# -*- coding: utf-8 *-*
import sys
import os
import errno
import time
# global configuration
import vprimer.glv as glv
import vprimer.utils as utl
from vprimer.logging_config import LogConf
log = LogConf.open_log(__name__)
import vcfpy
from vprimer.allele_select import AlleleSelect
class Variant(object):
def __init__(self):
pass
def pick_variant(self):
"""
"""
# open vcf through vcfpy
reader = vcfpy.Reader.from_path(glv.conf.vcf_file)
def open_log(self):
global log
log = LogConf.open_log(__name__)
def open_log_enzyme(self):
# in glv
global log
log = LogConf.open_log(__name__)
self.default_enzyme_names = [
['# A'],
['AluI', 'AGCT', 'AG^_CT', '4'],
['ApaI', 'GGGCCC', 'G_GGCC^C', '6'],
['AscI', 'GGCGCGCC', 'GG^CGCG_CC', '8'],
['AvrII', 'CCTAGG', 'C^CTAG_G', '6'],
[''],
['# B'],
['BamHI', 'GGATCC', 'G^GATC_C', '6'],
['BbsI', 'GAAGAC', 'GAAGACNN^NNNN_N', '6'],
['BclI', 'TGATCA', 'T^GATC_A', '6'],
['BglII', 'AGATCT', 'A^GATC_T', '6'],
['BsaI', 'GGTCTC', 'GGTCTCN^NNNN_N', '6'],
['BsiWI', 'CGTACG', 'C^GTAC_G', '6'],
['BsmFI', 'GGGAC', 'GGGACNNNNNNNNNN^NNNN_N', '5'],
['BspHI', 'TCATGA', 'T^CATG_A', '6'],
['BssHII', 'GCGCGC', 'G^CGCG_C', '6'],
['Bst1107I', 'GTATAC', 'GTA^_TAC', '6'],
['BstBI', 'TTCGAA', 'TT^CG_AA', '6'],
['BstEII', 'GGTNACC', 'G^GTNAC_C', '7'],
['BstXI', 'CCANNNNNNTGG', 'CCAN_NNNN^NTGG', '12'],
[''],
['# C'],
['ClaI', 'ATCGAT', 'AT^CG_AT', '6'],
[''],
['# D'],
['DdeI', 'CTNAG', 'C^TNA_G', '5'],
['DpnI', 'GATC', 'GA^_TC', '4'],
['DraI', 'TTTAAA', 'TTT^_AAA', '6'],
['DraIII', 'CACNNNGTG', 'CAC_NNN^GTG', '9'],
[''],
['# E'],
['Eco52I', 'CGGCCG', 'C^GGCC_G', '6'],
['EcoO109I', 'RGGNCCY', 'RG^GNC_CY', '7'],
['EcoO65I', 'GGTNACC', 'G^GTNAC_C', '7'],
['EcoRI', 'GAATTC', 'G^AATT_C', '6'],
['EcoRV', 'GATATC', 'GAT^_ATC', '6'],
['EcoT14I', 'CCWWGG', 'C^CWWG_G', '6'],
[''],
['# F'],
['FseI', 'GGCCGGCC', 'GG_CCGG^CC', '8'],
[''],
['# H'],
['HaeII', 'RGCGCY', 'R_GCGC^Y', '6'],
['HincII', 'GTYRAC', 'GTY^_RAC', '6'],
['HindIII', 'AAGCTT', 'A^AGCT_T', '6'],
['HinfI', 'GANTC', 'G^ANT_C', '5'],
['HpaI', 'GTTAAC', 'GTT^_AAC', '6'],
['HphI', 'GGTGA', 'GGTGANNNNNNN_N^N', '5'],
[''],
['# K'],
['KpnI', 'GGTACC', 'G_GTAC^C', '6'],
[''],
['# M'],
['MluI', 'ACGCGT', 'A^CGCG_T', '6'],
['MseI', 'TTAA', 'T^TA_A', '4'],
[''],
['# N'],
['NcoI', 'CCATGG', 'C^CATG_G', '6'],
['NdeI', 'CATATG', 'CA^TA_TG', '6'],
['NheI', 'GCTAGC', 'G^CTAG_C', '6'],
['NlaIII', 'CATG', '_CATG^', '4'],
['NotI', 'GCGGCCGC', 'GC^GGCC_GC', '8'],
['NruI', 'TCGCGA', 'TCG^_CGA', '6'],
['NsiI', 'ATGCAT', 'A_TGCA^T', '6'],
[''],
['# P'],
['PacI', 'TTAATTAA', 'TTA_AT^TAA', '8'],
['PmeI', 'GTTTAAAC', 'GTTT^_AAAC', '8'],
['PmlI', 'CACGTG', 'CAC^_GTG', '6'],
['Psp1406I', 'AACGTT', 'AA^CG_TT', '6'],
['PstI', 'CTGCAG', 'C_TGCA^G', '6'],
['PvuII', 'CAGCTG', 'CAG^_CTG', '6'],
[''],
['# R'],
['RsaI', 'GTAC', 'GT^_AC', '4'],
[''],
['# S'],
['SacI', 'GAGCTC', 'G_AGCT^C', '6'],
['SacII', 'CCGCGG', 'CC_GC^GG', '6'],
['SalI', 'GTCGAC', 'G^TCGA_C', '6'],
['SapI', 'GCTCTTC', 'GCTCTTCN^NNN_N', '7'],
['SbfI', 'CCTGCAGG', 'CC_TGCA^GG', '8'],
['ScaI', 'AGTACT', 'AGT^_ACT', '6'],
['SfiI', 'GGCCNNNNNGGCC', 'GGCCN_NNN^NGGCC', '13'],
['SmaI', 'CCCGGG', 'CCC^_GGG', '6'],
['SnaBI', 'TACGTA', 'TAC^_GTA', '6'],
['SpeI', 'ACTAGT', 'A^CTAG_T', '6'],
['SphI', 'GCATGC', 'G_CATG^C', '6'],
['SspI', 'AATATT', 'AAT^_ATT', '6'],
['StuI', 'AGGCCT', 'AGG^_CCT', '6'],
['SwaI', 'ATTTAAAT', 'ATTT^_AAAT', '8'],
[''],
['# T'],
['TaqI', 'TCGA', 'T^CG_A', '4'],
['Tth111I', 'GACNNNGTC', 'GACN^N_NGTC', '9'],
[''],
['# X'],
['XbaI', 'TCTAGA', 'T^CTAG_A', '6'],
['XhoI', 'CTCGAG', 'C^TCGA_G', '6'],
['XmaI', 'CCCGGG', 'C^CCGG_G', '6'],
[''],
['# end'],
]
def open_log_vcffile(self):
# in glv
global log
log = LogConf.open_log(__name__)