1. Sequence File Parsing using Biopython
BCHB524 Lecture 11
BCHB524 - Edwards

2. Review Modules in the standard-python library: Plus lots, lots more.
sys, os, os.path – access files, program environment
zipfile, gzip – access compressed files directly
urllib – access web-resources (URLs) as files
csv – read delimited line based records from files
Plus lots, lots more.
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3. BioPython
Additional modules that make many common bioinformatics tasks easier
File parsing (many formats) & web-retrieval
Formal biological alphabets, codon tables, etc
Lots of other stuff…
Have to install separately
Not part of standard python, or Enthought
biopython.org
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4. Biopython: Fasta format
Most common biological sequence data format
Header/Description line
>accession description
Multi-accession sometimes represented
accession1|accession2|accession3
lots of variations, no standardization
No prescribed format for the description
Other lines
sequence, one chunk per line.
Usually all lines, except the last, are the same length.
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5. BioPython: Bio.SeqIO
import Bio.SeqIO import sys # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "fasta"):     # Print out the various elements of the SeqRecord     print "\n------NEW SEQRECORD------\n"     print "seq_record.id:\n\t", seq_record.id     print "seq_record.description:\n\t",seq_record.description     print "seq_record.seq:\n\t",seq_record.seq seqfile.close()
import Bio.SeqIO
import sys
# Check the input
if len(sys.argv) < 2:
print >>sys.stderr, "Please provide a sequence file"
sys.exit(1)
# Get the sequence filename
seqfilename = sys.argv[1]
# Open the FASTA file and iterate through its sequences
seqfile = open(seqfilename)
for seq_record in Bio.SeqIO.parse(seqfile, "fasta"):
# Print out the various elements of the SeqRecord
print "repr(seq_record):", repr(seq_record)
print "seq_record.id:", seq_record.id
print "seq_record.description:",seq_record.description
print "repr(seq_record.seq):",repr(seq_record.seq)
print "seq_record.seq:",seq_record.seq
print "len(seq_record):",len(seq_record)
seqfile.close()
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6. Biopython: Other formats
Genbank format
From NCBI, also format for RefSeq sequence
UniProt/SwissProt flat-file format
From UniProt for SwissProt and TrEMBL
UniProt-XML format:
Use the gzip module to handle compressed sequence databases
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7. BioPython: Bio.SeqIO
import Bio.SeqIO import sys # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "genbank"):     # Print out the various elements of the SeqRecord     print "\n------NEW SEQRECORD------\n"     print "seq_record.id:\n\t", seq_record.id     print "seq_record.description:\n\t",seq_record.description     print "seq_record.seq:\n\t",seq_record.seq seqfile.close()
import Bio.SeqIO
import sys
# Check the input
if len(sys.argv) < 2:
print >>sys.stderr, "Please provide a sequence file"
sys.exit(1)
# Get the sequence filename
seqfilename = sys.argv[1]
# Open the FASTA file and iterate through its sequences
seqfile = open(seqfilename)
for seq_record in Bio.SeqIO.parse(seqfile, "fasta"):
# Print out the various elements of the SeqRecord
print "repr(seq_record):", repr(seq_record)
print "seq_record.id:", seq_record.id
print "seq_record.description:",seq_record.description
print "repr(seq_record.seq):",repr(seq_record.seq)
print "seq_record.seq:",seq_record.seq
print "len(seq_record):",len(seq_record)
seqfile.close()
BCHB524 - Edwards

8. BioPython: Bio.SeqIO
import Bio.SeqIO import sys # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "swiss"):     # Print out the various elements of the SeqRecord     print "\n------NEW SEQRECORD------\n"     print "seq_record.id:\n\t", seq_record.id     print "seq_record.description:\n\t",seq_record.description     print "seq_record.seq:\n\t",seq_record.seq seqfile.close()
import Bio.SeqIO
import sys
# Check the input
if len(sys.argv) < 2:
print >>sys.stderr, "Please provide a sequence file"
sys.exit(1)
# Get the sequence filename
seqfilename = sys.argv[1]
# Open the FASTA file and iterate through its sequences
seqfile = open(seqfilename)
for seq_record in Bio.SeqIO.parse(seqfile, "fasta"):
# Print out the various elements of the SeqRecord
print "repr(seq_record):", repr(seq_record)
print "seq_record.id:", seq_record.id
print "seq_record.description:",seq_record.description
print "repr(seq_record.seq):",repr(seq_record.seq)
print "seq_record.seq:",seq_record.seq
print "len(seq_record):",len(seq_record)
seqfile.close()
BCHB524 - Edwards

9. BioPython: Bio.SeqIO
import Bio.SeqIO import sys # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "uniprot-xml"):     # Print out the various elements of the SeqRecord     print "\n------NEW SEQRECORD------\n"     print "seq_record.id:\n\t", seq_record.id     print "seq_record.description:\n\t",seq_record.description     print "seq_record.seq:\n\t",seq_record.seq seqfile.close()
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10. BioPython: Bio.SeqIO and gzip
import Bio.SeqIO import sys import gzip # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = gzip.open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "fasta"):     # Print out the various elements of the SeqRecord     print "\n------NEW SEQRECORD------\n"     print "seq_record.id:\n\t", seq_record.id     print "seq_record.description:\n\t",seq_record.description     print "seq_record.seq:\n\t",seq_record.seq seqfile.close()
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11. What about the other "stuff"
BioPython makes it easy to get access to non-sequence information stored in "rich" sequence databases
Annotations
Cross-References
Sequence Features
Literature
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12. BioPython: Bio.SeqIO
import Bio.SeqIO import sys import gzip # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = gzip.open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "uniprot-xml"):     # What else is available in the SeqRecord?     print "\n------NEW SEQRECORD------\n"     print "repr(seq_record)\n\t",repr(seq_record)     print "dir(seq_record)\n\t",dir(seq_record)     break seqfile.close()
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13. BioPython: Bio.SeqRecord
import Bio.SeqIO import sys import gzip # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the FASTA file and iterate through its sequences seqfile = gzip.open(seqfilename) for seq_record in Bio.SeqIO.parse(seqfile, "uniprot-xml"):     # Print out the various elements of the SeqRecord     print "\n------NEW SEQRECORD------\n"     print "seq_record.annotations\n\t",seq_record.annotations     print "seq_record.features\n\t",seq_record.features     print "seq_record.dbxrefs\n\t",seq_record.dbxrefs     print "seq_record.format('fasta')\n",seq_record.format('fasta')     break seqfile.close()
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14. BioPython: Random access
Sometimes you want to access the sequence records "randomly"…
…to pick out the ones you want (by accession)
Why not make a dictionary, with accessions as keys, and SeqRecord values?
Use SeqIO.to_dict(…)
What if you don't want to hold it all in memory
Use SeqIO.index(…)
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15. BioPython: Bio.SeqIO.to_dict(…)
import Bio.SeqIO import sys # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Open the sequence database seqfile = open(seqfilename) # Use to_dict to make a dictionary of sequence records sprot_dict = Bio.SeqIO.to_dict(Bio.SeqIO.parse(seqfile, "uniprot-xml")) # Close the file seqfile.close() # Access and print a sequence record print sprot_dict['Q6GZV8']
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16. BioPython: Bio.SeqIO.index(…)
import Bio.SeqIO import sys # Check the input if len(sys.argv) < 2:     print >>sys.stderr, "Please provide a sequence file"     sys.exit(1) # Get the sequence filename seqfilename = sys.argv[1] # Use index to make an out of core dict of seq records sprot_index = Bio.SeqIO.index(seqfilename, "uniprot-xml") # Access and print a sequence record print sprot_index['Q6GZV8']
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17. Exercises
0. Read through and try the examples from Chapters 2-5 of BioPython's Tutorial.
1a. Download human proteins from RefSeq and compute amino-acid frequencies for the (RefSeq) human proteome.
Which amino-acid occurs the most? The least?
Hint: access RefSeq human proteins in human.protein.fasta.gz from the course data-folder.
1b. Download human proteins from SwissProt and compute amino-acid frequencies for the SwissProt human proteome.
Hint: access SwissProt human proteins from -> “Taxonomic divisions”
1c. How similar are the human amino-acid frequencies of in RefSeq and SwissProt?
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18. Homework 6 Due Monday, October 10. Exercise 1 from Lecture 10
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