From ff7fcec020a7012aa97bdc4ccd7f3a8e9c36fe3e Mon Sep 17 00:00:00 2001 From: ccedmendoza Date: Wed, 19 Sep 2018 15:58:30 +0200 Subject: [PATCH 1/3] add mm10 to xml --- tools/sicer/sicer_wrapper.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/sicer/sicer_wrapper.xml b/tools/sicer/sicer_wrapper.xml index 8c2fc03d..661da37c 100644 --- a/tools/sicer/sicer_wrapper.xml +++ b/tools/sicer/sicer_wrapper.xml @@ -31,7 +31,7 @@ - value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ] + value is not None and value.dbkey in [ 'mm8', 'mm9', 'mm10', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ] From b5bd7e37af62212c1cbd276e95ca71c8298ad657 Mon Sep 17 00:00:00 2001 From: ccedmendoza Date: Wed, 19 Sep 2018 15:59:17 +0200 Subject: [PATCH 2/3] add mm10 to .py --- tools/sicer/sicer_wrapper.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tools/sicer/sicer_wrapper.py b/tools/sicer/sicer_wrapper.py index 9ffcd68d..9c8c8aa5 100644 --- a/tools/sicer/sicer_wrapper.py +++ b/tools/sicer/sicer_wrapper.py @@ -7,10 +7,11 @@ import sys, optparse, os, tempfile, subprocess, shutil +print(os.getcwd()) CHUNK_SIZE = 2**20 #1mb #HACK! FIXME: allow using all specified builds, would currently require hacking SICER's "GenomeData.py" on the fly. -VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ] +VALID_BUILDS = [ 'mm8', 'mm9', 'mm10', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ] def cleanup_before_exit( tmp_dir ): if tmp_dir and os.path.exists( tmp_dir ): From 4cf2f84d583db9c766f6a528b6e4cbf71a47fb2e Mon Sep 17 00:00:00 2001 From: ccedmendoza Date: Wed, 19 Sep 2018 16:04:23 +0200 Subject: [PATCH 3/3] I'm not sure of where it should be added or how it should be updated. But added mm10 to GenomeData.py file --- tools/sicer/GenomeData.py | 206 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 206 insertions(+) create mode 100644 tools/sicer/GenomeData.py diff --git a/tools/sicer/GenomeData.py b/tools/sicer/GenomeData.py new file mode 100644 index 00000000..9bc28d53 --- /dev/null +++ b/tools/sicer/GenomeData.py @@ -0,0 +1,206 @@ +#!/usr/bin/env python +# Copyright (c) 2007 NHLBI, NIH +# Copyright (c) 2010 The George Washington University +# Authors: Chongzhi Zang, Weiqun Peng, Dustin E Schones and Keji Zhao +# +# This software is distributable under the terms of the GNU General +# Public License (GPL) v2, the text of which can be found at +# http://www.gnu.org/copyleft/gpl.html. Installing, importing or +# otherwise using this module constitutes acceptance of the terms of +# this License. +# +# Disclaimer +# +# This software is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# Comments and/or additions are welcome (send e-mail to: +# wpeng@gwu.edu). +# +# Version 1.1 6/9/2010 + +""" +This module contains classes of genome data, e.g. chromsomes +per species, the size of the chromosomes, etc. +""" + +import re, os, sys, shutil + +GenomeDataError = "Error in GenomeData class"; + +bg_number_chroms = 1; +bg_length_of_chrom = 100000000; + +background_chroms = []; +background_chrom_lengths = {}; +for i in range(0,bg_number_chroms): + background_chroms.append( 'chr' + str(i+1)); + background_chrom_lengths['chr' + str(i+1)] = bg_length_of_chrom; + + +mm8_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', + 'chr18','chr19','chrX', 'chrY', 'chrM'] + +mm9_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', + 'chr18','chr19','chrX', 'chrY', 'chrM'] + +mm10_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', + 'chr18','chr19','chrX', 'chrY', 'chrM'] + +rn4_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', + 'chr18','chr19','chr20','chrX','chrM'] + +hg18_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', + 'chr18','chr19','chr20','chr21','chr22','chrX','chrY','chrM'] + +hg19_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', + 'chr18','chr19','chr20','chr21','chr22','chrX','chrY','chrM'] + +sacCer1_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', + 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chrM'] + +dm2_chroms = ['chr2h', 'chr2L', 'chr2R', 'chr3h', 'chr3L', + 'chr3R','chr4','chr4h','chrM','chrU','chrX','chrXh','chrYh'] + +dm3_chroms = ['chr2L', 'chr2LHet', 'chr2R', 'chr2RHet', 'chr3L', 'chr3LHet', + 'chr3R', 'chr3RHet', 'chr4','chrX','chrXHet', 'chrYHet', 'chrU', 'chrUextra', 'chrM'] + +pombe_chroms = ['chr1','chr2', 'chr3', 'mat']; + +tair8_chroms = ['chr1','chr2','chr3','chr4','chr5']; + +mm8_chrom_lengths = {'chr1':197069962, 'chr2':181976762, 'chr3':159872112, + 'chr4':155029701, 'chr5':152003063, 'chr6':149525685, + 'chr7':145134094, 'chr8':132085098, 'chr9':124000669, + 'chr10':129959148, 'chr11':121798632, 'chr12':120463159, + 'chr13':120614378, 'chr14':123978870, 'chr15':103492577, + 'chr16':98252459, 'chr17':95177420, 'chr18':90736837, + 'chr19':61321190, 'chrX':165556469, 'chrY':16029404, + 'chrM':16299} + +mm9_chrom_lengths = {'chr1':197195432, 'chr2':181748087, 'chr3':159599783, + 'chr4':155630120, 'chr5':152537259, 'chr6':149517037, + 'chr7':152524553, 'chr8':131738871, 'chr9':124076172, + 'chr10':129993255, 'chr11':121843856, 'chr12':121257530, + 'chr13':120284312, 'chr14':125194864, 'chr15':103494974, + 'chr16':98319150, 'chr17':95272651, 'chr18':90772031, + 'chr19':61342430, 'chrX':166650296, 'chrY':15902555, + 'chrM':16299} + +mm10_chrom_lengths= {'chr1':195471971, 'chr2':182113224, 'chr3':160039680, + 'chr4':156508116, 'chr5':151834684, 'chr6':149736546, + 'chr7':145441459, 'chr8':129401213, 'chr9':124595110, + 'chr10':130694993, 'chr11':122082543, 'chr12':120129022, + 'chr13':120421639, 'chr14':124902244, 'chr15':104043685, + 'chr16':98207768, 'chr17':94987271, 'chr18':90702639, + 'chr19':61431566, 'chrX':171031299, 'chrY':91744698, + 'chrM':16299} + +rn4_chrom_lengths = {'chr1':267910886, 'chr2':258207540, 'chr3':171063335, + 'chr4':187126005, 'chr5':173096209, 'chr6':147636619, + 'chr7':143002779, 'chr8':129041809, 'chr9':113440463, + 'chr10':110718848, 'chr11':87759784, 'chr12':46782294, + 'chr13':111154910, 'chr14':112194335, 'chr15':109758846, + 'chr16':90238779, 'chr17':97296363, 'chr18':87265094, + 'chr19':59218465, 'chr20':55268282, 'chrX':160699376, + 'chrM':16300} + + + +hg18_chrom_lengths = {'chr1':247249719, 'chr2':242951149, 'chr3':199501827, + 'chr4':191273063, 'chr5':180857866, 'chr6':170899992, + 'chr7':158821424, 'chr8':146274826, 'chr9':140273252, + 'chr10':135374737, 'chr11':134452384, 'chr12':132349534, + 'chr13':114142980, 'chr14':106368585, 'chr15':100338915, + 'chr16':88827254, 'chr17':78774742, 'chr18':76117153, + 'chr19':63811651, 'chr20':62435964, 'chr21':46944323, + 'chr22':49691432, 'chrX':154913754, 'chrY':57772954, + 'chrM':16571} + +hg19_chrom_lengths = {'chr1':249250621, 'chr2':243199373, 'chr3':198022430, + 'chr4':191154276, 'chr5':180915260, 'chr6':171115067, + 'chr7':159138663, 'chr8':146364022, 'chr9':141213431, + 'chr10':135534747, 'chr11':135006516, 'chr12':133851895, + 'chr13':115169878, 'chr14':107349540, 'chr15':102531392, + 'chr16':90354753, 'chr17':81195210, 'chr18':78077248, + 'chr19':59128983, 'chr20':63025520, 'chr21':48129895, + 'chr22':51304566, 'chrX':155270560, 'chrY':59373566, + 'chrM':16571} + + +dm2_chrom_lengths = {'chr2h':1694122, 'chr2L':22407834, 'chr2R':20766785, + 'chr3h':2955737, 'chr3L':23771897, 'chr3R':27905053, + 'chr4h':88110, 'chr4':1281640, 'chrXh':359526, + 'chrX':22224390, 'chrYh':396896, 'chrM':19517, + 'chrU':8724946} + +dm3_chrom_lengths = {'chr2L':23011544, + 'chr2LHet':368872, + 'chr2R':21146708, + 'chr2RHet':3288761, + 'chr3L':24543557, + 'chr3LHet':2555491, + 'chr3R':27905053, + 'chr3RHet':2517507, + 'chr4':1351857, + 'chrX':22422827, + 'chrXHet':204112, + 'chrYHet':347038, + 'chrU':10049037, + 'chrUextra':29004656, + 'chrM':19517} + + +sacCer1_chrom_lengths = {'chr1':230208, 'chr2':813136, 'chr3':316613, + 'chr4':1531914, 'chr5':576869, 'chr6':270148, + 'chr7':1090944, 'chr8':562639, 'chr9':439885, + 'chr10':745446, 'chr11':666445, 'chr12':1078173, + 'chr13':924430, 'chr14':784328, 'chr15':1091285, + 'chr16':948060, 'chrM':85779} + + +pombe_chrom_lengths = {'chr1':5580032,'chr2':4541604,'chr3':2453783, + 'mat':41249} + +tair8_chrom_lengths = {'chr1':30427671, 'chr2':19698289, 'chr3':23459830, + 'chr4':18585056, 'chr5':26975502} + + +species_chroms = {'mm8':mm8_chroms, + 'mm9':mm9_chroms, + 'mm10':mm10_chroms, + 'hg18':hg18_chroms, + 'hg19':hg19_chroms, + "dm2":dm2_chroms, + "dm3":dm3_chroms, + "sacCer1":sacCer1_chroms, + "pombe":pombe_chroms, + 'rn4':rn4_chroms, + 'tair8':tair8_chroms, + 'background':background_chroms}; + + +species_chrom_lengths={'mm8':mm8_chrom_lengths, + 'mm9':mm9_chrom_lengths, + 'mm10':mm10_chrom_lengths, + 'hg18':hg18_chrom_lengths, + 'hg19':hg19_chrom_lengths, + 'dm2':dm2_chrom_lengths, + 'dm3':dm3_chrom_lengths, + 'sacCer1':sacCer1_chrom_lengths, + 'pombe':pombe_chrom_lengths, + 'rn4':rn4_chrom_lengths, + 'tair8':tair8_chrom_lengths, + 'background':background_chrom_lengths}; + + + +