https://bioinformaticsonline.com/snippets?offset=130 https://bioinformaticsonline.com/snippets/view/43350/remove-dupcates-in-multifasta-file Thu, 02 Sep 2021 06:48:43 -0500 https://bioinformaticsonline.com/snippets/view/43350/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[$0]++ } f' seqs.fa]]> LEGE https://bioinformaticsonline.com/snippets/view/43345/python-script-to-read-fasta-and-fastq-file Thu, 02 Sep 2021 02:01:39 -0500 https://bioinformaticsonline.com/snippets/view/43345/python-script-to-read-fasta-and-fastq-file # !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam.FastxFile`. Args: fasta_q_file (str): Path to FASTA/Q file. """ with FastxFile(fasta_q_file) as fh: for entry in fh: sequence_id = entry.name sequence = entry.sequence]]> LEGE https://bioinformaticsonline.com/snippets/view/43340/print-in-terminal-with-python Tue, 31 Aug 2021 03:48:58 -0500 https://bioinformaticsonline.com/snippets/view/43340/print-in-terminal-with-python #!/usr/bin/env python import time import curses def pbar(window): height, width = window.getmaxyx() for i in range(10): window.addstr(height -1, 0, "[" + ("=" * i) + ">" + (" " * (10 - i )) + "]") window.refresh() time.sleep(0.5) curses.wrapper(pbar)]]> Neel https://bioinformaticsonline.com/snippets/view/43333/install-jellyfish-on-linux Sat, 28 Aug 2021 02:32:55 -0500 https://bioinformaticsonline.com/snippets/view/43333/install-jellyfish-on-linux Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/$ sudo apt install jellyfish Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: linux-headers-4.15.0-144 linux-headers-4.15.0-144-generic linux-headers-4.15.0-147 linux-headers-4.15.0-147-generic linux-headers-4.15.0-151 linux-headers-4.15.0-151-generic linux-image-4.15.0-144-generic linux-image-4.15.0-147-generic linux-image-4.15.0-151-generic linux-modules-4.15.0-144-generic linux-modules-4.15.0-147-generic linux-modules-4.15.0-151-generic linux-modules-extra-4.15.0-144-generic linux-modules-extra-4.15.0-147-generic linux-modules-extra-4.15.0-151-generic Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: libjellyfish-2.0-2 The following NEW packages will be installed: jellyfish libjellyfish-2.0-2 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 418 kB of archives. After this operation, 808 kB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjellyfish-2.0-2 amd64 2.2.8-3build1 [60.7 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 jellyfish amd64 2.2.8-3build1 [358 kB] Fetched 418 kB in 1s (429 kB/s) Selecting previously unselected package libjellyfish-2.0-2:amd64. (Reading database ... 329798 files and directories currently installed.) Preparing to unpack .../libjellyfish-2.0-2_2.2.8-3build1_amd64.deb ... Unpacking libjellyfish-2.0-2:amd64 (2.2.8-3build1) ... Selecting previously unselected package jellyfish. Preparing to unpack .../jellyfish_2.2.8-3build1_amd64.deb ... Unpacking jellyfish (2.2.8-3build1) ... Setting up libjellyfish-2.0-2:amd64 (2.2.8-3build1) ... Setting up jellyfish (2.2.8-3build1) ... Processing triggers for libc-bin (2.27-3ubuntu1.4) ... Processing triggers for doc-base (0.10.8) ... Processing 1 added doc-base file... Processing triggers for man-db (2.8.3-2ubuntu0.1) ...]]> Neel https://bioinformaticsonline.com/snippets/view/43327/list-of-string-comparison-algorithms Fri, 27 Aug 2021 07:27:29 -0500 https://bioinformaticsonline.com/snippets/view/43327/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.html]]> Surabhi Chaudhary https://bioinformaticsonline.com/snippets/view/43314/commands-to-transfer-files-and-folder-in-docker Tue, 24 Aug 2021 03:25:08 -0500 https://bioinformaticsonline.com/snippets/view/43314/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_DIRECTORY]]> Jit https://bioinformaticsonline.com/snippets/view/43296/commandline-for-paired-end-reads-simulation-with-bbmap Thu, 19 Aug 2021 10:30:41 -0500 https://bioinformaticsonline.com/snippets/view/43296/commandline-for-paired-end-reads-simulation-with-bbmap (JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=600 gaussian java -ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=600 gaussian Executing align2.RandomReads3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interleaved, reads=100k, length=250, mininsert=400, maxinsert=600, gaussian] Writing reference. Executing dna.FastaToChromArrays2 [mixed.fa, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=500, nodisk=false] Set genScaffoldInfo=true Writing chunk 1 Waiting for writing to finish. Finished. snpRate=0.0, max=0, unique=true insRate=0.0, max=0, len=(0-0) delRate=0.0, max=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) genome=1 PERFECT_READ_RATIO=0.0 ADD_ERRORS_FROM_QUALITY=true REPLACE_NOREF=false paired=true read length=250 reads=100000 insert size=400-600 Wrote reads_BBMAP250.fq Time: 5.722 seconds.]]> Jit https://bioinformaticsonline.com/snippets/view/43295/install-bwise-using-conda Thu, 19 Aug 2021 09:21:02 -0500 https://bioinformaticsonline.com/snippets/view/43295/install-bwise-using-conda (JitMetaENV) ➜ test_phase_assebly conda install -c bioconda bwise Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - bwise The following packages will be downloaded: package | build ---------------------------|----------------- bcalm-2.2.3 | h2e03b76_2 4.6 MB bioconda bgreat-2.0.0 | h2e03b76_3 143 KB bioconda btrim-1.0.1 | h7d875b9_3 48 KB bioconda bwise-1.0.0 | h2e03b76_1 11 KB bioconda certifi-2021.5.30 | py36h5fab9bb_0 141 KB conda-forge ------------------------------------------------------------ Total: 4.9 MB The following NEW packages will be INSTALLED: bcalm bioconda/linux-64::bcalm-2.2.3-h2e03b76_2 bgreat bioconda/linux-64::bgreat-2.0.0-h2e03b76_3 btrim bioconda/linux-64::btrim-1.0.1-h7d875b9_3 bwise bioconda/linux-64::bwise-1.0.0-h2e03b76_1 The following packages will be UPDATED: ca-certificates 2021.4.13-h06a4308_1 --> 2021.7.5-h06a4308_1 certifi 2020.12.5-py36h5fab9bb_1 --> 2021.5.30-py36h5fab9bb_0 Proceed ([y]/n)? y Downloading and Extracting Packages certifi-2021.5.30 | 141 KB | ####################################################################### | 100% bcalm-2.2.3 | 4.6 MB | ####################################################################### | 100% bwise-1.0.0 | 11 KB | ####################################################################### | 100% btrim-1.0.1 | 48 KB | ####################################################################### | 100% bgreat-2.0.0 | 143 KB | ####################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (JitMetaENV) ➜ test_phase_assebly bwise *** This is BWISE - High order De Bruijn graph assembler *** The command line was: /home/urbe/anaconda3/envs/JitMetaENV/bin/bwise [Warning] /home/urbe/JitSimuStudy/test_phase_assebly directory already exists, BWISE will use it. Results will be stored in: /home/urbe/JitSimuStudy/test_phase_assebly usage: bwise [-h] [-x PAIRED_READFILES] [-u SINGLE_READFILES] [-s KMER_SOLIDITY] [-S KMER_COVERAGE] [-p SR_SOLIDITY] [-P SR_COVERAGE] [-k K_MIN] [-K K_MAX] [-e MAPPING_EFFORT] [-a ANCHOR_SIZE] [-i FRACTION_ANCHOR] [-A MAX_OCCURENCE] [-m MISSMATCH_ALLOWED] [-g GREEDY_K2000] [-t NB_CORES] [-o OUT_DIR] [-H HAPLO_MODE] [--version] [FATAL ERROR] BWISE requires at least a read file To find out why, try `Bwise --help` and/or check the logs files of the various steps of the pipeline (logs/logBloo coo, logs/logBcalm, logs/logTips, logs/logBgreat, logs/logK2000).]]> Jit https://bioinformaticsonline.com/snippets/view/43253/perl-onliner-to-print-fasta-headers Fri, 13 Aug 2021 07:35:49 -0500 https://bioinformaticsonline.com/snippets/view/43253/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.fa]]> Neel https://bioinformaticsonline.com/snippets/view/43252/commandline-to-extract-a-list-of-specific-read-ids-from-a-bam-file Fri, 13 Aug 2021 07:30:15 -0500 https://bioinformaticsonline.com/snippets/view/43252/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.txt]]> Neel