add exercises using biopython

source/Object_Oriented_Programming.rst

@@ -93,6 +93,85 @@ The following python code provides an example of the expected behaviour of objec
 
 :download:`point.py <_static/code/point.py>` .
 
+Exercise
+--------
+
+Use biopython to read a fasta file (:download:`sv40.fasta <_static/data/sv40.fasta>`)
+and display the attributes
+
+* id
+* name
+* description
+* seq
+
+use the module SeqIO in biopython
+A tutorial is available https://biopython.org/wiki/SeqIO ::
+
+    from Bio import SeqIO
+
+    sv40_rcd = SeqIO.read("sv40.fasta", "fasta")
+    print("id =", sv40_rcd.id)
+    print("name =", sv40_rcd.name)
+    print("description =", sv40_rcd.description)
+    print("sequence =", sv40_rcd.seq)
+
+
+Exercise
+--------
+
+Translate the sequence in phase 1, 2, -2 ::
+
+    sv40_seq_phase1 = sv40_rcd.seq
+    sv40_seq_phase2 = sv40_rcd[1:]
+    sv40_seq_phase_2 = sv40_rcd[1:].reverse_complement(id=True)
+
+Exercise
+--------
+
+* Create a sequence with the first 42 nucleotides
+* Translate this sequence
+* Mutate the nucleotide in position 18 'A' -> 'C'
+* and translate the mutated sequence
+
+see tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc28 ::
+
+    short_seq = sv40_seq_phase2[0:42]
+    short_seq.translate()
+    mutable_seq = short_seq.seq.tomutable()
+    mutable_seq[19] = 'C'
+    mutate_seq = mutable_seq.toseq()
+    mutate_seq.translate()
+
+
+Exercise
+--------
+
+Open the file abcd.fasta (:download:`abcd.fasta <_static/data/abcd.fasta>`) and convert it in genbank format
+
+**Hint**:
+the seq alphabet attribute must be set to extended_protein
+see  Bio.Alphabet.IUPAC module ::
+
+    from Bio.Alphabet.IUPAC import extended_protein
+    with open("abcd.fasta", "r") as fasta, open('abcd.gb', 'w') as genbank:
+        for record in SeqIO.parse(fasta, "fasta"):
+            record.seq.alphabet = extended_protein
+            print(len(record.seq))
+            SeqIO.write(record, genbank, 'genbank')
+
+
+Exercice
+--------
+
+Open the file abcd.fasta (:download:`abcd.fasta <_static/data/abcd.fasta>`) and filter out sequence <= 700
+Write the results in fasta file ::
+
+    with open("abcd.fasta", "r") as input, open("abcd_short.fasta", "w") as output:
+        for record in SeqIO.parse(input, "fasta"):
+            if len(record.seq) > 700:
+                SeqIO.write(record, output, 'fasta')
+
+
 Exercise
 --------
 

source/_static/code/bio.py

+from Bio import SeqIO
+
+
+sv40_rcd = SeqIO.read("sv40.fasta", "fasta")
+print("id =", sv40_rcd.id)
+print("name =", sv40_rcd.name)
+print("description =", sv40_rcd.description)
+print("sequence =", sv40_rcd.seq)
+
+translate the sequence in phase 1, 2, -2
+
+sv40_seq_phase1 = sv40_rcd.seq
+sv40_seq_phase2 = sv40_rcd[1:]
+sv40_seq_phase_2 = sv40_rcd[1:].reverse_complement(id=True)
+
+cree une seq avec les 42 premiers nucleotides en phase2
+traduire cette sequence
+muter le nucleotide 18 'A' -> 'C'
+et traduire la sequence muté
+
+
+short_seq = sv40_seq_phase2[0:42]
+short_seq.translate()
+mutable_seq = short_seq.seq.tomutable()
+mutable_seq[19] = 'C'
+mutate_seq = mutable_seq.toseq()
+mutate_seq.translate()
+
+
+from Bio.Alphabet.IUPAC import extended_protein
+with open("abcd.fasta", "r") as fasta, open('abcd.gb', 'w') as genbank:
+    for record in SeqIO.parse(fasta, "fasta"):
+        record.seq.alphabet = extended_protein
+        SeqIO.write(record, genbank, 'genbank')
+
+
+
+with open("abcd.fasta", "r") as input, open("abcd_short.fasta", "w") as output:
+    for record in SeqIO.parse(input, "fasta"):
+        if len(record.seq) > 700:
+            SeqIO.write(record, output, 'fasta')
+

source/_static/data/sv40.fasta

+>gi|965480|gb|J02400.1|SV4CG Simian virus 40 complete genome
+GCCTCGGCCTCTGCATAAATAAAAAAAATTAGTCAGCCATGGGGCGGAGAATGGGCGGAACTGGGCGGAG
+TTAGGGGCGGGATGGGCGGAGTTAGGGGCGGGACTATGGTTGCTGACTAATTGAGATGCATGCTTTGCAT
+ACTTCTGCCTGCTGGGGAGCCTGGGGACTTTCCACACCTGGTTGCTGACTAATTGAGATGCATGCTTTGC
+ATACTTCTGCCTGCTGGGGAGCCTGGGGACTTTCCACACCCTAACTGACACACATTCCACAGCTGGTTCT
+TTCCGCCTCAGAAGGTACCTAACCAAGTTCCTCTTTCAGAGGTTATTTCAGGCCATGGTGCTGCGCCGGC
+TGTCACGCCAGGCCTCCGTTAAGGTTCGTAGGTCATGGACTGAAAGTAAAAAAACAGCTCAACGCCTTTT
+TGTGTTTGTTTTAGAGCTTTTGCTGCAATTTTGTGAAGGGGAAGATACTGTTGACGGGAAACGCAAAAAA
+CCAGAAAGGTTAACTGAAAAACCAGAAAGTTAACTGGTAAGTTTAGTCTTTTTGTCTTTTATTTCAGGTC
+CATGGGTGCTGCTTTAACACTGTTGGGGGACCTAATTGCTACTGTGTCTGAAGCTGCTGCTGCTACTGGA
+TTTTCAGTAGCTGAAATTGCTGCTGGAGAGGCCGCTGCTGCAATTGAAGTGCAACTTGCATCTGTTGCTA
+CTGTTGAAGGCCTAACAACCTCTGAGGCAATTGCTGCTATAGGCCTCACTCCACAGGCCTATGCTGTGAT
+ATCTGGGGCTCCTGCTGCTATAGCTGGATTTGCAGCTTTACTGCAAACTGTGACTGGTGTGAGCGCTGTT
+GCTCAAGTGGGGTATAGATTTTTTAGTGACTGGGATCACAAAGTTTCTACTGTTGGTTTATATCAACAAC
+CAGGAATGGCTGTAGATTTGTATAGGCCAGATGATTACTATGATATTTTATTTCCTGGAGTACAAACCTT
+TGTTCACAGTGTTCAGTATCTTGACCCCAGACATTGGGGTCCAACACTTTTTAATGCCATTTCTCAAGCT
+TTTTGGCGTGTAATACAAAATGACATTCCTAGGCTCACCTCACAGGAGCTTGAAAGAAGAACCCAAAGAT
+ATTTAAGGGACAGTTTGGCAAGGTTTTTAGAGGAAACTACTTGGACAGTAATTAATGCTCCTGTTAATTG
+GTATAACTCTTTACAAGATTACTACTCTACTTTGTCTCCCATTAGGCCTACAATGGTGAGACAAGTAGCC
+AACAGGGAAGGGTTGCAAATATCATTTGGGCACACCTATGATAATATTGATGAAGCAGACAGTATTCAGC
+AAGTAACTGAGAGGTGGGAAGCTCAAAGCCAAAGTCCTAATGTGCAGTCAGGTGAATTTATTGAAAAATT
+TGAGGCTCCTGGTGGTGCAAATCAAAGAACTGCTCCTCAGTGGATGTTGCCTTTACTTCTAGGCCTGTAC
+GGAAGTGTTACTTCTGCTCTAAAAGCTTATGAAGATGGCCCCAACAAAAAGAAAAGGAAGTTGTCCAGGG
+GCAGCTCCCAAAAAACCAAAGGAACCAGTGCAAGTGCCAAAGCTCGTCATAAAAGGAGGAATAGAAGTTC
+TAGGAGTTAAAACTGGAGTAGACAGCTTCACTGAGGTGGAGTGCTTTTTAAATCCTCAAATGGGCAATCC
+TGATGAACATCAAAAAGGCTTAAGTAAAAGCTTAGCAGCTGAAAAACAGTTTACAGATGACTCTCCAGAC
+AAAGAACAACTGCCTTGCTACAGTGTGGCTAGAATTCCTTTGCCTAATTTAAATGAGGACTTAACCTGTG
+GAAATATTTTGATGTGGGAAGCTGTTACTGTTAAAACTGAGGTTATTGGGGTAACTGCTATGTTAAACTT
+GCATTCAGGGACACAAAAAACTCATGAAAATGGTGCTGGAAAACCCATTCAAGGGTCAAATTTTCATTTT
+TTTGCTGTTGGTGGGGAACCTTTGGAGCTGCAGGGTGTGTTAGCAAACTACAGGACCAAATATCCTGCTC
+AAACTGTAACCCCAAAAAATGCTACAGTTGACAGTCAGCAGATGAACACTGACCACAAGGCTGTTTTGGA
+TAAGGATAATGCTTATCCAGTGGAGTGCTGGGTTCCTGATCCAAGTAAAAATGAAAACACTAGATATTTT
+GGAACCTACACAGGTGGGGAAAATGTGCCTCCTGTTTTGCACATTACTAACACAGCAACCACAGTGCTTC
+TTGATGAGCAGGGTGTTGGGCCCTTGTGCAAAGCTGACAGCTTGTATGTTTCTGCTGTTGACATTTGTGG
+GCTGTTTACCAACACTTCTGGAACACAGCAGTGGAAGGGACTTCCCAGATATTTTAAAATTACCCTTAGA
+AAGCGGTCTGTGAAAAACCCCTACCCAATTTCCTTTTTGTTAAGTGACCTAATTAACAGGAGGACACAGA
+GGGTGGATGGGCAGCCTATGATTGGAATGTCCTCTCAAGTAGAGGAGGTTAGGGTTTATGAGGACACAGA
+GGAGCTTCCTGGGGATCCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAG
+TGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATA
+AACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGGTTCAGGGGGAGGTGTGGGAGGTTTTTTA
+AAGCAAGTAAAACCTCTACAAATGTGGTATGGCTGATTATGATCATGAACAGACTGTGAGGACTGAGGGG
+CCTGAAATGAGCCTTGGGACTGTGAATCAATGCCTGTTTCATGCCCTGAGTCTTCCATGTTCTTCTCCCC
+ACCATCTTCATTTTTATCAGCATTTTCCTGGCTGTCTTCATCATCATCATCACTGTTTCTTAGCCAATCT
+AAAACTCCAATTCCCATAGCCACATTAAACTTCATTTTTTGATACACTGACAAACTAAACTCTTTGTCCA
+ATCTCTCTTTCCACTCCACAATTCTGCTCTGAATACTTTGAGCAAACTCAGCCACAGGTCTGTACCAAAT
+TAACATAAGAAGCAAAGCAATGCCACTTTGAATTATTCTCTTTTCTAACAAAAACTCACTGCGTTCCAGG
+CAATGCTTTAAATAATCTTTGGGCCTAAAATCTATTTGTTTTACAAATCTGGCCTGCAGTGTTTTAGGCA
+CACTGTACTCATTCATGGTGACTATTCCAGGGGGAAATATTTGAGTTCTTTTATTTAGGTGTTTCTTTTC
+TAAGTTTACCTTAACACTGCCATCCAAATAATCCCTTAAATTGTCCAGGTTATTAATTCCCTGACCTGAA
+GGCAAATCTCTGGACTCCCCTCCAGTGCCCTTTACATCCTCAAAAACTACTAAAAACTGGTCAATAGCTA
+CTCCTAGCTCAAAGTTCAGCCTGTCCAAGGGCAAATTAACATTTAAAGCTTTCCCCCCACATAATTCAAG
+CAAAGCAGCTGCTAATGTAGTTTTACCACTATCAATTGGTCCTTTAAACAGCCAGTATCTTTTTTTAGGA
+ATGTTGTACACCATGCATTTTAAAAAGTCATACACCACTGAATCCATTTTGGGCAACAAACAGTGTAGCC
+AAGCAACTCCAGCCATCCATTCTTCTATGTCAGCAGAGCCTGTAGAACCAAACATTATATCCATCCTATC
+CAAAAGATCATTAAATCTGTTTGTTAACATTTGTTCTCTAGTTAATTGTAGGCTATCAACCCGCTTTTTA
+GCTAAAACAGTATCAACAGCCTGTTGGCATATGGTTTTTTGGTTTTTGCTGTCAGCAAATATAGCAGCAT
+TTGCATAATGCTTTTCATGGTACTTATAGTGGCTGGGCTGTTCTTTTTTAATACATTTTAAACACATTTC
+AAAACTGTACTGAAATTCCAAGTACATCCCAAGCAATAACAACACATCATCACATTTTGTTTCCATTGCA
+TACTCTGTTACAAGCTTCCAGGACACTTGTTTAGTTTCCTCTGCTTCTTCTGGATTAAAATCATGCTCCT
+TTAACCCACCTGGCAAACTTTCCTCAATAACAGAAAATGGATCTCTAGTCAAGGCACTATACATCAAATA
+TTCCTTATTAACCCCTTTACAAATTAAAAAGCTAAAGGTACACAATTTTTGAGCATAGTTATTAATAGCA
+GACACTCTATGCCTGTGTGGAGTAAGAAAAAACAGTATGTTATGATTATAACTGTTATGCCTACTTATAA
+AGGTTACAGAATATTTTTCCATAATTTTCTTGTATAGCAGTGCAGCTTTTTCCTTTGTGGTGTAAATAGC
+AAAGCAAGCAAGAGTTCTATTACTAAACACAGCATGACTCAAAAAACTTAGCAATTCTGAAGGAAAGTCC
+TTGGGGTCTTCTACCTTTCTCTTCTTTTTTGGAGGAGTAGAATGTTGAGAGTCAGCAGTAGCCTCATCAT
+CACTAGATGGCATTTCTTCTGAGCAAAACAGGTTTTCCTCATTAAAGGCATTCCACCACTGCTCCCATTC
+ATCAGTTCCATAGGTTGGAATCTAAAATACACAAACAATTAGAATCAGTAGTTTAACACATTATACACTT
+AAAAATTTTATATTTACCTTAGAGCTTTAAATCTCTGTAGGTAGTTTGTCCAATTATGTCACACCACAGA
+AGTAAGGTTCCTTCACAAAGATCAAGTCCAAACCACATTCTAAAGCAATCGAAGCAGTAGCAATCAACCC
+ACACAAGTGGATCTTTCCTGTATAATTTTCTATTTTCATGCTTCATCCTCAGTAAGCACAGCAAGCATAT
+GCAGTTAGCAGACATTTTCTTTGCACACTCAGGCCATTGTTTGCAGTACATTGCATCAACACCAGGATTT
+AAGGAAGAAGCAAATACCTCAGTTGCATCCCAGAAGCCTCCAAAGTCAGGTTGATGAGCATATTTTACTC
+CATCTTCCATTTTCTTGTACAGAGTATTCATTTTCTTCATTTTTTCTTCATCTCCTCCTTTATCAGGATG
+AAACTCCTTGCATTTTTTTAAATATGCCTTTCTCATCAGAGGAATATTCCCCCAGGCACTCCTTTCAAGA
+CCTAGAAGGTCCATTAGCTGCAAAGATTCCTCTCTGTTTAAAACTTTATCCATCTTTGCAAAGCTTTTTG
+CAAAAGCCTAGGCCTCCAAAAAAGCCTCCTCACTACTTCTGGAATAGCTCAGAGGCCGAGGCG
\ No newline at end of file