Biopython : librairie python pour la

bioinformartique
 Simple manipulation de sequences

from Bio.Seq import Seq

my_seq = Seq("AGTACACTGGT")
print(my_seq)
print(my_seq.complement())
print(my_seq.reverse_complement())
 Simple manipulation de sequences

from Bio.Seq import Seq

my_seq = Seq("AGTACACTGGT")
Affiche l’ADN complementaire
print(my_seq)
print(my_seq.complement())
print(my_seq.reverse_complement())

Affiche l’ADN reverse complementaire

 Lecture d’un fichier Fasta

from Bio import SeqIO

for seq_record in SeqIO.parse("SeqFasta.txt", "fasta"):
print(seq_record.id)
print(seq_record.seq)
print(len(seq_record))
 Lecture d’un fichier Fasta

from Bio import SeqIO

for seq_record in SeqIO.parse("SeqFasta.txt", "fasta"):
print(seq_record.id)
print(seq_record.seq)
print(len(seq_record))

Affiche le nom de la sequence Fasta

N’affiche pas le ‘>’
S’arrete au premier espace
 Lecture d’un fichier Fasta

from Bio import SeqIO

for seq_record in SeqIO.parse("SeqFasta.txt", "fasta"):
print(seq_record.id)
print(seq_record.seq)
print(len(seq_record))

Affiche la sequence nucleique/proteique

Les attributs de l’objet SeqIO en format Fasta

●
.seq → la sequence
●
.id → l’identifiant de la sequence (du > au premier espace non inclus)
●
.description → description (pour un humain) de la sequence
●
.dbxrefs → liste de liens vers les bases de donnees contenant la
sequence
●
.name
●
.letter_annotations
●
.annotations
●
.features
 Liste des formats de sequences lues

●
biopython.org/wiki/SeqIO et biopython.org/wiki/AlignIO
– 29 types de sequences lues
– Fasta, Fastq, Genbank ...
– 12 types d’alignements lus
– clustal, phylip, ...
Les objets de Seq sont des chaines de caracteres
...
my_seq = Seq("GATCG", IUPAC.unambiguous_dna)
for index, letter in enumerate(my_seq):
print("%i %s" % (index, letter))
0 G
1 A
2 T
print(len(my_seq))
5
Exemple de fonctionnalite pour les sequences

●
Calcul du GC%
● from Bio.Seq import Seq
● from Bio.Alphabet import IUPAC
● from Bio.SeqUtils import GC
● my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC",
IUPAC.unambiguous_dna)
● GC(my_seq) → 46.875
 Transcription d’une sequence d’ADN

coding_dna = Seq('ATGGCCATTGTAATG', IUPACUnambiguousDNA())

messenger_rna = coding_dna.transcribe()
print(messenger_rna)
→ Seq('AUGGCCAUUGUAAUG', IUPACUnambiguousRNA())

●
La fonction a change tous les T → U
●
Elle change aussi l’alphabet de la sequence
 Traduction d’une sequence
●
On peut traduire l’ARN mais aussi l’ADN comme avec cet exemple :
from Bio.Seq import Seq

from Bio.Alphabet import IUPAC

coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTTAG", IUPAC.unambiguous_dna)

coding_dna.translate()
→ Seq('MAIVMGR*KG*', HasStopCodon(IUPACProtein(), '*'))

●
La traduction est base sur les tables du NCBI. Par defaut, biopython
utilise le code genetic standard, mais il est possible d’utiliser d’autre
code genetique
coding_dna.translate(table="Vertebrate Mitochondrial")
→ Seq('MAIVMGRWKR*', HasStopCodon(IUPACProtein(), '*'))
 Affichage du code genetique standard

from Bio.Data import CodonTable

standard_table = CodonTable.unambiguous_dna_by_id[1]
print(standard_table)
 Ecrire avec biopython
from Bio.Seq import Seq

from Bio.SeqRecord import SeqRecord

from Bio.Alphabet import generic_protein

from Bio import SeqIO

rec1 = SeqRecord(Seq("MMYQQGCFAGGTVLRLAKDLAENHLDSMVGQAL" \

+"SSAC", generic_protein),

id="gi|14150838|gb|AAK54648.1|AF376133_1",

description="chalcone synthase [Cucumis sativus]")

rec2 = SeqRecord(Seq("YPDYYFRITNREHKAELNPSMCEYMAPSL", generic_protein),

id="gi|13919613|gb|AAK33142.1|",

description="chalcone synthase [Fragaria vesca]")

my_records = [rec1, rec2]

SeqIO.write(my_records, "my_example.faa", "fasta")

 Ecrire avec biopython
from Bio.Seq import Seq

from Bio.SeqRecord import SeqRecord

from Bio.Alphabet import generic_protein

from Bio import SeqIO Declaration et initialisation de l’objet rec1 et rec2

rec1 = SeqRecord(Seq("MMYQQGCFAGGTVLRLAKDLAENHLDSMVGQAL" \

+"SSAC", generic_protein),

id="gi|14150838|gb|AAK54648.1|AF376133_1",

description="chalcone synthase [Cucumis sativus]")

rec2 = SeqRecord(Seq("YPDYYFRITNREHKAELNPSMCEYMAPSL", generic_protein),

id="gi|13919613|gb|AAK33142.1|",

description="chalcone synthase [Fragaria vesca]")

my_records = [rec1, rec2]

SeqIO.write(my_records, "my_example.faa", "fasta")

 Ecrire avec biopython
from Bio.Seq import Seq

from Bio.SeqRecord import SeqRecord

from Bio.Alphabet import generic_protein

from Bio import SeqIO

rec1 = SeqRecord(Seq("MMYQQGCFAGGTVLRLAKDLAENHLDSMVGQAL" \

+"SSAC", generic_protein),

Ecriture des sequences id="gi|14150838|gb|AAK54648.1|AF376133_1",

au format Fasta
description="chalcone synthase [Cucumis sativus]")

rec2 = SeqRecord(Seq("YPDYYFRITNREHKAELNPSMCEYMAPSL", generic_protein),

id="gi|13919613|gb|AAK33142.1|",

description="chalcone synthase [Fragaria vesca]")

my_records = [rec1, rec2]

SeqIO.write(my_records, "my_example.faa", "fasta")

 Conversion de format de fichier

●
Conversion d’une sequence au format genbank en format fasta
● from Bio import SeqIO
● count = SeqIO.convert("orchid.gbk", "genbank",
"example.fasta", "fasta")
 Alignement des sequences
●
Un alignement global est realise par defaut.

● from Bio import pairwise2

● from Bio.SubsMat.MatrixInfo import blosum62
● alignments = pairwise2.align.localds("LSPADKTNVKAA", "PAEKSNV", blosum62, -10, -1)
● print(pairwise2.format_alignment(*alignments[0]))
● seq1 = SeqIO.read("alpha.fa", "fasta")
● seq2 = SeqIO.read("beta.fa", "fasta")
● alignments = pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -0.5)
● print(alignments)
 Alignement des sequences
●
Un alignement global est realise par defaut.

● from Bio import pairwise2

Alignement local
● from Bio.SubsMat.MatrixInfo import blosum62
● alignments = pairwise2.align.localds("LSPADKTNVKAA", "PAEKSNV", blosum62, -10, -1)
● print(pairwise2.format_alignment(*alignments[0]))
● seq1 = SeqIO.read("alpha.fa", "fasta")
● seq2 = SeqIO.read("beta.fa", "fasta")
● alignments = pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -0.5)
● print(alignments)
Alignement global
 Alignement des sequences
●
Un alignement global est realise par defaut.

● from Bio import pairwise2

● from Bio.SubsMat.MatrixInfo import blosum62
● alignments = pairwise2.align.localds("LSPADKTNVKAA", "PAEKSNV", blosum62, -10, -1)
● print(pairwise2.format_alignment(*alignments[0]))
● seq1 = SeqIO.read("alpha.fa", "fasta")
● seq2 = SeqIO.read("beta.fa", "fasta")
● alignments = pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -0.5)
● print(alignments)

Parametres de l’alignement
 Quelques parametres de l’alignement
●
match score
●
mismatch score
●
target open gap score
●
target extend gap score
●
query open gap score
●
query extend gap score
●
mode: local / global
●
aligner.algorithm Ex : 'Smith-Waterman'
●
...
●
En fonction des parametres des gaps, le PairwiseAligner de biopython
choisit le meilleur algorithme d’alignement
Exemple de lecture des fichiers de BLAST (1)

●
La sortie du fichier Blast doit etre en XML
blastx -query t.fa -db nr -out BLASTp.xml -outfmt 5

from Bio import SearchIO

blast_qresult = SearchIO.read("BLASTp.xml", "blast-xml")
blast_slice = blast_qresult[:3]
print(blast_slice)
Exemple de lecture des fichiers de BLAST (1)

●
La sortie du fichier Blast doit etre en XML
blastx -query t.fa -db nr -out BLASTp.xml -outfmt 5

from Bio import SearchIO

blast_qresult = SearchIO.read("BLASTp.xml", "blast-xml")
blast_slice = blast_qresult[:3]
print(blast_slice)
Recupere les 3 premiers hits
Exemple de lecture des fichiers de BLAST (1)

Program: blastp (2.8.1+)

Query: sp|Q5PP28|NAC3_ARATH (394)

NAC domain-containing protein 3 OS=Arabidopsis thaliana OX=3702 GN=...

Target: nr

Hits: ---- ----- ----------------------------------------------------------

# # HSP ID + description

---- ----- ----------------------------------------------------------

0 1 gi|15217677|ref|NP_171725.1| NAC domain containing pro...

1 1 gi|3258572|gb|AAC24382.1| Hypothetical protein [Arabid...

2 1 gi|297848422|ref|XP_002892092.1| NAC domain-containing...

Exemple de lecture des fichiers de BLAST (2)

from Bio import SearchIO

blast_qresult = SearchIO.read("BLASTp.xml", "blast-xml")
blast_hsp1 = blast_qresult[10]
print(blast_hsp1)
print('\n')
blast_hsp2 = blast_qresult[10][0]
print(blast_hsp2)
Exemple de lecture des fichiers de BLAST (2)

Affiche les informations numeriques du HSP

from Bio import SearchIO
blast_qresult = SearchIO.read("BLASTp.xml", "blast-xml")
blast_hsp1 = blast_qresult[10]
print(blast_hsp1)
print('\n')
blast_hsp2 = blast_qresult[10][0]
print(blast_hsp2)

Affiche les memes infos et

l’alignement du HSP
Exemple de lecture des fichiers de BLAST (2)

●
Resultat de blast_hsp1
Query: sp|Q5PP28|NAC3_ARATH

NAC domain-containing protein 3 OS=Arabidopsis thaliana OX=3702 GN=NA...

Hit: gi|1338503851|ref|XP_006305025.2| (389)

NAC domain-containing protein 3 [Capsella rubella]

HSPs: ---- -------- --------- ------ --------------- ---------------------

# E-value Bit score Span Query range Hit range

---- -------- --------- ------ --------------- ---------------------

0 3.5e-137 402.90 404 [0:394] [9:389]

Exemple de lecture des fichiers de BLAST (2)

●
Resultat de blast_hsp2
Query: sp|Q5PP28|NAC3_ARATH NAC domain-containing protein 3 OS=Arabidop...

Hit: gi|1338503851|ref|XP_006305025.2| NAC domain-containing protein ...

Query range: [0:394] (0)

Hit range: [9:389] (0)

Quick stats: evalue 3.5e-137; bitscore 402.90

Fragments: 1 (404 columns)

Query - METPVGLRFCPTDEEIVVDYLWPKNSDRDTSHVDRFINTVPVCRLDPWELPCQSRIKLK~~~SISRT

+E VG RF PTDEE V DYL PKN DTSHVDR I+T+ + DPWELP QSRIKLK~~~ ISRT

Hit - LENTVGFRFRPTDEEFVDDYLRPKNLKLDTSHVDRVISTLTISSFDPWELPSQSRIKLK~~~PISRT
Exemple de lecture des fichiers de BLAST (3)
from Bio.Blast import NCBIXML

result_handle = open('FichiersEtudiant/BLASTp.xml', 'r')

blast_record = NCBIXML.read(result_handle)

E_VALUE_THRESH = 0.01

for alignment in blast_record.alignments:

for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
print("\n****Alignment****")
print("sequence:", alignment.title)
print("length:", alignment.length)
print("e value:", hsp.expect)
print(hsp.query[0:75] + "...")
print(hsp.match[0:75] + "...")
print(hsp.sbjct[0:75] + "...")
Exemple de lecture des fichiers de BLAST (3)
from Bio.Blast import NCBIXML Limite l’affichage des resultats a un seuil
result_handle = open('FichiersEtudiant/BLASTp.xml', 'r')

blast_record = NCBIXML.read(result_handle)

E_VALUE_THRESH = 0.01

for alignment in blast_record.alignments:

for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH: Affiche quelques attributs
print("\n****Alignment****") des objets alignements et
print("sequence:", alignment.title) HSP
print("length:", alignment.length)
print("e value:", hsp.expect)
print(hsp.query[0:75] + "...")
print(hsp.match[0:75] + "...")
print(hsp.sbjct[0:75] + "...")

Limite l’affiche de l’alignement

au 75 premiers caracteres
 Variables contenues dans blast biopython
●
La lecture du fichier blast donne une liste d’objet
●
La variable blast_hsp une cellule de cette liste

● blast_hsp.query_range → (0, 61)

● blast_hsp.evalue → 4.91307e-23
● blast_hsp.hit_start → 0 # start coordinate of the hit sequence
● blast_hsp.query_span → 61 # how many residues in the query sequence
● blast_hsp.aln_span → 61 # how long the alignment is
● blast_hsp.gap_num → 0 # number of gaps
● blast_hsp.ident_num → 61 # number of identical residues
Phylogenie et classification avec biopython
● from Bio import Phylo
● tree = Phylo.read("FichiersEtudiant/simpleFichier.dnd", "newick")
● Phylo.draw_ascii(tree)
● ________________________ A

● ________________________|

● | |________________________ B

● ________________________|

● | | ________________________ C

● | |________________________|

● _| |________________________ D

● |

● | ________________________ E

● | |

● |________________________|________________________ F

● |

● |________________________ G
Connection a des base de donnees distantes

●
Telecharger et/ou parser les donnees de NCBI
– Genome ou sequence au format Fasta ou Genbank
– Obtenir la taxonomie d’une sequence

●
Telecharger les citations de Pubmed

●
Telecharger et/ou parser les donnees de Swiss-Prot, PDB ..
 Exercice

●
Refaites avec biopython l’exercice d’extraction du 10eme
alignement de BLAST