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# partial_gene_match.py
#
# Example showing how to use the CloseMatch class, to find strings in a gene with up to 'n' mismatches
#
import pyparsing as pp
import urllib.request
from contextlib import closing
# read in a bunch of genomic data
data_url = "http://toxodb.org/common/downloads/release-6.0/Tgondii/TgondiiApicoplastORFsNAs_ToxoDB-6.0.fasta"
with closing(urllib.request.urlopen(data_url)) as datafile:
fastasrc = datafile.read().decode()
# define parser to extract gene definitions
"""
Sample header:
>NC_001799-6-2978-2778 | organism=Toxoplasma_gondii_RH | location=NC_001799:2778-2978(-) | length=201
"""
integer = pp.pyparsing_common.integer
genebit = pp.Group(">" + pp.Word(pp.alphanums.upper() + "-_")("gene_id")
+ "|" + pp.Word(pp.printables)("organism")
+ "|" + pp.Word(pp.printables)("location")
+ "|" + "length=" + integer("gene_len")
+ pp.LineEnd()
+ pp.Word("ACGTN")[1, ...].addParseAction(''.join)("gene"))
# read gene data from .fasta file - takes just a few seconds
# An important aspect of this parsing process is the reassembly of all the separate lines of the
# gene into a single scannable string. Just searching the raw .fasta file could overlook matches
# if the match is broken up across separate lines. The parse action in the genebit parser does
# this reassembly work.
genedata = genebit[1, ...].parseString(fastasrc)
# using the genedata extracted above, look for close matches of a gene sequence
searchseq = pp.CloseMatch("TTAAATCTAGAAGAT", 3)
for g in genedata:
show_header = True
# scan for close matches, list out found strings, and mark mismatch locations
for t, startLoc, endLoc in searchseq.scanString(g.gene, overlap=True):
if show_header:
# only need to show the header once
print("%s/%s/%s (%d)" % (g.gene_id, g.organism, g.location, g.gene_len))
print("-" * 24)
show_header = False
matched = t[0]
mismatches = t['mismatches']
print("MATCH:", searchseq.match_string)
print("FOUND:", matched)
if mismatches:
print(" ", ''.join('*' if i in mismatches else ' '
for i, c in enumerate(searchseq.match_string)))
else:
print("<exact match>")
print("at location", startLoc)
print()
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