata (current_repodata.json): done Solv...4.6 MB bioconda bgreat-2.0.0 |...::bcalm-2.2.3-h2e03b76_2 bgreat bioconda/linux...################### | 100% bgreat-2.0.0 | 143 KB...
1054 days ago
Commandline for paired end reads simulation with BBMap !
...xedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k leng...-cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3 buil...ate=0.0, max=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRa...1054 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_DIRECTORY1049 days ago
List of string comparison algorithms !
String comparison: Levenshtein Distance Damerau-Levenshtein Distance Jaro Distance Jaro-Winkler Distance Match Rating Approach Comparison Hamming Distance More at https://jellyfish.readthedocs.io/en/latest/comparison.html1046 days ago
- ...sudo apt install jellyfish Reading package lists... Done Building dependency tree Reading state infor...ic linux-image-4.15.0-144-generic linux-image-4.15.0-147-g...fish libjellyfish-2.0-2 0 upgraded, 2 newly installed, 0 to...llyfish (2.2.8-3build1) ... Processing triggers for libc-bin...
1045 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)1042 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...FastxFile(fasta_q_file) as fh: for entry in fh: seq...1040 days ago
Remove dupcates in multifasta file !
#Using seqkit for duplicate sequence removal seqkit rmdup -n seqs.fa -o seqs_without_duplicate.fa #Awk for duplicate sequence removal awk '/^>/ { f = !a[$0]++ } f' seqs.fa1040 days ago
