Python for Bioinformatics

Transcription

1 Python for Bioinformatics A look into the BioPython world... Christian Skjødt csh@cbs.dtu.dk

2 Today s program 09-10: 10-12: 12-13: : : 16:00-17: Lecture: Introduction to BioPython Exercise: Working with sequences and Alignments Lunch Break Lecture: Accessing online databases and running BLAST using BioPython Exercise: A BLAST of BioPython Summary and Conclusion

3 FROM THE BEGINNING: A 10 minutes crash course in Python primitives...

4 Getting Python

5 Using Python: Two Modes

6 Using Python Data Types e-10

7 Using Python Data Types [1,5,3,6,2] ["The Holy Grail", "The Life of Brian"] [1,"yes",4.10,[1,2,3]]

8 Assigning Variables to Values A = 26 B = "Christian" Using Variables C = "My name is " + B + ", I am " + str(a) print C My name is Christian, I am 26

9 Arithmetical operations (math operations) x = y = x + y x - y x * y x / y x // y x % y x ** y pow(x, y) addition subtraction multiplication division floored division modulus - remainder of x/y exponentiation another way to do exponentiation

10 Accessing Data From Sequences: Strings, Lists and Tuples A = (1,2,3,4) print A[2] Obtaining a single item from a list using [2] 3 print A[0:2] (1,2) Obtaining multiple items from a list using [0:2] B = "ATTTGACGAATATATA" print B[-4:] TATA Can be used to access letters from strings as well. Obtaining the last 4 characters from a string using [-4:]

11 Accessing Data From Dictionaries IUPAC = {"A": "Ala", "C": "Cys", "E": "Glu"} print "C stands for the amino acid", IUPAC['C'] C stands for the amino acid Cys From A string within a List within a Dictionary D = {"sites": ["ATGCGT", "ATTGAG", "AGGTGC"]} print D["sites"][1][3:] GAG

12 Accessing Data Running Through Items in a Collection values = [4.12, 6.21, -0.21] for x in values: print x IUPAC = {"A": "Ala", "C": "Cys", "E": "Glu"} for amino in IUPAC: print IUPAC[ amino ] Ala Cys Glu

13 Using Calls Function Call A = "ATTGACGATTGAC" len(a) 13 Method Call A = "ATTGACGATTGAC" A.lower() attgacgattgac

14 INTRODUCTION TO BIOPYTHON Computational molecular biology made easy...

15 Getting started with BioPython...

16 Getting started with BioPython... To begin using BioPython inside Python we simply have to import the module! BioPython contain a number of nested modules (modules within modules). This can be a bit confusing at first, but you will get used to it! import Bio from Bio import Blast from Bio.Alphabet import IUPAC

17 SEQUENCES AND ALPHABETS

18 The Alphabet The BioPython module contains alphabets to declare a sequence type such as DNA and Proteins. from Bio import Alphabet print Alphabet.ThreeLetterProtein.letters ['Ala', 'Asx', 'Cys', 'Asp', 'Glu', 'Phe', 'Gly', 'His', 'Ile', 'Lys', 'Leu', 'Met', 'Asn', 'Pro', 'Gln', 'Arg', 'Ser', 'Thr', 'Sec', 'Val', 'Trp', 'Xaa', 'Tyr', 'Glx'] from Bio.Alphabet import IUPAC print IUPAC.IUPACProtein.letters print IUPAC.unambiguous_dna.letters ACDEFGHIKLMNPQRSTVWY GATC

19 The SeqObject This objects is composed of a sequence of a specific type (alphabet) from Bio.Seq import Seq my_gene = Seq("CCGGGTT", IUPAC.unambiguous_dna) my_gene Seq('CCGGGTT', IUPACUnambiguousDNA()) my_gene.transcribe() Seq('CCGGGUU', IUPACUnambiguousRNA()) my_gene.translate() Seq('PG', IUPACProtein()) my_gene[4:] Seq('GTT', IUPACUnambiguousDNA())

20 The SeqRecord SeqRecord is a python Class that represents a sequence record containing the sequence itself, name and id. Much like an entry from a fasta file. from Bio.SeqRecord import SeqRecord my_record = SeqRecord( my_gene, id="001", name="mygene1", description="my first gene") print my_record ID: 001 Name: MyGene1 Description: My first gene Number of features: 0 Seq('CCGGGTT', IUPACUnambiguousDNA())

21 INPUT/OUTPUT reading and writing biological file formats

22 The SeqIO module This module contains methods for reading and writing sequence files and handle them as SeqRecord objects. from Bio import SeqIO Reading Sequence files If there is only one sequence use SeqIO.read(): hbg = SeqIO.read( "../data/human_beta_globin.fasta", "fasta" ) print hbg ID: ENA V00499 V Name: ENA V00499 V Description: ENA V00499 V Human germ line gene for beta-globin. : Location: Number of features: 0 Seq ('CCCTGTGGAGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGA GCAGGGAGGG...ACT', SingleLetterAlphabet())

23 The SeqIO module If there is more than one sequence use SeqIO.parse() for record in SeqIO.parse( "../data/hiv-1_m-b.fasta", "fasta" ): print record.id, "- length:", len(record.seq) sp P03378 ENV_HV1A2 - length: 855 sp P03349 GAG_HV1A2 - length: 502 sp P03407 NEF_HV1A2 - length: 210 sp P03369 POL_HV1A2 - length: 1437 sp P04623 REV_HV1A2 - length: 116 sp P04614 TAT_HV1A2 - length: 101 sp P TAT_HV1A2 - length: 72 sp P03402 VIF_HV1A2 - length: 192 sp P05952 VPR_HV1A2 - length: 97 sp P05949 VPU_HV1A2 - length: 81

24 The SeqIO module Writing works in the opposite way, turning one or more SeqRecord objects into a file. SeqIO.write( my_record, "../data/my_gene.gbk", "genbank" ) 1 SeqIO.read( "../data/my_gene.gbk", "genbank" ) SeqRecord(seq=Seq('CCGGGTT', IUPACAmbiguousDNA()), id='001', name='mygene1', description='my first gene', dbxrefs=[])

25 ALIGNMENTS reading and analysing alignments

26 Parsing or Reading Sequence Alignments We have two functions for reading in sequence alignments, Bio.AlignIO.read() and Bio.AlignIO.parse() for files containing one or multiple alignments respectively from Bio import AlignIO alignment = AlignIO.read(open("PF05371_seed.sth"), "stockholm") print "Alignment length", alignment.get_alignment_length() Alignment length 52 for record in alignment : print record.seq, "-, record.id AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA - COATB_BPIKE/30-81 AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA - Q9T0Q8_BPIKE/1-52 DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA - COATB_BPI22/32-83 AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA - COATB_BPM13/24-72 AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA - COATB_BPZJ2/1-49

27 Writing Sequence Alignments We ve talked about using Bio.AlignIO.read() for alignment input (reading files), and now we ll look at Bio.AlignIO.write() which is for alignment output (writing files). from Bio.Align import MultipleSeqAlignment Use an alphabet to declare which sequence it is from Bio.Alphabet import generic_dna Create an empty alignment align = MultipleSeqAlignment([ SeqRecord(Seq("ACTGCTAGCTAG", generic_dna), id="alpha"), SeqRecord(Seq("ACT-CTAGCTAG", generic_dna), id="beta"), SeqRecord(Seq("ACTGCTAGDTAG", generic_dna), id="gamma"), ]) We can write them to a PHYLIP format file: AlignIO.write(align, "my_example.phy", "phylip") 1

28 EXERCISE 1 Working with sequences and alignments