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add sources and datasets

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BlastHit.py 0 → 100644
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#~~~~~~~GLOBAL IMPORTS~~~~~~~#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
class BlastHit(object):
"""
@class BlastHit
@brief Object oriented class containing informations of one blast hit
The following instance field are accessible :
* q_id : Query sequence name
* s_id : Subject sequence name
* identity : % of identity in the hit
* length : length of the hit
* mis : Number of mismatch in the hit
* gap : Number of gap in the hit
* q_orient : Orientation of the query along the hit
* q_start : Hit start position of the query
* q_end : Hit end position of the query
* s_orient : Orientation of the subject along the hit
* s_start : Hit start position of the subject
* s_end : Hit end position of the subject
* evalue : E value of the alignement
* bscore : Bit score of the alignement
A class list is used to track all instances generated.
"""
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#~~~~~~~CLASS FIELDS~~~~~~~#
id_count = 0
#~~~~~~~CLASS METHODS~~~~~~~#
@ classmethod
def next_id (self):
cur_id = self.id_count
self.id_count +=1
return cur_id
#~~~~~~~FONDAMENTAL METHODS~~~~~~~#
def __init__(self, q_id, s_id, identity, length, mis, gap, q_start, q_end, s_start, s_end, evalue, bscore):
"""
Create a BlastHit object which is automatically added to the class tracking instance list
The object with the following parameters are required for object initialisation
@param q_id Query sequence name
@param s_id Subject sequence name
@param identity % of identity in the hit
@param length length of the hit
@param mis Number of mismatch in the hit
@param gap Number of gap in the hit
@param q_start Hit start position of the query
@param q_end Hit end position of the query
@param s_start Hit start position of the subject
@param s_end Hit end position of the subject
@param evalue E value of the alignement
@param bscore Bit score of the alignement
"""
self.id = self.next_id()
self.q_id = q_id
self.s_id = s_id
self.identity = float(identity)
self.length = int(length)
self.mis = int(mis)
self.gap = int(gap)
self.evalue = float(evalue)
self.bscore = float(bscore)
# Orientation of the query and subject along the hit. True if positive
self.q_orient = int(q_start) < int(q_end)
self.s_orient = int(s_start) < int(s_end)
# Autoadapt start and end so that start is always smaller than end
self.q_start = int(q_start) if int(q_start) < int(q_end) else int(q_end)
self.q_end = int(q_end) if int(q_start) < int(q_end) else int(q_start)
self.s_start = int(s_start) if int(s_start) < int(s_end) else int(s_end)
self.s_end = int(s_end) if int(s_start) < int(s_end) else int(s_start)
def __repr__(self):
msg = "HIT {}".format(self.id)
msg += "\tQuery\t{}:{}-{}({})\n".format(self.q_id, self.q_start, self.q_end, "+" if self.q_orient else "-")
msg += "\tSubject\t{}:{}-{}({})\n".format(self.s_id, self.s_start, self.s_end, "+" if self.q_orient else "-")
msg += "\tLenght : {}\tIdentity : {}%\tEvalue : {}\tBit score : {}\n".format(self.length, self.identity, self.evalue, self.bscore)
return (msg)
def __str__(self):
return "<Instance of {} from {} >\n".format(self.__class__.__name__, self.__module__)
LICENSE supprimé 100644 → 0
+ 0
− 340
Voir le fichier @ 3af9ae6b
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MakeBlastDB.py 0 → 100644
+ 92
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# -*- coding: utf-8 -*-
"""
@package pyBlast
@brief Class to create a blast database through Shell Command line
@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2014
* <adrien.leger@gmail.com> <adrien.leger@inserm.fr> <adrien.leger@univ-nantes.fr>
* [Github](https://github.com/a-slide)
* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
"""
# Standard library packages import
from os import remove, path
from subprocess import Popen, PIPE
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
class MakeBlastDB(object):
"""
@class MakeBlastDB
@brief Wrapper for makeblastdb. Create a subject database from a fasta file
Blast+ 2.8+ needs to be install and correctly added to the path.
"""
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#~~~~~~~FONDAMENTAL METHODS~~~~~~~#
def __init__ (self, makeblastdb_exec="makeblastdb", makeblastdb_opt="", dbtype="nucl", input_type="fasta"):
"""
Create a blastdb from a reference fastq file
@param makeblastdb_exec Path of the makeblastdb executable by default "makeblastdb"
@param makeblastdb_opt makeblastdb command line options as a string
@param dbtype Molecule type of target db ('nucl', 'prot')
@param input_type Type of the data specified in input_file ('asn1_bin', 'asn1_txt', 'blastdb', 'fasta')
"""
# Creating object variables
self.makeblastdb_exec = makeblastdb_exec
self.makeblastdb_opt = "{} -dbtype {} -input_type {}".format(makeblastdb_opt, dbtype, input_type)
def __str__(self):
msg = "MAKEBLASTDB CLASS\n"
msg += "Makeblastdb path : {}\n".format(self.makeblastdb_exec)
msg += "Options : {}\n".format(self.makeblastdb_opt)
return msg
def __repr__(self):
return "\n<Instance of {} from {} >\n".format(self.__class__.__name__, self.__module__)
#~~~~~~~PUBLIC METHODS~~~~~~~#
def __call__(self, ref_path, db_path="./out"):
"""
Create a blastn database from ref_path using makeblastdb
@param ref_path Path of the fasta file containing the reference sequence. Cannot be gziped
@param db_path Outname for the blast db files basename.
@return The absolute path of the database basename
"""
# Build the command line
cmd = "{} {} -in {} -out {}".format(self.makeblastdb_exec, self.makeblastdb_opt, ref_path, db_path)
print ("CMD : " + cmd)
# Run the command line without stdin and asking both stdout and stderr
try:
# Execute the command line in the default shell
proc = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE)
stdout, stderr = proc.communicate()
# Verify the return code
if proc.returncode == 1:
msg = "An error occured during execution of following command :\n"
msg += "COMMAND : {}\n".format(cmd)
msg += "STDERR : {}\n".format(stderr)
raise Exception (msg)
# Verify the output
if not stdout:
raise Exception ("Error, no data received from standard output\n"+stderr)
return path.abspath(db_path)
# In case of exception during DB building remove the created files and reraise Exception
except Exception as E:
print("Remove database files")
for ext in ["00.nhr", "nhr", "00.nin", "nin", "00.nsq", "nsq"]:
f = "{}.{}".format(db_path, ext)
if path.isfile (f):
remove (f)
raise Exception (E.message+"Impossible to generate a valid database from the reference sequence")
MakeBlastn.py 0 → 100644
+ 124
− 0
Voir le fichier @ c09ef38a
# -*- coding: utf-8 -*-
"""
@package pyBlast
@brief Class to perform a blast alignment through Shell Command line
@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2014
* <adrien.leger@gmail.com> <adrien.leger@inserm.fr> <adrien.leger@univ-nantes.fr>
* [Github](https://github.com/a-slide)
* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
"""
# Standard library packages import
from os import remove, path
from multiprocessing import cpu_count
from subprocess import Popen, PIPE
# Local library packages
from BlastHit import BlastHit
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
class MakeBlastn(object):
"""
@class MakeBlast
@brief Perform a blastn of a query against a blast database. If hits are found, a list of
BlastHit objects is returned.
Blast+ 2.8+ needs to be install and eventually added to the path.
"""
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#~~~~~~~FONDAMENTAL METHODS~~~~~~~#
def __init__ (self, blast_exec="blastn", blastn_opt="", task="megablast", evalue=10,
best_per_query_seq = False):
"""
Initialize the object and index the reference genome if necessary
@param blast_exec Path ot the blast executable. By Default blastn will be used
@param blastn_opt Blastn command line options as a string
@param task Type of blast to be performed ('blastn' 'blastn-short' 'dc-megablast'
'megablast' 'rmblastn')
@param evalue E Value cuttoff to retain alignments
"""
# Creating object variables
self.blast_exec = blast_exec
self.blastn_opt = "{} -num_threads {} -task {} -evalue {} -outfmt 6 -dust no".format(
blastn_opt, cpu_count(), task, evalue)
self.best_per_query_seq = best_per_query_seq
self.evalue = evalue
def __str__(self):
msg = "BLAST WRAPPER\n"
msg += "Blastn path : {}\n".format(self.blast_exec)
msg += "Options : {}\n".format(self.blastn_opt)
msg += "Output best hit per query : {}\n".format("T" if self.best_per_query_seq else "F")
return msg
def __repr__(self):
return "<Instance of {} from {} >\n".format(self.__class__.__name__, self.__module__)
#~~~~~~~PUBLIC METHODS~~~~~~~#
def __call__ (self, query_path, db_path):
"""
Blast query against a subject database and return a list of BlastHit object
@param query Path to a fasta file containing the query sequences
@param blastdb Blast database object NewDB or ExistingDB
@return A list of BlastHit objects if at least one hit was found
"""
# Build the command line string
cmd = "{} {} -query {} -db {}".format(self.blast_exec, self.blastn_opt, query_path, db_path)
print ("CMD : " + cmd)
# Execute the command line in the default shell
proc = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE)
stdout, stderr = proc.communicate()
# Verify the return code
if proc.returncode == 1:
msg = "An error occured during execution of following command :\n"
msg += "COMMAND : {}\n".format(cmd)
msg += "STDERR : {}\n".format(stderr)
raise Exception (msg)
# If no hit were found
if not stdout:
return None
# Return a simple list if the unicity of hit per query is not required
if not self.best_per_query_seq:
hit_list = []
for line in stdout.splitlines():
h = line.split()
hit_list.append(BlastHit(h[0], h[1] , h[2], h[3], h[4], h[5], h[6], h[7], h[8], h[9], h[10], h[11]))
print ("\t{} hits found".format(len(hit_list)))
return hit_list
# The most complicated situation where only the best hit per query is returned
# Create an intermediate dictionary to store all hits per query
hit_dict = {}
# Parse each result lines and create a list of BlastHit objects per query
for i, line in enumerate(stdout.splitlines()):
h = line.split()
if h[0] in hit_dict:
hit_dict[h[0]].append(BlastHit(h[0], h[1] , h[2], h[3], h[4], h[5], h[6], h[7], h[8], h[9], h[10], h[11]))
else:
hit_dict[h[0]] = [BlastHit(h[0], h[1] , h[2], h[3], h[4], h[5], h[6], h[7], h[8], h[9], h[10], h[11])]
print ("\t{} hits found from {} query".format(i, len(hit_dict)))
# Flatten the dictionary in a list keeping only the best alignment per query
hit_list = []
for query_hits in hit_dict.values():
best_evalue = self.evalue
best_hit = None
for hit in query_hits:
if hit.evalue <= best_evalue:
best_evalue = hit.evalue
best_hit = hit
hit_list.append(best_hit)
print ("\t{} hits retained".format(len(hit_list)))
return hit_list
UniTest.py 0 → 100755
+ 65
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#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
import random
import string
if __name__ == '__main__':
msg = ""
###############################################################################################
print ("Testing MakeBlastDB")
try:
from MakeBlastDB import MakeBlastDB
db_maker = MakeBlastDB()
db_path = db_maker (ref_path="./test/Reference.fa" , db_path="./test/Reference")
msg += "PASS\t MakeBlastDB test\n"
except Exception as E:
msg += "FAIL\t MakeBlastDB test\t {}\n".format(E)
###############################################################################################
print ("Testing BlastHit")
try:
from BlastHit import BlastHit
hit_list = []
for i in range (100):
hit_list .append(BlastHit (
q_id = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(20)),
s_id = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(20)),
identity = random.uniform(0, 1),
length = random.randint(1, 100),
mis = random.randint(0, 100),
gap = random.randint(0, 100),
q_start = random.randint(0, 100),
q_end = random.randint(0, 100),
s_start = random.randint(0, 100),
s_end = random.randint(0, 100),
evalue = random.uniform(0, 1),
bscore = random.uniform(0, 1)))
assert len(hit_list) == 100, "Incorect number of hit generated"
msg += "PASS\t BlastHit test\n"
except Exception as E:
msg += "FAIL\t BlastHit test\t {}\n".format(E)
###############################################################################################
print ("Testing MakeBlastn")
try:
from MakeBlastn import MakeBlastn
for _ in range (50):
blast_maker = MakeBlastn (
task = random.choice(['blastn', 'blastn-short', 'dc-megablast', 'megablast', 'rmblastn']),
evalue = random.uniform(0, 1),
best_per_query_seq = random.choice([True, False]))
hits = blast_maker(query_path = "./test/query_sample.fa", db_path = db_path)
msg += "PASS\t MakeBlastn test\n"
except Exception as E:
msg += "FAIL\t MakeBlastn test\t {}\n".format(E)
print (msg)
###############################################################################################
__init__.py 0 → 100644
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# -*- coding: utf-8 -*-
"""
@package pyBlast
@brief **python 2.7 wrapper for ncbi blast+**
* MakeBlastDB :
* MakeBlastn :
* BlastHit
@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2015
* <adrien.leger@gmail.com>
* <adrien.leger@inserm.fr>
* <adrien.leger@univ-nantes.fr>
* [Github](https://github.com/a-slide)
* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
"""
__all__ = ["MakeBlastDB", "MakeBlastn", "BlastHit"]
__version__ = 0.1
test/Reference.fa 0 → 100644
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Ce diff est replié.
test/Reference.nhr 0 → 100644
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Fichier ajouté
test/Reference.nin 0 → 100644
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− 0
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Fichier ajouté
test/Reference.nsq 0 → 100644
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Fichier ajouté
test/query_sample.fa 0 → 100644
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>query_001%_mutation_forward
ATTTATCTAGGAACAGGAATGCACTTTTGGGGAAAGGTTTTCCATACCAAGGAAGGGGCAGTGGCTGGACTGATAGgACATTATTCTGtAAAAACTTATG
>query_002%_mutation_forward
ACAAGTTGCCAACCAAGCGTCAGAAATTGGTGGTCATGGTGGGAGAAAAGCCCATTACCATAACTCAGCACTCGGTAGAAACCGAAGGCTGCATTCACaC
>query_003%_mutation_forward
CGCTCTAGACCGTGCAAcAGGAGAGCCTGTAAGCGGGCACgCTTCCGTGGTCTGGTGGATAAATTCGCAAGGGTATCATGGCGGACGACCGGGGTTCGAG
>query_004%_mutation_forward
TCGGCTAAgATGGCCTGCTGCACCTGCGTGAGGGTAGACTGGAAGTCATCCATGTCCACAAAGCaGTGGTATGCGCCCGTGTTGgTGcTGTAAGTGgAGT
>query_005%_mutation_forward
TTgTaCTCTCGTGTGTaTGTGTCTGTTCGCCATCCCcTCTCCGCTCGTCACTTATCCTTaACTTTTCAGAGGGTCCCCCCGtAGAgCCCGGTCACCCTCA
>query_006%_mutation_forward
GGGCTCCAGTGAGCAGGAACTGAAAGCCATTGTCAgAGATCTTGGTTGTGtGCCATATTTTTTGGGCcCCTATGACAAtCGCTTaCCtGGCTTTGTTTCT
>query_007%_mutation_forward
GAATCTaATTGAGCAGGCACCCCTaACtGTGGCCGAGtAGgTGCAGCGCGACTTTCTGACGGtATGGCGCCGatTGAGTAAGGCCCgGGAGGCCCTTTgC
>query_008%_mutation_forward
AAACAACAGGcACATGAcTATATTTATCgAGGAACAGGAATGCACTTTTGGGGAAAGGTTTTCCATACCAAGGAAGGaGCAGTGGCTGGACTGATcGAAC
>query_009%_mutation_forward
GTCATACCTGATATCGCCTCcCTCAACGAAGTcCCggAAATCTTTGAGGGcCTTGGACGCGACGtGAAcCaCGCGGCAAACGCTCTGCAACAGGAAAACA
>query_010%_mutation_forward
AACTACGTCgTCTCCcGCcGCCACACaCccCGCCAGCACCTGTCGTCAGCGCCATTATGAGCAgcGAAATTCaCACGCCCTACATGTGGAGTTACCAGaC
>query_011%_mutation_forward
AAcGGCGtGGCaCGCCGCGcCTACGTCCGaGACTGCGTTaACcTATTTCTATGCTACACCaGtgAGcCGGCCATGccCaTTTGGCAGCAGTGCTTGGAGG
>query_012%_mutation_forward
cTCGCtTaGgGCGAGCtCcTACTCcGATGGtAGaCGGTCgTGTgGATtAGGATGATCTGGACaAAtAGCATCAGGGGCTCGCGCCAcCCcgAacaTTCcC
>query_013%_mutation_forward
CGatAGaCAATCCTAcCTCTGCAGACCTCGTCCTtTGAaCCGCGCTgTtGtGGCATTGGgAtTCTGCAATTTgTTGAGcAGccTGgGCCATCGGTCaACT
>query_014%_mutation_forward
CCCCATAGGAGGTATAACAAAATTgATAtGAGAGAAAAtCACATAAACACgTGAAAAACCCTCCTGgCTgGGCAAAtTcGCgCCCTCCCGCTtCAGAcCA
>query_015%_mutation_forward
AGACtCTGcGCGGTCTggAAGATCTTtTTCCCTTcAACTAtTAAAAcAAAAgAATcAAGCATCACTTACgcAcAATaAGTTAGtAAATTTCTGTCCAGcT
>query_016%_mutation_forward
TTGATGcTGTgAGTGCAGcTGGCCATAACGcAgCAGTTAACGGTCaGGTGACCCGtCTGCGAGAGCgCGGcGTACCTGAGACGCGAGTAAGCCCTCGAGT
>query_017%_mutation_forward
CGACCACCTgCAACCgGTCAAAGtTcAAgTtaTTgATCACGCcATACAGCAaCGaACAGGTCAGCGTGGAAATTGAATGGGAGCTGCgGAAGGAAAACct
>query_018%_mutation_forward
tTTtCCTGTTgATCAATcAcCCGGTTGAcTCGTaTtAGTTGAAtcTTGGTaTCTGCattGGGCGcATTCGcTcCGATGCgTaTCCTgGGGaCCGGCCTGa
>query_019%_mutation_forward
CaGCGCGCaCACACGTGGCGGCCGCCGACCTGGTAcCCGCATcacAGgAGAtGGTGAgCCcGGGCGATCtCACCCTTTGGCGgAcCCCATTCTCtAGTcA
>query_020%_mutation_forward
GaTGCCTGAacCCCCGcgGTGTAGcTAACaACGATACGGGAGGGgccAgCATCTtGCCCgAGTGCTtCAAcGATAaCGCGAGAaCtACGCTCACCGGCTC
>query_021%_mutation_forward
CAtTGtAACACTATgAGCGCCGGGTGGTGCACtCTGcCgAGgACGCTCgaGTCGGAGtTCAGATtCaCGcCCAGGTgCTCaGCGcTcCTCAGtGCGtACG
>query_022%_mutation_forward
TCTatGtCCGGCaGGACTGCGGCGtACGGcGaggTtagTaCtCGTCtTGCgAGAgCCCGCTaGCAAAcTCCTCCGGAAACAGGGtgGAGCCtCTTTaTTG
>query_023%_mutation_forward
CGCCCcCCGCTTgaTTCTCTACCATCACaGCGTGGCaTcCaCCtGTAACAcCCTtgtTgAgTACCtTCATCTCTACAtgCtAaAgTaacCCGGCGGCAct
>query_024%_mutation_forward
GcgGATgGCTAatCTGaGCGcTTTTAgGGtCAGCAAGCGAACtGGgtTTGCCAGCaGGaGCGCCCTCTcGTAAGGTcGGGAAGgCCTGCAAAGTAAACTG
>query_025%_mutation_forward
CGGGGgcCgCAACTCCATGCcCAcCgGaCCCCAaGTAtAGCtCAaCCTGCaTtGCcgCggGGActAtgTCTtCtGCTTCCcGGAGCGCCACTgGtCtgAC
>query_026%_mutation_forward
cGCAAcaaGAGAAGatAGAGAGCcACTTCCAgcTGCACtTGCgCcTGGAAAgCAgCGGaGTGAAAaCCATGtTTaTccagCcTTTCCTtAtgCAGATTCG
>query_027%_mutation_forward
aCCaGTTCCGAgtCataCtacTgCgcGAaACCTGTCCGCCTTTCTCCCTTaGGGAAGCGTcGCcacaTCTCtcAaCTCACGCTGTAatTcTaTCAGgTCG
>query_028%_mutation_forward
AaAtaCacTcgTaCAagcGCGcCAGCGtCAGCtGCtGgAACAGCAtCGaaCtaACtGAAGCAAAGGCGtCCcGATAGCtAGAaTCcGACAtAGCCCAgGA
>query_029%_mutation_forward
gGTCCctTGAGCCGCtaTCTGGAGGCcTTGGAACTaTGCAATcaATTGgcGAaTaTGTGCCAgtcGTCcAtTcgAACCCCTTCTacaGAaCTCaCGGCCt
>query_030%_mutation_forward
gGTTCGCTCaAgGCcGtGaTGTagcCACGAACCCgCCGgTCAGgCatACCGCTGacCgTaAcCCtGTAACTtTaGTCaTaAGTCCAACCCtccAAtgCAC
>query_031%_mutation_forward
TTtCCtcaGCTcAgaaAGaGAtGCtCCTATCggttCGAgCaGTCgtTTgCGcTCtTCCgTAcTTGCCcGACcCCgCGTCcTGaAGATgAtTAtGATAtGG
>query_032%_mutation_forward
agCcAgACCTgCaTgGGgTAgAGCACaCCtTGGcGGTATTTctACTcgAtgAGATcCtACTcCCACTTTTttagtCGTcgCTGGCAGCcAgaCATCAgtA
>query_033%_mutation_forward
CTGACAGTTcCCAATGgggAAgCgGTGAGGgACCaATCggAGCGATCgGTCTATTTCGTTCgTCCAgAaTgGCCTGAgTCCCCGTgcctTgGccgttaAC
>query_034%_mutation_forward
CTctAtCGTGtTACGCGTGgaGaGgAacccCCGCGatAttctgTGTggCGaGtCCctGAaGGAGAcGcGCtCGtGagGATGaGGtATtGAAtGTTtCACG
>query_035%_mutation_forward
TaAGGGCAcTCGCGAGcGGTacaCtCTGAgAgCTcGAtCCCCGAAtCCCAAAGCCAACCAcacAActCAGGACcACGtCCGaGtTCTGGgGCTTCgTGGC
>query_036%_mutation_forward
GCAgCaGgCCcAACCCTGaAaggCAcCcAGATCgTcGTctCCgTtTagGTGCaGAGTAcAcTAAAccCAGAtATTcAAAagggCatGaGCTtCTATCGCC
>query_037%_mutation_forward
CAgGaCAAAgcGcACGCCctACaTAGaCgTAaTTatTcggGCgtAtgCcGGgGCGcGCGTGACAAcCccATCTGCGaCTCCaGcCTCGgCGCTTAGtTCG
>query_038%_mutation_forward
TgTGtCAtGtATcCTCcGAGaTccGCTtACCAttaTAGgCCCaATGTAAGgTgGTaGCtaaGtCGGtcATATAgAATGatAGaTGCaaCTatAAAAATCc
>query_039%_mutation_forward
ACcGaaCAttCTGCtctcCtACagccAACAGgTCTACAatgTCCTaGAGtGtCAtTtGaCaTtgggaCGgAGCCACAaatCGgAGATTAGGAcCGCCACa
>query_040%_mutation_forward
ATTACAGgCtCatTtctAGGTcTAttAAAAaTAATAaGcaccAgctgCgCtTAgAtACtaGAAcAACCtTCtaGCaagGGCAgAATAGtACCgcCCCaCa
>query_041%_mutation_forward
acGCAACgGCGttTGctgtAtCTttTggACTcTgGCCGatACAAtTGCTcaaCCCGCagCaCtGaTcAtTcgTagaACaTTtgAaTGtataAGGgcggag
>query_042%_mutation_forward
tAAAtCtAGTCAgACATgAACtTGGcAccATCTaCACCtCTactAGgTACCTCAGAAGCCgTtACTGaGcCaGtCatgGCctaaaTAgTGagttCGtGCA
>query_043%_mutation_forward
aCAtAtaaAAAtCctcaCaTGCAAAatTgAGGtCgCCTaACttgCcCCGtcgtCAaTACCgcTgCcAagAaaGCtatggCCgCcggAACTgtTctCAtTG
>query_044%_mutation_forward
CGTTTctaTAaTagTgTcgaACACCacGCAacaGGgtAaGatgaTTTcGtAaCAGTGCcTGGgGGAGgGCAAgCTCtctGcGCTtCcaAAgCTGCTAccG
>query_045%_mutation_forward
CtAGttAAAACtCAAagGCttttgtgAgcCAGcgAGCTTcCttTcGtgcTctATGaCGATtGCgAaACTGcGCctTcTTAgGtACAtCAActtAAaCGGc
>query_046%_mutation_forward
tCTCGtTCACTaAaaCcgTGCGgcCGGTgtcaCGGCgGgGtCGcaCGGagaCgctTCAgcCttgGcCGGTAAccgGGTcATCCttAacgTCcGGGGAatt
>query_047%_mutation_forward
GCGCCTTATCCGaTAttTgTCcTgcTttcTgaAAggtaGaAttctAgGggTTAggGtgAgTGGCAtCtGCCAaTGGcgcgAaGAgcgaCAtAttGctcTA
>query_048%_mutation_forward
CAgTtGcgtACTAcaAGCaCCaaGgttacCAtGgcGcCCcGtACtCTCTTGTgGcctATgAGcTCCGCGctgcGacCCTCCagtTTctcCcGGGgatAac
>query_049%_mutation_forward
aAtGTtaGtAgCgctccgAcctaaCtGAtcGgGttgcttGGacCTtgAcTTaGAgcCGGcAcGgTTGAggatcCAGtacCCATaCCatGaTaaaAtGttt
>query_050%_mutation_forward
TtaACtCTtAtGGGCtgGaCGCGCCGgatCcAgtgCCGaGcCaGCtTaTACTTcgTTaTtTcCTgCgCCatGtccgttctagTaGGaGTgatGCcGgAGT
>query_001%_mutation_reverse
CCAACCTTACCAGAGGGCGCCCCAGCTGGCAATTCCGGTTCGCTTGCTGTCCATAAAACCGCCCAGTCTAGCTATCGCCATGTAAGCCCACTGCAAGCTA
>query_002%_mutation_reverse
TAAATTCTCTGAATCAGTTTTTCGCGAATCTGACTCAGcAAACGTCCCAAAACCATGGATTTCACCCCGGTGGTTTCCACGAGCACGTGCATGTGGAAGT
>query_003%_mutation_reverse
TACCCACTCCGTCGGCGCCTTCGTTAaTGTCTGCCATTGGTGCGCCACCGCCTGCAGCCATTGTATTAGGTCCCACACCAGAGGGCGCTGCTGGAGGTTC
>query_004%_mutation_reverse
AACCATCGGCAGCCATACCTGATTaAAATCATTTATTcTTgAAAGATGCAGTCATCCAAATCCACtTTGACCtGATCGCAGGCAGTGCAAGCGTCTGGCA
>query_005%_mutation_reverse
GTGCACGACGCGGtaTGTCCGGCCAATCgGTTTTCCGGCAAGTCTTGCcGtATGTTCTTCTCTGAAGGCGCAAAGGCTCAGGTGGCTcTTAAGCAGATCA
>query_006%_mutation_reverse
CCGTACAGTAGGGgTCGTCTACCTCCTTTTGAaACAGAAACCtGCGCTgCCATACTGGAGGATCATCCGCTGCTGCCCGAATGTAACACTTaGACAAaGC
>query_007%_mutation_reverse
GTAACTTGTATGTGTTGGcAATcGTAGTTTTCTcAAAATGGGAAGTGACGTAACGTGGGAgAACGGAAGTtACGATTTGAaGAAGTTGTatGTTTTTTGG
>query_008%_mutation_reverse
TTTTGCgTAGGCAGGAGGGTTTTTCAGGTGTTTATGTGTTTTTCTCTCCTATTAATTTTGgTATACCTCCTAgGGGGGCTGTcATaTTGTaTCTACGCCT
>query_009%_mutation_reverse
GGCCGAAAaGTGaTGCcGATCTCCAACACCGgCGCAAGGTGCTGCGTGCACGACtCGGCCTGTCCGGCCgcTCAGTTTTCCGGCAAcgCaTGCGGCATaT
>query_010%_mutation_reverse
TTAcACtGGTCTGTGAGGtgCCTGAcTTTacGCAATtATGATTCGCTGCTTGAcGCTGAAGGTGGAGGGCGCTacGGAGCAGATTTcTgCAATGGCCGGA
>query_011%_mutation_reverse
ACaAAGCCTGGGGCgTGGCCGACCGtCTGCGCATTCAGCcGaCCGGACCCAAGGACATGCATCGgAACGAATTCGCCCTTCGCAGAGACCAAAGTTtgAg
>query_012%_mutation_reverse
GgtGCCCTAGACcAATATTACGCGCTATGAaTAACACAAAATTAaaCAGATTTCAgTTCCTCTTcTTCAGTTTTCCCGCGAAAATGGCCAAATCTTAtTC
>query_013%_mutation_reverse
TTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTgTTTCCTGCGTTATCCtCaGAcTCTGTGGgTAACtGTATTACCGCCTTTGtGTtAGCT
>query_014%_mutation_reverse
CCTCACaGAgTAAGCATTGGTAACTGTCAGACCAAGTTTACTCgTgTATAtTTTAGAcTGAcTTAAAACTTCATTTTTAATTgAAAAGcATCTAGcTGAA
>query_015%_mutation_reverse
ATCTGGAaCaGGTGAtCGTGGGTCTCGCGGcATCcTTGCAGCACcGGGGCCAGcTGGTAAGCCCTCCCGgATCGTAGTTATCTAaACGAgGGGGAGTCAG
>query_016%_mutation_reverse
TATTAcGTaCCACACCAGAGtGtGCTGCcGccGGTTCTCCtAGAGGTTGAGGGTCTGGtACTGACTCTGAGTtGCCAcTCTGACCAcAATTGAGTCTTTT
>query_017%_mutation_reverse
CATaGCTGCAGCAATGGCccCAACGTTGCGCAAACTATTAACTcaCGAACTACgTAgTCTgcCTTCCCGGCAACtATTAATAGACTGGAcaattGCGGcT
>query_018%_mutation_reverse
AATAAaAAAgCGCCAtaTTTGACCCGGcACGCGGtAAACcCCgcAGAAAAACACCTGGGtcAGctTCCctGggAAacGTCtAAGTtCCtGCGGgCCTAGA
>query_019%_mutation_reverse
TTttGCATAAATCCAACAGCGcTTGTATAGGCTtTGCCcTCAGaAAtATCTCaATTTCTAAAGTTCCAATATTtTGGcTCCAtGtAaGAATTGTTTAGTA
>query_020%_mutation_reverse
GGtCCGCGGCTGCcGCTGATAGGGCTGCGttGcCGGGGGGATTGGGTTGAGaTtCatagtGGACTtGGGGTCCAAGTcgACCCtCCGTCCCTTgCaTAcC
>query_021%_mutation_reverse
CAtGTTTATGTTTcACTaGGTcTTTaTGAacGtTGGGCaCACAGTGGTTgCATTTTGGGAGGTtAGaaTGCCccCgcCaaCCAGtGAcgaGCCGgTGCCC
>query_022%_mutation_reverse
tAcAacCCAACTaTGACCCGcgACGCGGcAAACgCaTGAaAAAAcCACCTGGGCGAcTCTCCACcaAAACGGTatAccTtCagGCGGCCCcAGACgcAcA
>query_023%_mutation_reverse
ATTgAcAGcttCAAAACcCAaCaaAGcCGCtaGCAAAGaACTTGTGGCtaCttCAaTttAaCAtGgGTTaCAGGattAGcTGCTtTaagTCTCCtaTaAA
>query_024%_mutation_reverse
aGtaACtCgTTgTTGACtACAGAAAgGGtTTGcGATTCTGAaAaGGGtAAGCcCTCTAAACAGcCTTTCTcTaCGTGAGaGAAGCAGATATTTtAtTTaT
>query_025%_mutation_reverse
CTCCGCGcCgTCCAGCaTGCGtgGAtGCgGATCTTCGCTTTTGTGcTACAcGgtGaTGCGGcTGAGGttTCGCAGAGACCTacTTTTTATTTTtAGCTCT
>query_026%_mutation_reverse
AaaCTtggCTGTgCGGTGCTGTATTGgaTGcTGAAAGAGTTCcGCTTaGtCTGaTgGAAcGaGtTCacAGGcTCCGCAGGTgCAaGCGTaTcacTGcTCA
>query_027%_mutation_reverse
AcagTCCaGtcCcACtAtACCGGCTTCCcTCCGAtTtCtTGCcCGCaCGAccCGATGaTgCGCTTGaTccTgGAATGGaCAGGaAtCCGGAgCAAtCGaA
>query_028%_mutation_reverse
gaTTGcaCTGgAGATGgAtGGTCCCCgtgtAGTCCgTGGTcGaCctCcaCTGTCTtgTgTTTTGACtAACggtCTCTTTaTgCCCTaTgTctaTTaTAGc
>query_029%_mutation_reverse
ActTAgTaaCCcTCaAGTGaAcCCGTccTTAaGCCACCACgTtAccAACTaccaAGgACCGCaTAatacCCTCGCcCTcCTAATCgTGTTACCAGgGaaT
>query_030%_mutation_reverse
TCCAAcCTGGAACAAttCTCAAaCCTAgtTCGGTCTATTaaaTgGAaTccTtAGcatTTaTGtCGATTTCGagaTtTTtGTTAAAAAATGgGCaGAaTTc
>query_031%_mutation_reverse
GAtTCTGGgaGCAACTCCCATgCCTgCcgaGaCcCCCtccTCAgAAAGgTtTCAcAAAcGtCGaGgAGATaCgCGaacAcagCGCTtcGGgCCTTAATCA
>query_032%_mutation_reverse
AAaATCgaGGcTcGtCtgCGgTATtTCCTtATAGCccTCCGCCAgACaCAtCCGtCCACAaTtGAcGAtatCAGAAAAttGtCgcTTTTgCACCtgtATA
>query_033%_mutation_reverse
AgcGGTTCTGCgcCatCAtaagCGggTCACGCGaATCcacCagCtGtaGCACCCTTGGGgACttaTCAGGAttGGcCtgTttTAtCCGCGCtgGGgtgTt
>query_034%_mutation_reverse
ATTACAtATTACGtGTGtGGTAACGGGTGgtAgTGGtGCtGGGcTttagtTACctGCaTTCaGTATTAtCAtCAggGTCCAagtTTGTAagTcgGTtcTt
>query_035%_mutation_reverse
gCTCAGTgAGCATggACCctGGAttaCcAGgTaTtaCGAGTCTTcCAacAAcGGGGgGcaGgaGGcgaTGTtTAAtACTgTATcGCCGcTGtaTGaGACC
>query_036%_mutation_reverse
GtCCAGtTGCcatTCCGtaaGGCTGgGGTcGGCAaGtCAtGATAtGGGgAgCTacCAGTcaTGGAAAAAaATtTGAgAaGccaCAAGCACgaCTaGCACG
>query_037%_mutation_reverse
gATCTctGaCaAtATaGGgCCtTcgAGGgAaAgGTaCCGGaTgTGCCAGACCgTtCCacGTgAGGCCtCCTGGCTGaTaAtAGTTCCAAccTGAatAcaC
>query_038%_mutation_reverse
tTgGcAgGGGtAGcggatCGGgTaAAGCtTAaGCcatCGtCGCATaGgATCtcCCgcGAcGcATgtTTTaTCGttgtGtGtgAaGTaAacTGtCcGGAGA
>query_039%_mutation_reverse
AAgCAcGTtgCaGcTtTcTgAcGTatTCaTTCgtTcgTCAGTagGgAcAacCCAgGcAGcTgTAtCTCccaCGAtcCTcTggCGAAgttGcAGtGcAGcG
>query_040%_mutation_reverse
GAtAAaAagGGtccCCATCCGAGTACtgGaTCttcCcATaCGtgGTTggtgccGtcGcTCGAAaGGGCAGGaAGCgatcTCAgGCtTATGaAGCCaCCGC
>query_041%_mutation_reverse
gTTGctACacCtTGTcaACACCccCGaACAaCtAcAACtaCAtgTcccCCcCAgCCcaCGCTTAacTGTaaagCaCCcatCTTGtAcaccgtgAtTcaCc
>query_042%_mutation_reverse
CcaTgGCCcAAGaAGGTccTtTCGgaGcTGGtaCtcCCCcgTGTaCgGggGaAGAgggaaTgcTcGAGGgGaaTGTgGccaGTGGaacGGGCCCgatTcC
>query_043%_mutation_reverse
CatGCgaaGaGACCctTACAtgatCCAcCGgaCcctCGaCCGaTaCaaatGCggTCTTtCtTTCCgcTggCGaCctGTTCGtCGaCTTTgaCtGTCcAGg
>query_044%_mutation_reverse
ACtTCgaGTggaaGTggACAcAGcTcTccAGGcCcacCCGGActAcaTagGGaTggttaTCgGGgGGTcGGTGcGGTcCAaCttgtGGgGAgGCACTgcc
>query_045%_mutation_reverse
CTGttTGCACggAAcCTCCcCGGcAgttAGCgCTttaGatAaCcTTcGTTTaCtTaGCTgCaCCAAcTgaGacGGaaCGCaCGcaTtggGgCAGCcCGCc
>query_046%_mutation_reverse
tGaggaaTCgcTagGggccCTgCCCccCaaTaaTaaCCcCGTTCaaCaGCgTTCgCtaTCAtcgaCTtAcaacttttCgCCaTaTAGGGTcCCacaTTAt
>query_047%_mutation_reverse
CATcTtcTagagAAACCctcTCcGGAtgggACTTGcCgtAgATCgagcTgTccgGtgtgtcTaGcAcgaATgtcggaATTcgcACCCcGtGgcCCcgAAG
>query_048%_mutation_reverse
CgCAcCAGgCCAGcgAAcGTTtagATTtTTGaTaatCCCGGTTGcCaTTagGACGCtTgGTTaGtccagtCtGGcTCCctGCAGttAcTgggggGCCTGg
>query_049%_mutation_reverse
gcgCaacaTCcgAgaGtACctgGAAAAGaGtCTCCcGttgCgTAtcCAgACtattCCAaTtCGaCgcAtgGTtGCtgatagGCTTtTacGCCcgccaCAG
>query_050%_mutation_reverse
aACggcTGCTGTaAgctaTAAGctaAGggCCcAGTTTAtatAttATAGCgcTcaaTtAAaatgAgTtgActCCATtcaCAATTTagGTggTGAGcGtAag
test/query_small.fa 0 → 100644
+ 8
− 0
Voir le fichier @ c09ef38a
>query_001%_mutation_forward
CTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGAT
>query_025%_mutation_forward
CGTccGCTCGTGATGCTTGgAGGTCAtCTCgGCAAACGACTGCAGGaACGCCTGaAcGtATCGtCCCtTCAcCtcCgttAcGtTCTTGTgaCTGGTGAAt
>query_006%_mutation_reverse
ACGTGAAAAGGATgTAGGTGAAGATCCTTTTTGATAATCTCATaGCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCT
>query_026%_mutation_reverse
GtCGTgtcGAtGGggTcGGCaCAaGTCTGTGAGTGCGCCCATaGAaATAAAGTTACcGtAGtAaGGGATGgGCCAcAGtGTGCaAgCGCCCTGGTaCACC
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