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YAPBLAST.py
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YAPBLAST.py
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########################################################################################
## This file is a part of YAP package of scripts. https://github.com/shpakoo/YAP
## Distributed under the MIT license: http://www.opensource.org/licenses/mit-license.php
## Copyright (c) 2011-2013 Sebastian Szpakowski
########################################################################################
#################################################
## A pipeline for cleaning up sff files
#################################################
import sys
from optparse import OptionParser, OptionGroup
from StepsLibrary import *
from StepsLibrary_EXP import *
from collections import defaultdict
from Queue import Queue
_author="Sebastian Szpakowski"
_date="2012/08/27"
_version="Version 1"
#################################################
## Classes
##
#################################################
### Iterator over input file.
### every line is converted into a dictionary with variables referred to by their
### header name
class GeneralPurposeParser:
def __init__(self, file, skip=0, sep="\t"):
self.filename = file
self.fp = open(self.filename, "rU")
self.sep = sep
self.linecounter = 0
self.currline=""
def __iter__(self):
return (self)
def next(self):
otpt = dict()
for currline in self.fp:
currline = currline.strip().split(self.sep)
self.currline = currline
self.linecounter = self.linecounter + 1
return(currline)
raise StopIteration
def __str__(self):
return "%s [%s]\n\t%s" % (self.filename, self.linecounter, self.currline)
#################################################
## Functions
##
################################################
### Read in a file and return a list of lines
###
def loadLines(x):
try:
fp = open(x, "rU")
cont=fp.readlines()
fp.close()
#print "%s line(s) loaded." % (len(cont))
except:
cont=""
#print "%s cannot be opened, does it exist? " % ( x )
return cont
def getOligoFlip(filename):
if filename.find(".R.")>-1:
return "T"
else:
return "F"
#################################################
## Arguments
##
parser = OptionParser()
group = OptionGroup(parser, "Required", description="Will not run without these !")
group.add_option("-P", "--PROJECT", dest="project", default="",
help="project code", metavar="#")
group.add_option("-E", "--EMAIL", dest="email", default="",
help="e-mail address", metavar="@")
group.add_option("-b", "--database", dest="db",
help="absolute path to a database", metavar="blast")
parser.add_option("-d", "--directory", dest="dn_fasta", default="",
help="directory that will be scanned to fasta files", metavar="samples.group")
parser.add_option("-f", "--fasta", dest="fn_fasta", default="",
help="fasta file", metavar="reads.fasta")
parser.add_option_group(group)
group = OptionGroup(parser, "Optional Configuration", description="parameters to alter if necessary")
group.add_option("-m", "--mode", dest="blast_mode", default="blastn",
help="which blast application to use#\n[%default]", metavar="?blast?")
group.add_option("-s", "--split", dest="split_size", default=5000, type="int",
help="split input fasta into chunks with n sequences#\n[%default]", metavar="#")
parser.add_option_group(group)
group = OptionGroup(parser, "Technical", description="could be useful sometimes")
group.add_option("-T", "--threads",
dest="maxThreads",type="int", default=4,
help="maximum number of threads to spawn. [default: %default]")
group.add_option("-N", "--nodes",
dest="maxNodes",type="int", default=200,
help="maximum number of grid-nodes to use. [default: %default]")
group.add_option("-F", "--filesOpen",
dest="maxFiles",type="int", default=50,
help="maximum number of files opened at a given time. [default: %default]")
group.add_option("-C", "--NODESIZE", dest="nodesize", default=30,
help="maximum number of grid node's CPUs to use", metavar="#")
parser.add_option_group(group)
(options, args) = parser.parse_args()
#################################################
## Begin
##
if (options.fn_fasta == "" and options.dn_fasta=="") or options.email == "" or options.project =="" or options.db =="":
parser.print_help()
sys.exit(1)
files = list()
if options.fn_fasta != "":
files.extend(options.fn_fasta.split(","))
if options.dn_fasta != "":
for ext in ("fa", "fasta", "fna"):
tmp = glob.glob("%s/*.%s" % (options.dn_fasta, ext) )
if len(tmp)>0:
files.extend(tmp)
blasts = list()
init(options.project, options.email, maxnodes = options.maxNodes)
for file in files:
tmp = file.strip().split("/")[-1].split(".")
if len(tmp)>=3:
sample = tmp[1]
else:
sample = tmp[0]
INS= {"fasta": ["%s~%s" % (file, sample)]}
S1 = FileImport(INS)
#S2 = FastaSort({"types": "fasta"}, [S1])
S3 = FastaSplit({"types": "fasta", "chunk": options.split_size}, [S1])
args = { "mode" : options.blast_mode,
"-db" : options.db,
"-max_target_seqs" : "10",
"-html": "",
"-num_threads": "1"
}
S4 = BLAST(args, [S3])
S5 = FileMerger("blast6", [S4], prefix = sample)
blasts.append(S5)
OutputStep("FIN", "blast6", blasts)
##########################################################################
#
#################################################
## Finish
#################################################