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Parsing data records I

Two sequence records in FASTA format:

>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN

>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN

Challenge #1

Open the file SingleSeq.fasta, read its content line by line and print it

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See the solution to challenge #1

Challenge #2

Open the file SingleSeq.fasta, read its content line by line and write it to another file.

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See the solution to challenge #2

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
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN

Making choices: The if/elif/else statements

if condition1 #if expression in condition1is TRUE
    statements1   #execute statements1
elif condition2 #else if expression in condition2is TRUE
    statements2 #execute statements2...
elif condition3 #etc...
...
…

else:
  statementN

Check these conditions:

• 'ACTC'[0] == 'C' is True or false?
• 'ACTC'[0] == 'A' is True or false?

Operators:

==    !=     =>    <=    >      <

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

  nucl = ['A','C','T','G']
  if 'A' in nucl: print 'A'
  elif 'C' in nucl: print 'C'
  elif 'T' in nucl: print 'T'
  else: print 'G'

nucl = ['A','C','T','G']
if 'A' in nucl: print 'A'
if 'C' in nucl: print 'C'
if 'T' in nucl: print 'T'
if 'G' in nucl: print 'G'

Challenge #3

Read a sequence in FASTA format from the file SingleSeq.fasta and print only the header of the sequence

>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN

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See the solution to challenge #3

Challenge #4

Read a file in FASTA format and write to a new file only the header of the record.

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See the solution to challenge #4

Challenge #5

Read a file in FASTA format and write to a new file only the sequence (without the header).

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See the solution to challenge #5

Challenge: Merge programs 4 and 5

In other words, read a file in FASTA format and write the header to a file and the sequence to a different one.

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See the solution to challenges #4 and #5 merged

Challenge #6

Let’s increase the difficulty just a bit…

• Read a FASTA file line by line
• Save the header in a variable and the sequence in a different one
• Print header and sequence separately

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See the solution to challenge #6

Challenge #7

• Implement challenge #6 by counting the number of cysteine (“C”) residues in the sequence
• Print separately header, sequence and the number of cysteine residues

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See the solution to challenge #7

Challenge #8

• Read a file in FASTA format line-by-line.
• Print or write the record to a file only if the sequence is from Homo sapiens.

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See the solution to challenge #8

Challenge #9

Very often in reality you will need to analyze several sequences….

Consider the content of the file SwissProt-Human.fasta

SwissProt-Human.fasta

>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
>sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ
>sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GNYWHAHMGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN
...
...
...

Download a Uniprot multiple sequence FASTA file. Write the record headers to a new file.

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See the solution to challenge #9

Challenge #10

Read a multiple sequence FASTA file and write the sequences to a new file separated by a blank line

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See the solution to challenge #10

Challenge #11

Read a file in FASTA format and copy to a new file the records’ Accession Numbers (AC).

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See the solution to challenge #11

Challenge #12

• Read FASTA records from a file
• Count (and print) the cysteine residues in each sequence.

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See the solution to challenge #12

Challenge #13

Read the multiple sequence FASTA file sprot_prot.fasta and write to a new file only the records from Homo sapiens.

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See the solution to challenge #13

Challenge #14 homework

• Read a multiple sequence file in FASTA format and only write to a new file the records the sequences of which start with a methionine (‘M’) and have at least two tryptophan residues (‘W’)

First:

• 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’)

Then

• 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’)

Finally merge the two steps

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See the solution to challenge #14

Challenge #15 homework

Read a Genbank record and write to a file the nucleotide sequence in FASTA format. Extract and write to a file the gene sequence from the Candida albicans genomic DNA, chromosome 7, complete sequence (file ap006852.gbk)

Try to write it in FASTA format:

AP006852
ccactgtccaatggctcaacacgccaatcatcatacaatacccccaacaggaatcaccaa
agtactgatgcttctcactatcaatagtttgtactttcaccacacaatagcagatgatcc
atctaaatccaccttcctatcgatcgtgaccacccccataaaataggtcaactccataaa
cacctccatcaccaacgctagactcacaacccagaacatgttaatcaaccggtgggccaa
Gtaccgttgtagctctctcgtaaacacaagaaccaacaccaaacaacatactacaactga
...
...

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See the solution to challenge #15

Parsing data records

• Start by visually inspecting the file you want to parse

• Identify the information you want to extract

• Identify separators to select your information using if conditions

• Use lists if you have to compare data from different files

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