#!/usr/bin/env python
# Remove sequences shorter than
from sys import argv, exit
from FB_functions import read_fasta
if len(argv) < 3:
print "usage: script.py seqfile.fasta 10"
print "removes sequences shorter than 10 nucleotides/amino acids"
exit()
sequences = read_fasta(argv[1])
for sequence in sequences:
if len(sequence[1]) > int(argv[2]):
print sequence[0] + "\n" + sequence[1]
help="Set a fixed fraglength to create fragments of [default=%default]",
default=False)
parser.add_option("-o", "--outputfile", dest="outputfile", type="string", default="fragments.pfa",
help="Filename for output file")
(options, args) = parser.parse_args()
if len(args)<1:
print parser.print_help()
print "ERROR: Need fasta file to work on!"
exit()
# Read QNR-sequences from fasta and store sequences in list of tuples
seqlist = read_fasta(args[0])
##---------------------------------------------------------------------------##
## DATA FOR FRAGMENT CREATION ##
##---------------------------------------------------------------------------##
# The number of different fragment lengths to be created:
MAXIMUM_FRAGMENT_LENGTH = options.fraglength # max value is ~210 (213) for Qnr
# Number of fragments per fragment length:
NUMBER_OF_FRAGMENTS_PER_LENGTH = options.replicates
# Determine the minimum sequence length
# (sets upper limit for fragment starting point)
SEQUENCE_MINLENGTH = 5000 # sufficiently large number
for seqid,sequence in seqlist:
#!/usr/bin/env python
# Classify cluster members according to
# fasta file of reference sequences.
from sys import argv, exit
from FB_functions import read_fasta
import re
if len(argv)<2:
print "usage: script.py cluster.fasta..."
exit()
refseqs = read_fasta("/home/boulund/qnr-search_project/qnrsequences/pmqr.pfa")
# Compile a regex to find the Qnr-tag of the reference sequences
qnrname_regex = re.compile(r'(Qnr\w\d*)')
for file in argv[1:]:
#print "\n"+file+"\n"
outfile = open(file+".classified","w")
cluster = read_fasta(file)
for seq in cluster:
success = False
for refseq in refseqs:
qnrname = re.search(qnrname_regex,refseq[0])
if qnrname is not None:
if seq[1] in refseq[1]:
success = True
outfile.write(">-"+qnrname.group(0)+"-"+seq[0][1:]+"\n")