def initialize():
global dataSavePath, post_list_file_name, img_list_file_name, comments_list_file_name, repeat
dataSavePath = osPathJoin(osGetcwd(), 'CrawlerDataFile')
post_list_file_name = "post_list.json"
img_list_file_name = "img_list.json"
comments_list_file_name = "comments_list.json"
repeat = False
def blastall_seq2db(header,
sequence,
dbname="",
blastprogram="blastp",
output="ncbiparsed",
extra_blastp_params={
'F': 'F',
'e': '10'
}):
"""
"""
if blastprogram not in ['blastp', 'tblastn', 'blastn', 'blastx']:
raise "only blastp and tblastn are supported"
extra_params = " ".join(
["-%s %s" % (k, v) for k, v in extra_blastp_params.iteritems()])
# generate (semi ;-) unique filename
uniquetag = get_random_string_tag()
fname = "_".join(
[uniquetag,
str(header).replace(" ", "_"), sequence[0:10] + ".fa"])
fname = osPathJoin(OSgetcwd(), fname)
fh = open(fname, 'w')
fh.write(">%s\n%s\n" % (header, sequence))
fh.close()
command = "%s -p %s %s -i %s -d %s " % (BLASTALL_PATH, blastprogram,
extra_params, fname, dbname)
try:
ci, co, ce = osPopen3(command)
ci.close()
if output == "ncbiparsed":
b_parser = NCBIStandalone.BlastParser()
blastallout = b_parser.parse(co)
else:
blastallout = co.read()
co.close()
ce.close()
except:
# for some kind of - obvious or freak accident case -
# Blast or parsing of the blast record failed
# No debugging here; just cleanup and return False
print "BLAST CRASHED::"
print command
blastallout = False
# remove the created Query file
osRemove(fname)
# and return!
return blastallout
def blastall_seq2db(header,sequence,dbname="",blastprogram="blastp",output="ncbiparsed",extra_blastp_params={'F': 'F', 'e': '10'}):
"""
"""
if blastprogram not in ['blastp','tblastn','blastn','blastx']:
raise "only blastp and tblastn are supported"
extra_params = " ".join(["-%s %s" % (k,v) for k,v in extra_blastp_params.iteritems()])
# generate (semi ;-) unique filename
uniquetag = get_random_string_tag()
fname = "_".join( [ uniquetag, str(header).replace(" ","_"), sequence[0:10]+".fa" ] )
fname = osPathJoin(OSgetcwd(),fname)
fh = open(fname,'w')
fh.write(">%s\n%s\n" % (header,sequence))
fh.close()
command = "%s -p %s %s -i %s -d %s " % (BLASTALL_PATH,blastprogram,extra_params,fname,dbname)
try:
ci,co,ce = osPopen3(command)
ci.close()
if output == "ncbiparsed":
b_parser = NCBIStandalone.BlastParser()
blastallout = b_parser.parse(co)
else:
blastallout = co.read()
co.close()
ce.close()
except:
# for some kind of - obvious or freak accident case -
# Blast or parsing of the blast record failed
# No debugging here; just cleanup and return False
print "BLAST CRASHED::"
print command
blastallout = False
# remove the created Query file
osRemove(fname)
# and return!
return blastallout
def abgpsysexit(input,OPTIONS,message=""):
""" """
if input.has_key(OPTIONS.target):
key = OPTIONS.target
elif OPTIONS.target == None:
key = None
else:
# find by protein fref
for k in input.keys():
if input[k]['gldobj'].protein_fref() == OPTIONS.target:
key = k
break
else:
key = None
# get filename to write to
if key:
fname = "%s.bailout.log" % input[key]['gldobj'].protein_fref()
elif key == None and OPTIONS.filewithloci:
hdr = OPTIONS.filewithloci.split("/")[-1].split(".")[0]
fname = "%s.bailout.log" % hdr
elif key == None and OPTIONS.dirwithloci:
hdr = OPTIONS.dirwithloci.split("/")[-1].split(".")[0]
fname = "%s.bailout.log" % hdr
else:
fname = "%s.bailout.log" % ("Notargetapplied")
# clean the complete directory from all files
_file_cleanup( osListdir(OPTIONS.outdir), include_directories=True )
fname = osPathJoin(OPTIONS.outdir,fname)
fh = open(fname,'w')
fh.write(message+"\n")
fh.close()
# safely break out of the ABGP algorithm
sysExit()
def HistoryDataLoad():
post_list_history = []
# img_list_history = []
# comments_list_history = []
if FilePathGlobals.repeat == False:
post_list_path = osPathJoin(FilePathGlobals.dataSavePath,
FilePathGlobals.post_list_file_name)
# img_list_path = osPathJoin(FilePathGlobals.dataSavePath,
# FilePathGlobals.img_list_file_name)
# comments_list_path = osPathJoin(FilePathGlobals.dataSavePath,
# FilePathGlobals.comments_list_file_name)
# 確認檔案是否存在
if CheckFile(post_list_path):
with open(post_list_path,
encoding='utf-8',
errors='ignore') as f:
post_list_history = json.load(f, strict=False)
# # 確認檔案是否存在
# if CheckFile(img_list_path):
# with open(img_list_path,
# encoding='utf-8',
# errors='ignore') as f:
# img_list_history = json.load(f, strict=False)
# # 確認檔案是否存在
# if CheckFile(comments_list_path):
# with open(comments_list_path,
# encoding='utf-8',
# errors='ignore') as f:
# comments_list_history = json.load(f, strict=False)
return post_list_history
def abgpsysexit(input, OPTIONS, message=""):
""" """
if input.has_key(OPTIONS.target):
key = OPTIONS.target
elif OPTIONS.target == None:
key = None
else:
# find by protein fref
for k in input.keys():
if input[k]['gldobj'].protein_fref() == OPTIONS.target:
key = k
break
else:
key = None
# get filename to write to
if key:
fname = "%s.bailout.log" % input[key]['gldobj'].protein_fref()
elif key == None and OPTIONS.filewithloci:
hdr = OPTIONS.filewithloci.split("/")[-1].split(".")[0]
fname = "%s.bailout.log" % hdr
elif key == None and OPTIONS.dirwithloci:
hdr = OPTIONS.dirwithloci.split("/")[-1].split(".")[0]
fname = "%s.bailout.log" % hdr
else:
fname = "%s.bailout.log" % ("Notargetapplied")
# clean the complete directory from all files
_file_cleanup(osListdir(OPTIONS.outdir), include_directories=True)
fname = osPathJoin(OPTIONS.outdir, fname)
fh = open(fname, 'w')
fh.write(message + "\n")
fh.close()
# safely break out of the ABGP algorithm
sysExit()
""" Alignment Based Gene Predictions settings: settings for (PSSM) Translational Start Sites (TSS) """ from settings.abgp import MAIN_ABGP_PATH from os.path import join as osPathJoin ################################################################################ # PSSM_IC file for Translational Start Sites ################################################################################ IC_TSS_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,"datafiles/ic_start_5fungi.txt") IC_TSS_PATTERN_OFFSET = (9,7) ################################################################################ # Threshold values for TranslationalStartSite (ATG) PSSM cutoffs # Recommended to set spatiously low! # Non-cannonical splice sites are not supported yet ################################################################################ TSS_MIN_PSSM_SCORE = float(-1) TSS_ALLOW_NON_CANONICAL = False TSS_NON_CANONICAL_MIN_PSSM_SCORE = float(0) ################################################################################ # Threshold for defining if a TSS is optimal in a given range ################################################################################ TCODE_TSS_5P_WINDOW = 201 # nt coords TCODE_TSS_3P_WINDOW = 201 # nt coords TCODE_AVERAGE_SCORE = 0.845
def __init__(self): pass
# end of class AcceptorPSSMOptions
################################################################################
# Which (Non)canonical splice sites are recognized/accepted?
################################################################################
CANONICAL_DONOR_SITES = ['GT']
NON_CANONICAL_DONOR_SITES = ['GC']
CANONICAL_ACCEPTOR_SITES = ['AG']
################################################################################
# PSSM_IC files for donors & acceptors
################################################################################
IC_DONOR_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,
"datafiles/ic_donor_5fungi.txt")
IC_DONOR_PATTERN_OFFSET = (3,4)
IC_ACCEPTOR_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,
"datafiles/ic_acceptor_5fungi.txt")
IC_ACCEPTOR_PATTERN_OFFSET = (6,3)
IC_DONOR_NCGC_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,
"datafiles/ic_ncdonorgc_5fungi.txt")
################################################################################
# Threshold values for donor site PSSM cutoffs
# Recommended to set spatiously low!
# Non-cannonical donor sites are supported yet, but disabled by default
################################################################################
MIN_DONOR_PSSM_SCORE = 0.0
ALLOW_NON_CANONICAL_DONOR = True
NON_CANONICAL_MIN_DONOR_PSSM_SCORE = float(3.0)
def CrawlerAction(days):
try:
# 初始化全域變數
FilePathGlobals.initialize()
# 取得指定天數的 post list 資料，存成陣列
post_list_temp = get_post_list(days)
# print("\n\n post_list:", post_list)
# 從陣列裡面把每個 url 丟進 post_crawler 爬取 po 文內容，回傳 post_time, author, comments, img_name_list, img_url_list
post_list = []
# img_list = []
# comments_list = []
for index, post in enumerate(post_list_temp):
post_time, author, comments, img_name_list, img_url_list = post_crawler(
post['url'], index)
post_list_temp[index]['post_time'] = post_time
post_list_temp[index]['author'] = author
post_list_temp[index]['imgs'] = img_url_list
post_list_temp[index]['comments'] = comments
post_list.append(post_list_temp[index])
# # img_list
# for imgUrl in img_url_list:
# imgs_dict = {}
# imgs_dict['post_index'] = postIndex
# # print(post_time, author, img_name_list, img_url_list)
# imgs_dict['img_url'] = imgUrl
# img_list.append(imgs_dict)
# # comments_list
# for comment_info in comments:
# comments_dict = {}
# comments_dict = comment_info
# comments_dict['post_index'] = postIndex
# comments_list.append(comments_dict)
# 顯示每一頁的資料
print(post_list[index]['title'])
print(post_list[index]['url'], '\n')
# 確認保存資料夾是否存在
CheckDir(FilePathGlobals.dataSavePath)
# 從歷史數據中剔除重複資料
from Model.Crawler.HistoryData.JsonHistoryDataModel import HistoryDataLoad, UpdateRepeatData
post_list_history = HistoryDataLoad()
post_list, post_list_history = UpdateRepeatData(
post_list, post_list_history)
post_list.extend(post_list_history)
# 存成字典post_list
with open(osPathJoin(FilePathGlobals.dataSavePath,
FilePathGlobals.post_list_file_name),
'w',
encoding="utf-8") as file:
json.dump(post_list, file, ensure_ascii=False)
# # img_list
# with open(osPathJoin(FilePathGlobals.dataSavePath, FilePathGlobals.img_list_file_name),
# 'w', encoding="utf-8") as file:
# json.dump(img_list, file, ensure_ascii=False)
# # comments_list
# with open(osPathJoin(FilePathGlobals.dataSavePath, FilePathGlobals.comments_list_file_name),
# 'w', encoding="utf-8") as file:
# json.dump(comments_list, file, ensure_ascii=False)
except Exception as e:
from traceback import format_exc
print(format_exc())
def createblastdbs(input,GSG,OPTIONS,dbfraction=None,organism=None,acceptorfids=[],rejectorfids=[]):
"""
(Re)create blast-db's by masking the areas thar are incorporated in the GSG
@type input: dict
@param input: `input` data structure dictionary
@type GSG: GenestructureOfCodingBlockGraphs
@param GSG: GenestructureOfCodingBlockGraphs instance
@type OPTIONS: optparse options instance
@param OPTIONS: optparse options instance (with attribute 'abinitio')
@type dbfraction: string
@param dbfraction: None, 'all', 'GSGupstream', 'GSGcentral', 'GSGdownstream', 'annotation'
@type organism: organism identifier
@param organism: only recreate blastdb for this organism/gene identifier
@type acceptorfids: list with integers
@param acceptorfids: list of orf ids to accept
@type rejectorfids: list with integers
@param rejectorfids: list of orf ids to reject
@attention: acceptorfids and rejectorfids are only used when organism is specified!
"""
seqsindb = {}
for org in input.keys():
# if organism is given, do only this one
if organism and org!=organism: continue
# acceptorfids anc rejectorfids only valid in combi with `organism`
if not organism: acceptorfids, rejectorfids = [], []
# assign blast database name / multi fasta file and open filehandle
uniquetag = get_random_string_tag()
fname = '%s-blastdb-%s.fa' % (uniquetag,org)
fullpath = osPathJoin(OPTIONS.outdir,fname)
fh = open(fullpath,'w')
seqsindb[org] = 0
# distinct cases possible:
if len(GSG):
# there is already a GSG, so this is not the first blast iteration
# do not apply a shortcut when OPTIONS.abinitio == False
coords = GSG.omsr2mask(org)
if dbfraction == 'GSGupstream':
# take only orfs LEFT of the first CBG in GSG
max_orf_nt_start = max(GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
elif dbfraction == 'GSGdownstream':
# take only orfs RIGTH of the last CBG in GSG
min_orf_nt_end = min(GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(min_orf_end=min_orf_nt_end,
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
elif dbfraction == 'GSGcentral':
# take only orfs in between FIRST and LAST CBG in GSG (can be only one CBG!)
max_orf_nt_start = max(GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
min_orf_nt_end = min(GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(min_orf_end=min_orf_nt_end,
max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
else:
# dbfraction equals 'all' or None -> no limitation, just take all orfs!
# do only the general limitation on sublists of orfids
orflist = input[org]['orfs'].get_elegiable_orfs(
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
# create masked fasta of this sequence part only
newfasta = input[org]['orfs'].tomaskedfasta(coords=coords,orflist=orflist,header_prefix=org)
# write to file and count accessions in this file -> seqsindb[org]
fh.write(newfasta)
seqsindb[org] = newfasta.count(">")
else:
# No filled GSG objects -> no a priori knowledge yet
# When dbfraction=='annotated' and !OPTIONS.abinitio -> take annotated orfs only
# TODO: dbfraction is not checked/used here -> just OPTIONS.abinitio
for orf in input[org]['orfs'].orfs:
# in case not abinitio, make only a db of orfs in teh current annotation!
if OPTIONS.abinitio == False and orf.id not in input[org]['orfid-genestructure']:
continue
if orf.id in rejectorfids:
# ignore Orfs that are listed as to-be-ignored
continue
if acceptorfids and orf.id not in acceptorfids:
# ignore Orfs that are not listed as to-be-accepted
continue
# write fasta of orf to file
fh.write(orf.tofasta(header="%s_orf_%s" % (org,orf.id))+"\n")
# increase seqsindb[org] counter
seqsindb[org]+=1
# close the filehandle
fh.close()
# run formatdb
formatdb(fname=fullpath)
# set name of blastdb in infodict
input[org]['blastdb'] = fullpath
# return the counter of how much orf sequences are stored in the blast database
return seqsindb
# >85 BLOSUM-62 (11,1)
#
##############################################################################
#
# blosum62 = parse_emboss_matrix_file("/opt/ab/share/EMBOSS/data/EBLOSUM62")
# pam30 = parse_emboss_matrix_file("/opt/ab/share/EMBOSS/data/EPAM30")
#
##############################################################################
# Python Imports
from os.path import join as osPathJoin
# import paths to BLOSUM and PAM matrices
from executables import EMBOSS_DATA_DIRECTORY
BLOSUM45_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EBLOSUM45")
BLOSUM62_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EBLOSUM62")
BLOSUM80_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EBLOSUM80")
PAM30_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EPAM30")
PAM70_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EPAM70")
def parse_emboss_matrix_file(fname):
"""
Parse an EMBOSS protein similarity matrix file
Supported types are BLOSUM and PAM matrices
"""
lines = []
matrix = {}
aas = []
for line in open(fname).readlines():
# python
PYTHON_PATH = "/usr/bin/python2.6" # tested are 2.4, 2.6 and 2.7.4
PYTHON_VERSION = "python2.6.2"
# emboss
EMBOSS_EXECUTABLES_PATH = "/usr/bin"
EMBOSS_DATA_DIRECTORY = "/usr/share/EMBOSS/data"
EMBOSS_VERSION = "4.0.0"
# perl
PERL_PATH = "perl" # only required in case a MySQL GGB database is
# coupled to store and visualize ABFGP output.
PERL_VERSION = "?" # not used at all.
################################################################################
# Full paths to executables
################################################################################
EXECUTABLE_BLASTALL = osPathJoin(BASEPATH, "software/blast-2.2.8/blastall")
EXECUTABLE_FORMATDB = osPathJoin(BASEPATH, "software/blast-2.2.8/formatdb")
EXECUTABLE_GETORF = osPathJoin(EMBOSS_EXECUTABLES_PATH, "getorf")
EXECUTABLE_TCODE = osPathJoin(EMBOSS_EXECUTABLES_PATH, "tcode")
EXECUTABLE_TRANSEQ = osPathJoin(EMBOSS_EXECUTABLES_PATH, "transeq")
EXECUTABLE_CLUSTALW = osPathJoin(BASEPATH, "software/clustalw-1.83/clustalw")
EXECUTABLE_SIGNALP = osPathJoin(BASEPATH, "software/signalp-3.0/signalp")
EXECUTABLE_TMHMM = osPathJoin(BASEPATH, "software/tmhmm-2.0/bin/tmhmm")
EXECUTABLE_SFM = osPathJoin(BASEPATH,
"software/ScanForMatches/scan_for_matches")
EXECUTABLE_HMMPATH = osPathJoin(BASEPATH, "software/hmmer-2.3.2")
EXECUTABLE_HMMSEARCH = osPathJoin(EXECUTABLE_HMMPATH, "hmmsearch")
EXECUTABLE_HMMBUILD = osPathJoin(EXECUTABLE_HMMPATH, "hmmbuild")
EXECUTABLE_CEXPANDER_PATH = osPathJoin(BASEPATH, "software/cexpander-1.0")
EXECUTABLE_CEXPANDER_ALLVSALL = osPathJoin(EXECUTABLE_CEXPANDER_PATH,
# Module metadata
__authors__ = "Ate van der Burgt"
__license__ = "MIT"
# Python imports
import gzip
from subprocess import Popen, PIPE
from os.path import (
join as osPathJoin,
abspath as osPathAbspath,
dirname as osPathDirname,
)
# absolute paths to executables located within the same directory
EXECUTABLE_ISSINGLEFASTADNA = osPathJoin(osPathDirname(osPathAbspath(__file__)),"issinglefastadna.sh")
EXECUTABLE_ISSINGLEFASTAPROTEIN = osPathJoin(osPathDirname(osPathAbspath(__file__)),"issinglefastaprotein.sh")
########################################################################
#### Exceptions
########################################################################
class NoSingleFastaFile(Exception):
pass
########################################################################
#### Validation functions
########################################################################
def IsSingleFastaDna(fname,executable=EXECUTABLE_ISSINGLEFASTADNA):
"""
# >85 BLOSUM-62 (11,1)
#
##############################################################################
#
# blosum62 = parse_emboss_matrix_file("/opt/ab/share/EMBOSS/data/EBLOSUM62")
# pam30 = parse_emboss_matrix_file("/opt/ab/share/EMBOSS/data/EPAM30")
#
##############################################################################
# Python Imports
from os.path import join as osPathJoin
# import paths to BLOSUM and PAM matrices
from executables import EMBOSS_DATA_DIRECTORY
BLOSUM45_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EBLOSUM45")
BLOSUM62_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EBLOSUM62")
BLOSUM80_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EBLOSUM80")
PAM30_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EPAM30")
PAM70_PATH = osPathJoin(EMBOSS_DATA_DIRECTORY, "EPAM70")
def parse_emboss_matrix_file(fname):
"""
Parse an EMBOSS protein similarity matrix file
Supported types are BLOSUM and PAM matrices
"""
lines = []
matrix = {}
aas = []
for line in open(fname).readlines():
def favicon():
return send_from_directory(osPathJoin(webShellRootPath, 'static'),
'images/favicon.ico',
mimetype='image/vnd.microsoft.icon')
def robots():
return send_from_directory(osPathJoin(webShellRootPath, 'static'),
'robots.txt',
mimetype='text/plain')
# python
PYTHON_PATH = "/usr/bin/python2.6" # tested are 2.4, 2.6 and 2.7.4
PYTHON_VERSION = "python2.6.2"
# emboss
EMBOSS_EXECUTABLES_PATH = "/usr/bin"
EMBOSS_DATA_DIRECTORY = "/usr/share/EMBOSS/data"
EMBOSS_VERSION = "4.0.0"
# perl
PERL_PATH = "perl" # only required in case a MySQL GGB database is
# coupled to store and visualize ABFGP output.
PERL_VERSION = "?" # not used at all.
################################################################################
# Full paths to executables
################################################################################
EXECUTABLE_BLASTALL = osPathJoin(BASEPATH,"software/blast-2.2.8/blastall")
EXECUTABLE_FORMATDB = osPathJoin(BASEPATH,"software/blast-2.2.8/formatdb")
EXECUTABLE_GETORF = osPathJoin(EMBOSS_EXECUTABLES_PATH,"getorf")
EXECUTABLE_TCODE = osPathJoin(EMBOSS_EXECUTABLES_PATH,"tcode")
EXECUTABLE_TRANSEQ = osPathJoin(EMBOSS_EXECUTABLES_PATH,"transeq")
EXECUTABLE_CLUSTALW = osPathJoin(BASEPATH,"software/clustalw-1.83/clustalw")
EXECUTABLE_SIGNALP = osPathJoin(BASEPATH,"software/signalp-3.0/signalp")
EXECUTABLE_TMHMM = osPathJoin(BASEPATH,"software/tmhmm-2.0/bin/tmhmm")
EXECUTABLE_SFM = osPathJoin(BASEPATH,"software/ScanForMatches/scan_for_matches")
EXECUTABLE_HMMPATH = osPathJoin(BASEPATH,"software/hmmer-2.3.2")
EXECUTABLE_HMMSEARCH = osPathJoin(EXECUTABLE_HMMPATH,"hmmsearch")
EXECUTABLE_HMMBUILD = osPathJoin(EXECUTABLE_HMMPATH,"hmmbuild")
EXECUTABLE_CEXPANDER_PATH = osPathJoin(BASEPATH,"software/cexpander-1.0")
EXECUTABLE_CEXPANDER_ALLVSALL = osPathJoin(EXECUTABLE_CEXPANDER_PATH,
"prep_launch.py")
# Python imports that might be absent depending on the version of Python from sets import Set # deprecated but backwards compatible in newer verions of python from optparse import OptionParser from optparse import OptionGroup from optparse import OptionValueError from StringIO import StringIO # Most likely Numeric is not installed; this is solved by having it installed # within the ABFGP code tree # The path to Numeric is obtained either from the settings dir (absolute) # or the path is reconstructed (relative) # absolute path acquisition from settings.abgp import MAIN_ABGP_PATH as BASEPATH sys.path.append(osPathJoin(BASEPATH, "requiredmodules")) from Numeric import zeros, where, greater, greater_equal # relative path acquisition sys.path.append(osPathJoin(osPathDirname(osPathAbspath(__file__)), "requiredmodules")) from Numeric import zeros, where, greater, greater_equal from abgp_etc import abgpsysexit from abgp_etc import _blastdb_cleanup from abgp_etc import _blastdb_cleanup, _file_cleanup from abgp_exceptions import InproperlyAppliedArgument from abgp_exceptions import NoCrossdataApplied, NoInputApplied from abgp_geneconfirmation import * from abgp_geneconfirmation import geneconfirmation from abgpgenelocusdirectory import AbgpGeneLocusDirectory from abgpgenelocusdirectory import IsAbgpGeneLocusDirectory
""" Alignment Based Gene Predictions settings: EMBOSS data files """ from os.path import join as osPathJoin from abgp import MAIN_ABGP_PATH ################################################################################ # Full paths to Amino Acid similarity matrices ################################################################################ BLOSUM62_PATH = osPathJoin(MAIN_ABGP_PATH,"datafiles/EMBOSS/EBLOSUM62") BLOSUM80_PATH = osPathJoin(MAIN_ABGP_PATH,"datafiles/EMBOSS/EBLOSUM80") BLOSUM45_PATH = osPathJoin(MAIN_ABGP_PATH,"datafiles/EMBOSS/EBLOSUM45") PAM30_PATH = osPathJoin(MAIN_ABGP_PATH,"datafiles/EMBOSS/EPAM30") PAM70_PATH = osPathJoin(MAIN_ABGP_PATH,"datafiles/EMBOSS/EPAM70")
""" Alignment Based Gene Predictions settings: settings for (PSSM) Translational Start Sites (TSS) """ from settings.abgp import MAIN_ABGP_PATH from os.path import join as osPathJoin ################################################################################ # PSSM_IC file for Translational Start Sites ################################################################################ IC_TSS_DATA_FILE = osPathJoin(MAIN_ABGP_PATH, "datafiles/ic_start_5fungi.txt") IC_TSS_PATTERN_OFFSET = (9, 7) ################################################################################ # Threshold values for TranslationalStartSite (ATG) PSSM cutoffs # Recommended to set spatiously low! # Non-cannonical splice sites are not supported yet ################################################################################ TSS_MIN_PSSM_SCORE = float(-1) TSS_ALLOW_NON_CANONICAL = False TSS_NON_CANONICAL_MIN_PSSM_SCORE = float(0) ################################################################################ # Threshold for defining if a TSS is optimal in a given range ################################################################################ TCODE_TSS_5P_WINDOW = 201 # nt coords TCODE_TSS_3P_WINDOW = 201 # nt coords TCODE_AVERAGE_SCORE = 0.845 TSS_IS_OPTIMAL_5P_WINDOW = 200 # nt coords, was 250 in the juli2009 abgp_tssanalyses test TSS_IS_OPTIMAL_3P_WINDOW = 100 # nt coords
################################################################################
### PssmObjectCollectionGraph class and inheriting classes ####
################################################################################
# Python imports
from sets import Set
# Make sure Numeric is installed somewhere!!!
# For convenience, it is installed in ./requiredmodules
import sys
from os.path import join as osPathJoin
from settings.abgp import MAIN_ABGP_PATH as BASEPATH
sys.path.append(osPathJoin(BASEPATH,"requiredmodules"))
from Numeric import zeros
# graphAbgp imports
from graph_organism import OrganismGraph
from subclass_sitealignment import BasalSiteAlignmentFunctions, sort_by_cumulative_score
from subclass_pssmobjects import BasalPSSMObjectGraphFunctions
import conversion
import ordering
import graphPlus
from exceptions import *
# Global Varibale Imports
from settings.translationalstartsites import TCODE_TSS_5P_WINDOW, TCODE_TSS_3P_WINDOW
class PssmObjectCollectionGraph(OrganismGraph,BasalSiteAlignmentFunctions,BasalPSSMObjectGraphFunctions):
"""
"""
# Python imports that might be absent depending on the version of Python
from sets import Set # deprecated but backwards compatible in newer verions of python
from optparse import OptionParser
from optparse import OptionGroup
from optparse import OptionValueError
from StringIO import StringIO
# Most likely Numeric is not installed; this is solved by having it installed
# within the ABFGP code tree
# The path to Numeric is obtained either from the settings dir (absolute)
# or the path is reconstructed (relative)
# absolute path acquisition
from settings.abgp import MAIN_ABGP_PATH as BASEPATH
sys.path.append(osPathJoin(BASEPATH, "requiredmodules"))
from Numeric import zeros, where, greater, greater_equal
# relative path acquisition
sys.path.append(
osPathJoin(osPathDirname(osPathAbspath(__file__)), "requiredmodules"))
from Numeric import zeros, where, greater, greater_equal
from abgp_etc import abgpsysexit
from abgp_etc import _blastdb_cleanup
from abgp_etc import _blastdb_cleanup, _file_cleanup
from abgp_exceptions import InproperlyAppliedArgument
from abgp_exceptions import NoCrossdataApplied, NoInputApplied
from abgp_geneconfirmation import *
from abgp_geneconfirmation import geneconfirmation
from abgpgenelocusdirectory import AbgpGeneLocusDirectory
""" Alignment Based Gene Predictions settings: EMBOSS data files """ from os.path import join as osPathJoin from abgp import MAIN_ABGP_PATH ################################################################################ # Full paths to Amino Acid similarity matrices ################################################################################ BLOSUM62_PATH = osPathJoin(MAIN_ABGP_PATH, "datafiles/EMBOSS/EBLOSUM62") BLOSUM80_PATH = osPathJoin(MAIN_ABGP_PATH, "datafiles/EMBOSS/EBLOSUM80") BLOSUM45_PATH = osPathJoin(MAIN_ABGP_PATH, "datafiles/EMBOSS/EBLOSUM45") PAM30_PATH = osPathJoin(MAIN_ABGP_PATH, "datafiles/EMBOSS/EPAM30") PAM70_PATH = osPathJoin(MAIN_ABGP_PATH, "datafiles/EMBOSS/EPAM70")
def createblastdbs(input,
GSG,
OPTIONS,
dbfraction=None,
organism=None,
acceptorfids=[],
rejectorfids=[]):
"""
(Re)create blast-db's by masking the areas thar are incorporated in the GSG
@type input: dict
@param input: `input` data structure dictionary
@type GSG: GenestructureOfCodingBlockGraphs
@param GSG: GenestructureOfCodingBlockGraphs instance
@type OPTIONS: optparse options instance
@param OPTIONS: optparse options instance (with attribute 'abinitio')
@type dbfraction: string
@param dbfraction: None, 'all', 'GSGupstream', 'GSGcentral', 'GSGdownstream', 'annotation'
@type organism: organism identifier
@param organism: only recreate blastdb for this organism/gene identifier
@type acceptorfids: list with integers
@param acceptorfids: list of orf ids to accept
@type rejectorfids: list with integers
@param rejectorfids: list of orf ids to reject
@attention: acceptorfids and rejectorfids are only used when organism is specified!
"""
seqsindb = {}
for org in input.keys():
# if organism is given, do only this one
if organism and org != organism: continue
# acceptorfids anc rejectorfids only valid in combi with `organism`
if not organism: acceptorfids, rejectorfids = [], []
# assign blast database name / multi fasta file and open filehandle
uniquetag = get_random_string_tag()
fname = '%s-blastdb-%s.fa' % (uniquetag, org)
fullpath = osPathJoin(OPTIONS.outdir, fname)
fh = open(fullpath, 'w')
seqsindb[org] = 0
# distinct cases possible:
if len(GSG):
# there is already a GSG, so this is not the first blast iteration
# do not apply a shortcut when OPTIONS.abinitio == False
coords = GSG.omsr2mask(org)
if dbfraction == 'GSGupstream':
# take only orfs LEFT of the first CBG in GSG
max_orf_nt_start = max(
GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(
max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,
rejectorfids=rejectorfids)
elif dbfraction == 'GSGdownstream':
# take only orfs RIGTH of the last CBG in GSG
min_orf_nt_end = min(
GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(
min_orf_end=min_orf_nt_end,
acceptorfids=acceptorfids,
rejectorfids=rejectorfids)
elif dbfraction == 'GSGcentral':
# take only orfs in between FIRST and LAST CBG in GSG (can be only one CBG!)
max_orf_nt_start = max(
GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
min_orf_nt_end = min(
GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(
min_orf_end=min_orf_nt_end,
max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,
rejectorfids=rejectorfids)
else:
# dbfraction equals 'all' or None -> no limitation, just take all orfs!
# do only the general limitation on sublists of orfids
orflist = input[org]['orfs'].get_elegiable_orfs(
acceptorfids=acceptorfids, rejectorfids=rejectorfids)
# create masked fasta of this sequence part only
newfasta = input[org]['orfs'].tomaskedfasta(coords=coords,
orflist=orflist,
header_prefix=org)
# write to file and count accessions in this file -> seqsindb[org]
fh.write(newfasta)
seqsindb[org] = newfasta.count(">")
else:
# No filled GSG objects -> no a priori knowledge yet
# When dbfraction=='annotated' and !OPTIONS.abinitio -> take annotated orfs only
# TODO: dbfraction is not checked/used here -> just OPTIONS.abinitio
for orf in input[org]['orfs'].orfs:
# in case not abinitio, make only a db of orfs in teh current annotation!
if OPTIONS.abinitio == False and orf.id not in input[org][
'orfid-genestructure']:
continue
if orf.id in rejectorfids:
# ignore Orfs that are listed as to-be-ignored
continue
if acceptorfids and orf.id not in acceptorfids:
# ignore Orfs that are not listed as to-be-accepted
continue
# write fasta of orf to file
fh.write(
orf.tofasta(header="%s_orf_%s" % (org, orf.id)) + "\n")
# increase seqsindb[org] counter
seqsindb[org] += 1
# close the filehandle
fh.close()
# run formatdb
formatdb(fname=fullpath)
# set name of blastdb in infodict
input[org]['blastdb'] = fullpath
# return the counter of how much orf sequences are stored in the blast database
return seqsindb
pass
# end of class AcceptorPSSMOptions
################################################################################
# Which (Non)canonical splice sites are recognized/accepted?
################################################################################
CANONICAL_DONOR_SITES = ['GT']
NON_CANONICAL_DONOR_SITES = ['GC']
CANONICAL_ACCEPTOR_SITES = ['AG']
################################################################################
# PSSM_IC files for donors & acceptors
################################################################################
IC_DONOR_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,
"datafiles/ic_donor_5fungi.txt")
IC_DONOR_PATTERN_OFFSET = (3, 4)
IC_ACCEPTOR_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,
"datafiles/ic_acceptor_5fungi.txt")
IC_ACCEPTOR_PATTERN_OFFSET = (6, 3)
IC_DONOR_NCGC_DATA_FILE = osPathJoin(MAIN_ABGP_PATH,
"datafiles/ic_ncdonorgc_5fungi.txt")
################################################################################
# Threshold values for donor site PSSM cutoffs
# Recommended to set spatiously low!
# Non-cannonical donor sites are supported yet, but disabled by default
################################################################################
MIN_DONOR_PSSM_SCORE = 0.0
ALLOW_NON_CANONICAL_DONOR = True
NON_CANONICAL_MIN_DONOR_PSSM_SCORE = float(3.0)