Python Assignment 5

Parsing a FASTA file with Biopython

Exercise 1

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#!/usr/bin/env python
from Bio import SeqIO, SeqUtils
import re
handle = open('./exons.fasta', 'r')
records = SeqIO.parse(handle, 'fasta')
q1 = 0
len2id = dict()
seq2time = dict()
exon2GC = dict()
# iterate through records
for r in records:
    q1 += 1
    # sequence
    seq = str(r.seq)
    # length
    l = str(len(seq))
    try:
        len2id[l].append(r.id)
    except KeyError:
        len2id[l] = [r.id]
    # repeats
    pattern = r'A{20,}|C{20,}|G{20,}|T{20,}'
    q5 = re.findall(pattern, seq.upper())
    q5 = len(q5)
    # identical sequence
    try:
        seq2time[seq] += 1
    except KeyError:
        seq2time[seq] = 1
    # q7 and q8
    ids = r.id.split('|')
    if ids[0] == 'ENSG00000006831':
        exon = ids[-1]
        GC = SeqUtils.GC(seq)
        exon2GC[exon] = GC
 
# calculate
q2 = len(len2id['3408'])
lengths = map(int, len2id.keys())
q3a = len2id[str(min(lengths))]
q3b = len(q3a) > 1
q4a = len2id[str(max(lengths))]
q4b = len(q4a) > 1
times = seq2time.values()
q6 = any([time > 1 for time in times])
q7b = exon2GC.keys()
q7a = len(q7b)
maxGC = max(exon2GC.values())
q8 = [(exon, exon2GC[exon]) for exon in q7b if exon2GC[exon] == maxGC]
 
# print results
print '1. How many records are in the file?\nAnswer:', q1
print '2. How many records have a sequence length of 3408?\nAnswer:', q2
print '3. What is the header for the record with the shortest sequence? Is there more than one record with that length?\nAnswer:', q3a, '\nAnswer:', q3b
print '4. What is the title for the record with the longest sequence? Is there more than one record with that length?\nAnswer:', q4a, '\nAnswer:', q4b
print '5. How many records have sequences which contain 20-nucleotide repeats (the same nucleotide repeated at least 20 consecutive times) in their sequences?\nAnswer:', q5
print '6. Do any records contain 100% identical sequences?\nAnswer:', q6
print '7. The records in the file represent exons. How many exons can you find for the gene with Ensembl id ENSG00000006831? What are their exon IDs?\nAnswer:', q7a, '\nAnswer', q7b
print '8. Which of the exons of ENSG00000006831 has the highest GC content?\nAnswer:', q8


result: 

[bionc01: Assignment5] python e1.py
1. How many records are in the file?
Answer: 212645
2. How many records have a sequence length of 3408?
Answer: 4
3. What is the header for the record with the shortest sequence? Is there more than one record with that length?
Answer: ['ENSG00000139737|ENST00000358679|13|78272023|78338377|1|ENSE00001735712', 'ENSG00000157224|ENST00000394605|7|90013035|90142716|1|ENSE00001702414'] 
Answer: True
4. What is the title for the record with the longest sequence? Is there more than one record with that length?
Answer: ['ENSG00000124942|ENST00000378024|11|62201016|62314332|-1|ENSE00001475929'] 
Answer: False
5. How many records have sequences which contain 20-nucleotide repeats (the same nucleotide repeated at least 20 consecutive times) in their sequences?
Answer: 0
6. Do any records contain 100% identical sequences?
Answer: True
7. The records in the file represent exons. How many exons can you find for the gene with Ensembl id ENSG00000006831? What are their exon IDs?
Answer: 8 
Answer ['ENSE00001426014', 'ENSE00001402644', 'ENSE00000712257', 'ENSE00001334428', 'ENSE00000816807', 'ENSE00000816806', 'ENSE00001334430', 'ENSE00000816808']
8. Which of the exons of ENSG00000006831 has the highest GC content?
Answer: [('ENSE00001426014', 76.36363636363636)]
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