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Parsing data records

Parsing data records. > sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY

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Parsing data records

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  1. Parsing data records

  2. >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN

  3. A sequence record in FASTA format >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN

  4. seq = ">sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens \ MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS\ WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY\ LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY\ YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD\ AGEGEN" for i in seq: print i

  5. seq = open("SingleSeq.fasta") for line in seq: print line

  6. seq = open("SingleSeq.fasta") seq_2 = open("SingleSeq-2.fasta") for line in seq: seq_2.write(line) seq_2.close()

  7. Writing different things depending on a condition Read a sequence in FASTA format and print only the header of the sequence >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN

  8. seq = open("SingleSeq.fasta") for line in seq: if line[0] == '>': print line >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN

  9. Making choices: The if/elif/else statements if <condition 1>: if expression in <condition1> is TRUE <statements 1> execute statements 1 [elif <condition 2>]: else if exp in <condition2> is TRUE <statements 2>] execute statements 2.... [elif <condition 3>]: etc... pass] … [else: <statements N>]

  10. Write different things depending on a condition >>> s="MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAE" >>> s_len = float(len(s)) >>> G_num = s.count('G’) >>> A_num= s.count('A’) >>> freq_G = G_num/s_len >>> freq_A = A_num/s_len >>> print freq_G 0.116666666667 >>> print freq_A 0.216666666667

  11. Write different things depending on a condition >>> s="MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAE" >>> s_len = float(len(s)) >>> G_num = s.count('G’) >>> A_num = s.count('A’) >>> freq_G = G_num/s_len >>> freq_A = A_num/s_len >>> print freq_G 0.116666666667 >>> print freq_A 0.216666666667 >>> if freq_G > freq_A: ... print "Gly is more frequent than Ala" ... eliffreq_G < freq_A: ... print "Ala is more frequent than Gly" ... else: ... print "The frequency of Gly and Ala is the same" ... Ala is more frequent than Glycines

  12. The if/elif/else construct produces different effects compared with the use of a series ofif conditions

  13. seq = open("SingleSeq.fasta") for line in seq: if line[0] == '>': print line seq = open("SingleSeq.fasta") for line in seq: if line[0] != '>': print line

  14. seq = open("SingleSeq.fasta") for line in seq: if line[0] != '>': print line == != => <= > <

  15. Exercises 1, 2, and 3 1) Read a file in FASTA format and write to a new file only the header of the record. 2) Read a file in FASTA format and write to a new file only the sequence (without the header). 3) Merge 1) and 2). In other words, read a file in FASTA format and write the header to a file and the sequence to a different one.

  16. fasta = open('SingleSeq.fasta') header = open('header.txt', 'w’) for line in fasta: if line[0] == '>': header.write(line) header.close()

  17. fasta = open('SingleSeq.fasta') seq= open('seq.txt','w') for line in fasta: if line[0] != '>': seq.write(line) seq.close()

  18. fasta = open('SingleSeq.fasta') header = open('header.txt', 'w') seq = open('seq.txt','w') for line in fasta: if line[0] == '>': header.write(line) else: seq.write(line) header.close() seq.close()

  19. Let’s increase the difficulty just a bit…

  20. seq_fasta = open("SingleSeq.fasta") seq = '' for line in seq_fasta: if line[0] == '>': header = line else: seq = seq + line.strip() num_cys = seq.count("C") print header, seq, num_cys

  21. Exercise 4 4) Read a file in FASTA format. Print or write the record to a file only if the sequence is from Homo sapiens.

  22. seq_fasta = open("SingleSeq.fasta") seq = '' header = '' for line in seq_fasta: if line[0] == '>': if "Homo sapiens" in line: header = line else: if header: seq = seq + line if header: print header + seq else: print "The record is not from H. sapiens"

  23. In general, you will need to analyse several sequences….

  24. SwissProt-Human.fasta >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN >sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE EQNKEALQDVEDENQ >sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSW RVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESK VFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFS VFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDE EAGEGN ... ... ...

  25. Read the records from a file and write them to a new file fasta = open('SwissProt-Human.fasta') fasta_2 = open('SwissProt-Human_2.fasta', 'w') for line in fasta: fasta_2.write(line) this must be a string

  26. Strings can be concatenated >>> print "ACTGGTA" + "ATGTAACTT" ACTGGTAATGTAACTT Strings can be indexed and sliced >>> s = "ACTGGTA" >>> s[0] 'A' >>> s[1:3] 'CT' String elements cannot be re-assigned >>> s[2] = 'Z' Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: 'str' object does not support item assignment

  27. Read the sequences from a file and write them to a new file Number the lines starting from 1 fasta = open('SwissProt-Human.fasta') fasta_2 = open('SwissProt-Human_2.fasta', 'w') n = 0 for line in fasta: n = n + 1 l_n = str(n) fasta_2.write(l_n + "\t" + line) fasta_2.close()

  28. >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN >sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE EQNKEALQDVEDENQ >sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSW RVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESK VFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFS VFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDE EAGEGN ... ... ...

  29. Exercise 5 5) Download a Uniprot multiple sequence FASTA file. Write the record headers to a new file.

  30. fasta = open('SwissProt-Human.fasta') headers = open('headers.txt', 'w') for line in fasta: if line[0] == '>': headers.write(line) headers.close()

  31. >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN >sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE EQNKEALQDVEDENQ >sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSW RVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESK VFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFS VFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDE EAGEGN ... ... ...

  32. Exercise 6 6) Read a multiple sequence FASTA file and write the sequences to a new file separated by a blank line

  33. fasta = open('SwissProt-Human.fasta.fasta') seqs = open('seqs.txt', 'w') for line in fasta: if line[0] == '>’: seqs.write('\n') elifline[0] != '>': seqs.write(line) seqs.close() seqs.write(line.strip() + '\n’)

  34. Exercise 7 7) Read a multiple sequence FASTA file and write to a new file only the records from Homo sapiens.

  35. fasta = open('sprot_prot.fasta') output = open('homo_sapiens.fasta', 'w') seq = '' for line in fasta: if line[0] == '>' and seq == '': header = line elif line[0] != '>': seq = seq + line elif line[0] == '>' and seq != '': if "Homo sapiens" in header: output.write(header + seq) header = line seq = '' if "Homo sapiens" in header: output.write(header + seq) output.close()

  36. Exercise 8 8) Read FASTA records from a file and count the cysteine residues in each sequence.

  37. Read the records from a file and count the cysteine residues in each sequence fasta = open('sprot_prot.fasta') seq = '' for line in fasta: if line[0] == '>' and seq == '': header = line[4:10] elif line[0] != '>': seq = seq + line.strip() elif line[0] == '>' and seq != '': cys_num = seq.count('C') print header, ': ', cys_num header = line[4:10] seq = '' print header, ': ', cys_num

  38. Exercises 9, 10, and 11 9) Read a multiple sequence file in FASTA format and write to a new file only the records of the sequences starting with a methionine ('M'). 10) Read a multiple sequence file in FASTA format and write to a new file only the records of the sequences having at least two tryptophan residues ('W'). 11) Read a multiple sequence file in FASTA format and write to a new file only the records the sequences of which start with a methionine ('M') and have at least two tryptophans ('W').

  39. outfile = open('SwissProtHuman-Filtered.fasta','w') fasta = open('SwissProtHuman.fasta','r') seq = '' for line in fasta: if line[0:1] == '>' and seq == '': header = line elif line [0:1] != '>': seq= seq + line elif line[0:1] == '>' and seq != '': TRP_num= seq.count('W') if seq[0] == 'M' and TRP_num > 1: outfile.write(header + seq) seq= '' header = line TRP_num = seq.count('W') if seq[0] == 'M' and TRP_num > 1: outfile.write(header + seq) outfile.close()

  40. In many cases you will need to compare data from different files

  41. SwissProt-Human.fasta >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD AGEGEN >sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE EQNKEALQDVEDENQ >sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSW RVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESK VFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFS VFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDE EAGEGN ... ... ... cancer-expressed.txt

  42. 1) Read 10 SwissProt ACs from a file 2) Store them into a data structure cancer_file = open('cancer-expressed.txt') cancer_list = [] for line in cancer_file: AC = line.strip() cancer_list.append(AC) print cancer_list

  43. List data structure A list is a mutableordered collection of objects The elements of a list can be any kind of object: numbers strings tuples lists dictionaries function calls etc. L = [1, [2,3], 4.52, ‘DNA’] L = [] The empty list

  44. >>> L = [1,”hello”,12.1,[1,2,”three”],”seq”,(1,2)] >>> L[0] # indexing 1 >>> L[3] # indexing [1, 2, ’three'] >>> L[3][2] # indexing ‘three’ >>> L[-1] # negative indexing (1, 2) >>> L[2:4] # slicing [12.1, [1, 2, ‘three’]] >>> L[2:] # slicing shorthand [12.1, [1, 2, ‘three’], ‘seq’, (1, 2)] >>>

  45. The elements of a list can be changed/replaced after the list has been defined These operations CHANGE the list >>> l = [2,3,5,7,8,['a','b'],'a','b','cde'] >>> l[0] = 1 >>> l [1, 3, 5, 7, 8, ['a', 'b'], 'a', 'b', 'cde'] >>> l[0:3] = 'DNA' >>> l ['D', 'N', 'A', 7, 8, ['a', 'b'], 'a', 'b', 'cde'] >>> del l[0:5] >>> l [['a', 'b'], 'a', 'b', 'cde'] >>> l.append('DNA') >>> l [['a', 'b'], 'a', 'b', 'cde', 'DNA'] >>> l.extend('dna') >>> l [['a', 'b'], 'a', 'b', 'cde', 'DNA', 'd', 'n', 'a'] >>>

  46. The elements of a list can be changed/replaced after the list has been defined >>> l = [1,3,5,7,8,['a','b'],'a','b','cde'] >>> l.count(‘a’) >>> l 1 >>> l.index(8) 4 >>> l.insert(4, 80) >>> l [1, 3, 5, 7, 80, 8, [‘a’, ‘b’], ‘a’, ‘b’, ‘cde’] >>> l.pop(4) 80 >>> l [1, 3, 5, 7, 8, [‘a’, ‘b’], ‘a’, ‘b’, ‘cde’] >>> l.pop() ‘cde’ >>> l [1, 3, 5, 7, 8, [‘a’, ‘b’], ‘a’, ‘b’] >>> l.remove(8) [1, 3, 5, 7, [‘a’, ‘b’], ‘a’, ‘b’]

  47. The elements of a list can be changed/replaced after the list has been defined >>> l = [4, 3, 2, 1, 5, 6, 7, 8] >>> l.reverse() >>> l [8, 7, 6, 5, 1, 2, 3, 4] >>> new = sorted(l) >>> new [1, 2, 3, 4, 5, 6, 7, 8] >>> l [8, 7, 6, 5, 1, 2, 3, 4] >>> l.sort() >>> l [1, 2, 3, 4, 5, 6, 7, 8]

  48. Putting together lists and loops range()andxrange() built-in functions >>> range(10) [0, 1, 2, 3, 4, 5, 6, 7, 8, 9] >>> range(1, 11) [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] >>> range(0, 30, 5) [0, 5, 10, 15, 20, 25] >>> range(0, 10, 3) [0, 3, 6, 9] >>> range(0, -10, -1) [0, -1, -2, -3, -4, -5, -6, -7, -8, -9] >>> range(0) [] >>> range(1, 0) [] # the xrange()method ismore commonly used in for loops than range() >>>for i in xrange(5): … print i … 0,1,2,3,4 Thexrange()method generates the values upon call, i.e. it does not store them into a variable

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