#!/usr/bin/env python

# Author: Mitchell Stanton-Cook (https://github.com/mscook)

# Affiliation: Scott Beatson Lab Group University of Queensland St Lucia

# Date: March 2014

############## Script to parse IS from embl file with flanking sequence ###################

### Description:

# This script takes in an embl file from a 'genomes' folder and parses out gene features,

# as well as flanking sequence of a predefined length, that match a specific feature type.

## Usage:

# Execute script from above a 'genomes' directory containing embl files that you want to extract

# particular sequences from.

# The header has been modified to suit usage with SeqFindR (https://github.com/mscook/seqfindr).

# The amount of flanking sequence desired, as well as the feature type that you want extracted,

# can be changed to suit the user.

import glob

from Bio import SeqIO

from Bio.SeqFeature import FeatureLocation

import os

in_files = glob.glob('genomes/*.embl')

flanking_region = 100

try:

os.mkdir("results")

except OSError:

print "a 'results' dir already exists"

print "Overwriting"

stored = {}

for f in in_files:

cur_genome = SeqIO.parse(f, "embl")

#print cur_genome

for record in cur_genome:

for feat in record.features:

if feat.type == 'mobile_element':

s, e, strand = feat.location.start, feat.location.end, feat.location.strand

header = '>'+feat.qualifiers['mobile_element_type'][0].split(':')[-1]+","+feat.qualifiers['mobile_element_type'][0].split(':')[-1]+".."+str(s+1)+".."+str(e)+"("+str(strand)+"),""100bp flanked,[EC958 IS]"

flanked = FeatureLocation(s-flanking_region, e+flanking_region, strand)

out_seq = flanked.extract(record.seq)

fname = header[1:].split(',')[0].replace('unclassified','unc').replace('family', 'fam').replace('(', '').replace('partial', 'p').replace(')', '').replace(' ', '_').replace('/', '-').strip()+'.fna'

if fname in stored.keys():

old = fname

fname = fname.replace(".fna", "_"+str(stored[fname])+".fna")

stored[old] = stored[old]+1

else:

stored[fname] = 1

with open(os.path.join('results', fname), 'w') as out:

out.write(header+'\n')

out.write(str(out_seq)+'\n')