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Add mm10 to sicer #514

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Add mm10 to sicer #514

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ff7fcec
add mm10 to xml
ccedmendoza Sep 19, 2018
b5bd7e3
add mm10 to .py
ccedmendoza Sep 19, 2018
4cf2f84
I'm not sure of where it should be added or how it should be updated.…
ccedmendoza Sep 19, 2018
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206 changes: 206 additions & 0 deletions tools/sicer/GenomeData.py
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#!/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:
# [email protected]).
#
# 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};




3 changes: 2 additions & 1 deletion tools/sicer/sicer_wrapper.py
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Expand Up @@ -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 ):
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2 changes: 1 addition & 1 deletion tools/sicer/sicer_wrapper.xml
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Expand Up @@ -31,7 +31,7 @@
</requirements>
<inputs>
<param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
<validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator>
<validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'mm10', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator>
</param>
<param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys -->
<options>
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