rumble-tools | Open source tools, libraries, and datasets related | Genomics library

by RumbleDiscovery Go Version: Current License: MIT

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kandi X-RAY | rumble-tools Summary

rumble-tools is a Go library typically used in Artificial Intelligence, Genomics applications. rumble-tools has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Open source tools, libraries, and datasets related to the Rumble Network Discovery product and associated research

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rumble-tools has a low active ecosystem.
It has 87 star(s) with 16 fork(s). There are 16 watchers for this library.
It had no major release in the last 12 months.
There are 1 open issues and 1 have been closed. There are 1 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of rumble-tools is current.

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rumble-tools has no bugs reported.

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rumble-tools Quality

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security Security

rumble-tools has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

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license License

rumble-tools is licensed under the MIT License. This license is Permissive.
Permissive licenses have the least restrictions, and you can use them in most projects.

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Top functions reviewed by kandi - BETA

kandi has reviewed rumble-tools and discovered the below as its top functions. This is intended to give you an instant insight into rumble-tools implemented functionality, and help decide if they suit your requirements.

handleReflect handles reflection requests
SMBExtractFieldsFromSecurityBlob extracts fields from a security blob .
doHunt runs a job to the given dst .
SMB2ParseNegotiateContext is used to parse the SMB2 response .
doMonitor runs a monitor on the given destination directory .
SMBReadFrame is like SMBReadFrame but returns a byte slice .
SMB2ExtractFieldsFromNegotiateReply extracts the fields from the reply message .
probe is used to negotiate a new protocol
SMB2NegotiateProtocolRequest builds the SMB2NegotiateProtocolRequest message
BatchPorts splits a string into a list of ports .

rumble-tools Key Features

Open source tools, libraries, and datasets related to the Rumble Network Discovery product and associated research

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Community Discussions

Trending Discussions on Genomics

search for regex match between two files using python
Is there a way to permute inside using to variables in bash?
BigQuery Regex to extract string between two substrings
how to stop letter repeating itself python
Split multiallelic to biallelic in vcf by plink 1.9 and its variant name
Delete specific letter in a FASTA sequence
How to get the words within the first single quote in r using regex?
Does Apache Spark 3 support GPU usage for Spark RDDs?
Aggregating and summing columns across 1500 files by matching IDs in R (or bash)
Usage of compression IO functions in apache arrow

Trending Discussions on Genomics

QUESTION

search for regex match between two files using python

Asked 2022-Apr-09 at 00:49

I´m working with two text files that look like this: File 1

#   See ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt for a description of the columns in this file.
# assembly_accession    bioproject  biosample   wgs_master  refseq_category taxid   species_taxid   organism_name   infraspecific_name  isolate version_status  assembly_level  release_type    genome_rep  seq_rel_date    asm_name    submitter   gbrs_paired_asm paired_asm_comp ftp_path    excluded_from_refseq    relation_to_type_material   asm_not_live_date
GCF_000739415.1 PRJNA224116 SAMN02732406        na  837 837 Porphyromonas gingivalis    strain=HG66     latest  Chromosome  Major   Full    2014/08/14  ASM73941v1  University of Louisville    GCA_000739415.1 identical   https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/739/415/GCF_000739415.1_ASM73941v1         na
GCF_001263815.1 PRJNA224116 SAMN03366764        na  837 837 Porphyromonas gingivalis    strain=A7436        latest  Complete Genome Major   Full    2015/08/11  ASM126381v1 University of Florida   GCA_001263815.1 identical   https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/263/815/GCF_001263815.1_ASM126381v1            na
GCF_001297745.1 PRJNA224116 SAMD00040429    BCBV00000000.1  na  837 837 Porphyromonas gingivalis    strain=Ando     latest  Scaffold    Major   Full    2015/09/17  ASM129774v1 Lab. of Plant Genomics and Genetics, Department of Plant Genome Research, Kazusa DNA Research Institute GCA_001297745.1 identical   https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/297/745/GCF_001297745.1_ASM129774v1            an
...

File 2:

#   See ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt for a description of the columns in this file.
# assembly_accession    bioproject  biosample   wgs_master  refseq_category taxid   species_taxid   organism_name   infraspecific_name  isolate version_status  assembly_level  release_type    genome_rep  seq_rel_date    asm_name    submitter   gbrs_paired_asm paired_asm_comp ftp_path    excluded_from_refseq    relation_to_type_material   asm_not_live_date
GCA_000739415.1 PRJNA245225 SAMN02732406        na  837 837 Porphyromonas gingivalis    strain=HG66     latest  Chromosome  Major   Full    2014/08/14  ASM73941v1  University of Louisville    GCF_000739415.1 identical   https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/739/415/GCA_000739415.1_ASM73941v1         na
GCA_001263815.1 PRJNA276132 SAMN03366764        na  837 837 Porphyromonas gingivalis    strain=A7436        latest  Complete Genome Major   Full    2015/08/11  ASM126381v1 University of Florida   GCF_001263815.1 identical   https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/263/815/GCA_001263815.1_ASM126381v1            na

So, I want to search for a specific pattern using regex. For example, file 1 has this pattern:

GCF_000739415.1

and file 2 this one:

GCA_000739415.1

The difference is the third character: F versus A. However, sometimes numbers differ. Difference between files is the third row of data. These two files have a lot of patterns like the previous one, however, there are some differences. My goal is to search for the pattern that only exists in one file and not in the other file. For example, "GCF_001297745.1 in the third row in the file 1 but not in the file 2. This should be a GCA_001297745.1"

I´m working on a python code:

# PART 1: Open and read text file
with open("assembly_summary_genbank.txt", 'r') as f_1:
    contents_1 = f_1.readlines()
with open("assembly_summary_refseq.txt", 'r') as f_2:
    contents_2 = f_2.readlines()

# PART 2: Search for IDs
matches_1 = re.findall("GCF_[0-9]*\.[0-9]", str(contents_1))
matches_2 = re.findall("GCA_[0-9]*\.[0-9]", str(contents_2))

# PART 3: Match between files
# Seudocode
for line in matches_1:
    if matches_1 == matches_2:
        print("PATTERN THAT ONLY EXIST IN ONE FILE")

Part 3 refers to doing a for loop that searches for each line in both files and prints the patterns that only exist in one file and not in the other one. Any idea for doing this for loop?

ANSWER

Answered 2022-Apr-09 at 00:49

Perhaps you are after this?

import re

given_example = "GCA_000739415.1 PRJNA245225 SAMN02732406        na  837 837 Porphyromonas gingivalis    strain=HG66     latest  Chromosome  Major   Full    2014/08/14  ASM73941v1  University of Louisville    GCF_000739415.1 identical   https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/739/415/GCA_000739415.1_ASM73941v1         an"
altered_example = "GCA_000739415.1 GCTEST_000739415.1"

# GX[A or F]_[number; digit >= 1].[number; digit >= 1]
regex = r"GC[AF]_\d+.\d+"

matches_1 = re.findall(regex, given_example)
matches_2 = re.findall(regex, altered_example)

# Iteration for intersection
for match in matches_1:
    if match in matches_2:
        print(f"{match} is in both files")

Prints

GCA_000739415.1 is in both files
GCA_000739415.1 is in both files

But I would recommend:

# The preferred method for intersection, where order is not important
matches = list(set(matches_1) & set(matches_2))

Which saves as:

['GCA_000739415.1']

Note the regex matches in a form of GX[A or F]_[number; digit >= 1].[number; digit >= 1]. Let me know if this is not what you are after

Regex demo here

Edit

I believe you are after the symmetric difference of sets for files 1 and 2. Which is a fancy way of saying "things in A & B, that are not in both"

Which can be done with literation:

# Iteration
# A set has no duplicates, and is unordered
sym_dif = set()
for match in matches_1:
    if match not in matches_2:
        sym_dif.add(match)

>>> list(sym_dif)
['GCF_001297745.1', 'GCA_001297745.1']

I think your mistake was not using a set, you should't have any duplicates, and using matches_1 == matches_2. The lists won't be the same. You should check if it is not in the other set.

Or using this set notation which is the preferred method:

>>> list(set(matches_1).symmetric_difference(set(matches_2)))
['GCF_001297745.1', 'GCA_001297745.1']

Source https://stackoverflow.com/questions/71789818

QUESTION

Is there a way to permute inside using to variables in bash?

Asked 2021-Dec-09 at 23:50

I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

Input files: Highland.ped - Midland.ped - Lowland.ped
Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

The general code is:

plink2 --file Highland --exclude HighlandMidland.txt --out HighlandMidland
plink2 --file Highland --exclude HighlandLowland.txt --out HighlandLowland
plink2 --file Midland --exclude HighlandMidland.txt --out MidlandHighland
plink2 --file Midland --exclude MidlandLowland.txt --out MidlandLowland
plink2 --file Lowland --exclude HighlandLowland.txt --out LowlandHighland
plink2 --file Lowland --exclude MidlandLowland.txt --out LowlandMidland

To avoid repeating this code 6 different times I would like to use the variables listed above (1, 2 and 3) to create single output files. Outputfiles are a permutation with replacements of the inputfile names.

ANSWER

Answered 2021-Dec-09 at 23:50

Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

lands=(Highland Midland Lowland)
for (( i = 0 ; i < ${#lands[@]} ; ++i )) ; do
  for (( j = i + 1 ; j < ${#lands[@]} ; ++j )) ; do
    plink2 --file "${lands[i]}" --exclude "${lands[i]}${lands[j]}.txt" --out "${lands[i]}${lands[j]}"
    plink2 --file "${lands[j]}" --exclude "${lands[i]}${lands[j]}.txt" --out "${lands[j]}${lands[i]}"
  done
done

and here's another:

lands=(Highland Midland Lowland)
for (( i = 0 ; i < ${#lands[@]} ; ++i )) ; do
  for (( j = 0 ; j < ${#lands[@]} ; ++j )) ; do
    if [[ "$i" != "$j" ]] ; then
      plink2 \
        --file "${lands[i]}" \
        --exclude "$lands[i < j ? i : j]}$lands[i < j ? j : i]}.txt" \
        --out "${lands[i]}${lands[j]}"
    fi
  done
done

. . . but one common factor between both of the above is that they're much less clear than your current code!

Source https://stackoverflow.com/questions/70298074

QUESTION

how to stop letter repeating itself python

Asked 2021-Nov-25 at 18:33

I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it

import json

val = open("data.json")
val1 = json.load(val)#loads the list


a = input("Enter a Jumbled word ")#takes a word from user
a = list(a)#changes into list to iterate


for x in val1:#iterates words from list
    for somethin in a:#iterates letters from list
        if somethin in list(x):#checks if the letter is in the iterated word
            continue
        else:
            break
    else:#checks if the loop ended correctly (that means word has same letters)
        if len(a) != len(list(x)):#checks if it has same number of letters
            continue#returns
        else:
            print(x)#continues the loop to see if there are more like that

EDIT: many people wanted the json file so here it is

['Torres Strait Creole', 'good bye', 'agon', "queen's guard", 'animosity', 'price list', 'subjective', 'means', 'severe', 'knockout', 'life-threatening', 'entry into the war', 'dominion', 'damnify', 'packsaddle', 'hallucinate', 'lumpy', 'inception', 'Blankenese', 'cacophonous', 'zeptomole', 'floccinaucinihilipilificate', 'abashed', 'abacterial', 'ableism', 'invade', 'cohabitant', 'handicapped', 'obelus', 'triathlon', 'habitue', 'instigate', 'Gladstone Gander', 'Linked Data', 'seeded player', 'mozzarella', 'gymnast', 'gravitational force', 'Friedelehe', 'open up', 'bundt cake', 'riffraff', 'resourceful', 'wheedle', 'city center', 'gorgonzola', 'oaf', 'auf', 'oafs', 'galoot', 'imbecile', 'lout', 'moron', 'news leak', 'crate', 'aggregator', 'cheating', 'negative growth', 'zero growth', 'defer', 'ride back', 'drive back', 'start back', 'shy back', 'spring back', 'shrink back', 'shy away', 'abderian', 'unable', 'font manager', 'font management software', 'consortium', 'gown', 'inject', 'ISO 639', 'look up', 'cross-eyed', 'squinting', 'health club', 'fitness facility', 'steer', 'sunbathe', 'combatives', 'HTH', 'hope that helps', 'How The Hell', 'distributed', 'plum cake', 'liberalization', 'macchiato', 'caffè macchiato', 'beach volley', 'exult', 'jubilate', 'beach volleyball', 'be beached', 'affogato', 'gigabyte', 'terabyte', 'petabyte', 'undressed', 'decameter', 'sensual', 'boundary marker', 'poor man', 'cohabitee', 'night sleep', 'protruding ears', 'three quarters of an hour', 'spermophilus', 'spermophilus stricto sensu', "devil's advocate", 'sacred king', 'sacral king', 'myr', 'million years', 'obtuse-angled', 'inconsolable', 'neurotic', 'humiliating', 'mortifying', 'theological', 'rematch', 'varıety', 'be short', 'ontological', 'taxonomic', 'taxonomical', 'toxicology testing', 'on the job training', 'boulder', 'unattackable', 'inviolable', 'resinous', 'resiny', 'ionizing radiation', 'citrus grove', 'comic book shop', 'preparatory measure', 'written account', 'brittle', 'locker', 'baozi', 'bao', 'bau', 'humbow', 'nunu', 'bausak', 'pow', 'pau', 'yesteryear', 'fire drill', 'rotted', 'putto', 'overthrow', 'ankle monitor', 'somewhat stupid', 'a little stupid', 'semordnilap', 'pangram', 'emordnilap', 'person with a sunlamp tan', 'tittle', 'incompatible', 'autumn wind', 'dairyman', 'chesty', 'lacustrine', 'chronophotograph', 'chronophoto', 'leg lace', 'ankle lace', 'ankle lock', 'Babelfy', 'ventricular', 'recurrent', 'long-lasting', 'long-standing', 'long standing', 'sea bass', 'reap', 'break wind', 'chase away', 'spark', 'speckle', 'take back', 'Westphalian', 'Aeolic Greek', 'startup', 'abseiling', 'impure', 'bottle cork', 'paralympic', 'work out', 'might', 'ice-cream man', 'ice cream man', 'ice cream maker', 'ice-cream maker', 'traveling', 'special delivery', 'prizefighter', 'abs', 'ab', 'churro', 'pilfer', 'dehumanize', 'fertilize', 'inseminate', 'digitalize', 'fluke', 'stroke of luck', 'decontaminate', 'abandonware', 'manzanita', 'tule', 'jackrabbit', 'system administrator', 'system admin', 'springtime lethargy', 'Palatinean', 'organized religion', 'bearing puller', 'wheel puller', 'gear puller', 'shot', 'normalize', 'palindromic', 'lancet window', 'terminological', 'back of head', 'dragon food', 'barbel', 'Central American Spanish', 'basis', 'birthmark', 'blood vessel', 'ribes', 'dog-rose', 'dreadful', 'freckle', 'free of charge', 'weather verb', 'weather sentence', 'gipsy', 'gypsy', 'glutton', 'hump', 'low voice', 'meek', 'moist', 'river mouth', 'turbid', 'multitude', 'palate', 'peak of mountain', 'poetry', 'pure', 'scanty', 'spicy', 'spicey', 'spruce', 'surface', 'infected', 'copulate', 'dilute', 'dislocate', 'grow up', 'hew', 'hinder', 'infringe', 'inhabit', 'marry off', 'offend', 'pass by', 'brother of a man', 'brother of a woman', 'sister of a man', 'sister of a woman', 'agricultural farm', 'result in', 'rebel', 'strew', 'scatter', 'sway', 'tread', 'tremble', 'hog', 'circuit breaker', 'Southern Quechua', 'safety pin', 'baby pin', 'college student', 'university student', 'pinus sibirica', 'Siberian pine', 'have lunch', 'floppy', 'slack', 'sloppy', 'wishi-washi', 'turn around', 'bogeyman', 'selfish', 'Talossan', 'biomembrane', 'biological membrane', 'self-sufficiency', 'underevaluation', 'underestimation', 'opisthenar', 'prosody', 'Kumhar Bhag Paharia', 'psychoneurotic', 'psychoneurosis', 'levant', "couldn't-care-less attitude", 'noctambule', 'acid-free paper', 'decontaminant', 'woven', 'wheaten', 'waste-ridden', 'war-ridden', 'violence-ridden', 'unwritten', 'typewritten', 'spoken', 'abiogenetically', 'rasp', 'abstractly', 'cyclically', 'acyclically', 'acyclic', 'ad hoc', 'spare tire', 'spare wheel', 'spare tyre', 'prefabricated', 'ISO 9000', 'Barquisimeto', 'Maracay', 'Ciudad Guayana', 'San Cristobal', 'Barranquilla', 'Arequipa', 'Trujillo', 'Cusco', 'Callao', 'Cochabamba', 'Goiânia', 'Campinas', 'Fortaleza', 'Florianópolis', 'Rosario', 'Mendoza', 'Bariloche', 'temporality', 'papyrus sedge', 'paper reed', 'Indian matting plant', 'Nile grass', 'softly softly', 'abductive reasoning', 'abductive inference', 'retroduction', 'Salzburgian', 'cymotrichous', 'access point', 'wireless access point', 'dynamic DNS', 'IP address', 'electrolyte', 'helical', 'hydrometer', 'intranet', 'jumper', 'MAC address', 'Media Access Control address', 'nickel–cadmium battery', 'Ni-Cd battery', 'oscillograph', 'overload', 'photovoltaic', 'photovoltaic cell', 'refractor telescope', 'autosome', 'bacterial artificial chromosome', 'plasmid', 'nucleobase', 'base pair', 'base sequence', 'chromosomal deletion', 'deletion', 'deletion mutation', 'gene deletion', 'chromosomal inversion', 'comparative genomics', 'genomics', 'cytogenetics', 'DNA replication', 'DNA repair', 'DNA sequence', 'electrophoresis', 'functional genomics', 'retroviral', 'retroviral infection', 'acceptance criteria', 'batch processing', 'business rule', 'code review', 'configuration management', 'entity–relationship model', 'lifecycle', 'object code', 'prototyping', 'pseudocode', 'referential', 'reusability', 'self-join', 'timestamp', 'accredited', 'accredited translator', 'certify', 'certified translation', 'computer-aided design', 'computer-aided', 'computer-assisted', 'management system', 'computer-aided translation', 'computer-assisted translation', 'machine-aided translation', 'conference interpreter', 'freelance translator', 'literal translation', 'mother-tongue', 'whispered interpreting', 'simultaneous interpreting', 'simultaneous interpretation', 'base anhydride', 'binary compound', 'absorber', 'absorption coefficient', 'attenuation coefficient', 'active solar heater', 'ampacity', 'amorphous semiconductor', 'amorphous silicon', 'flowerpot', 'antireflection coating', 'antireflection', 'armored cable', 'electric arc', 'breakdown voltage','casing', 'facing', 'lining', 'assumption of Mary', 'auscultation']

Just a example and the dictionary is full of items

ANSWER

Answered 2021-Nov-25 at 18:33

As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

sorted_jumbled_word = sorted(a)
for word in val1:
    if len(sorted_jumbled_word) == len(word) and sorted(word) == sorted_jumbled_word:
        print(word)

Checking by length first reduces unnecessary sorting. If doing this repeatedly, you might want to create a dictionary of the words in the data file with their sorted versions, to avoid having to repeatedly sort them.

There are spaces and punctuation in some of the terms in your word list. If you want to make the comparison ignoring spaces then remove them from both the jumbled word and the list of unjumbled words, using e.g. word = word.replace(" ", "")

Source https://stackoverflow.com/questions/70112201

QUESTION

Delete specific letter in a FASTA sequence

Asked 2021-Oct-12 at 21:00

I have a FASTA file that has about 300000 sequences but some of the sequences are like these

>Spike|hCoV-19/Wuhan/WH02/2019|2019-12-31|EPI_ISL_406799|Original|hCoV-19^^Wuhan|Human|General Hospital of Central Theater Command of People's Liberation Army of China|BGI & Institute of Microbiology|Hunter|China
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVITEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*

>Spike|hCoV-19/England/PORT-2DE4EF/2020|2020-00-00|EPI_ISL_1310367|Original|hCoV-19^^England|Human|Centre for Enzyme Innovation|COVID-19 Genomics UK (COG-UK) Consortium|Robson|United Kingdom
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSVLEPLVDLPIGINITRFQTLLALHRSYLTPGDSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLDILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*

>Spike|hCoV-19/England/PORT-2DE616/2020|2020-00-00|EPI_ISL_1310384|Original|hCoV-19^^England|Human|Centre for Enzyme Innovation|COVID-19 Genomics UK (COG-UK) Consortium|Robson|United Kingdom
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSVLEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGSAAYYVGYLQLRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYYLLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*

I want to delete all the sequences that contain the letter x in them, how can I do that?

ANSWER

Answered 2021-Oct-12 at 20:28

You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

For example:

no_X_FASTA = "".join(re.findall(r">.+\n[^X]+\n",text))

Source https://stackoverflow.com/questions/69545912

QUESTION

Usage of compression IO functions in apache arrow

Asked 2021-Jun-02 at 18:58

I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.

ANSWER

Answered 2021-Jun-02 at 18:58

Here is an example program that inflates a compressed zlib file and reads it as CSV.

#include <iostream>

#include <arrow/api.h>
#include <arrow/csv/api.h>
#include <arrow/io/api.h>
#include <arrow/util/compression.h>
#include <arrow/util/logging.h>

arrow::Status RunMain(int argc, char **argv) {

  if (argc < 2) {
    return arrow::Status::Invalid(
        "You must specify a gzipped CSV file to read");
  }

  std::string file_to_read = argv[1];
  ARROW_ASSIGN_OR_RAISE(auto in_file,
                        arrow::io::ReadableFile::Open(file_to_read));
  ARROW_ASSIGN_OR_RAISE(auto codec,
                        arrow::util::Codec::Create(arrow::Compression::GZIP));
  ARROW_ASSIGN_OR_RAISE(
      auto compressed_in,
      arrow::io::CompressedInputStream::Make(codec.get(), in_file));

  auto read_options = arrow::csv::ReadOptions::Defaults();
  auto parse_options = arrow::csv::ParseOptions::Defaults();
  auto convert_options = arrow::csv::ConvertOptions::Defaults();
  ARROW_ASSIGN_OR_RAISE(
      auto table_reader,
      arrow::csv::TableReader::Make(arrow::io::default_io_context(),
                                    std::move(compressed_in), read_options,
                                    parse_options, convert_options));

  ARROW_ASSIGN_OR_RAISE(auto table, table_reader->Read());
  std::cout << "The table had " << table->num_rows() << " rows and "
            << table->num_columns() << " columns." << std::endl;

  return arrow::Status::OK();
}

int main(int argc, char **argv) {
  arrow::Status st = RunMain(argc, argv);
  if (!st.ok()) {
    std::cerr << st << std::endl;
    return 1;
  }
  return 0;
}

Compression is handled in different ways in different parts of Arrow. The file readers typically accept an arrow::io::InputStream. You should be able to use arrow::io::CompressedInputStream to wrap an arrow::io::InputStream with decompression. This gives you whole-file compression. This is fine for something like CSV.

For Parquet, this approach does not work (ParquetFileReader::Open expects arrow::io::RandomAccessFile). For IPC, this approach is inefficient (unless you are reading the entire file). Effective reading of these formats involves seekable reads which is not possible with whole-file compression. Both formats support their own format-specific compression options. You only need to specify these options on write. On read the compression will be detected from the metadata (the metadata is stored uncompressed) of the file itself. If you are writing data you can find the information in parquet::ArrowWriterProperties and arrow::ipc::WriteOptions.

Since whole-file compression is still a thing for CSV the datasets API has recently (as of 4.0.0) added support for detecting compression from file extensions for CSV datasets. More details can be found here.

As for documentation and an object diagram, those are excellent topics for the user mailing list, or you are welcome to provide a pull request.

Source https://stackoverflow.com/questions/67799265

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