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color_process.py
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color_process.py
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#!/usr/bin/env python
import sys
import copy
import logging
import argparse
from BCBio import GFF
# from gff3 import feature_lambda, feature_test_type
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)
def feature_lambda(feature_list, test, test_kwargs, subfeatures=True, parent=None, invert=False, recurse=True):
# Either the top level set of [features] or the subfeature attribute
for feature in feature_list:
feature._parent = parent
test_result = test(feature, **test_kwargs)
# if (not invert and test_result) or (invert and not test_result):
# print feature.type, test_kwargs, test_result, invert ^ test_result
if invert ^ test_result:
if not subfeatures:
feature_copy = copy.deepcopy(feature)
feature_copy.sub_features = []
yield feature_copy
else:
yield feature
if recurse and hasattr(feature, 'sub_features'):
for x in feature_lambda(feature.sub_features, test, test_kwargs, subfeatures=subfeatures, parent=feature, invert=invert, recurse=recurse):
yield x
def feature_test_type(feature, **kwargs):
if 'type' in kwargs:
return feature.type == kwargs['type']
elif 'types' in kwargs:
return feature.type in kwargs['types']
raise Exception("Incorrect feature_test_type call, need type or types")
coloring = {
'Petty': {
'13': '#FFFF00',
'15': '#FFFF00',
'16': '#FFFF00',
'17': '#FFFF00',
'18': '#FFFF00',
'22': '#FFFF00',
'23': '#FFFF00',
'24': '#FFA500',
'25': '#FFA500',
'26': '#FFA500',
'30': '#87CEFA',
'31': '#87CEFA',
'32': '#87CEFA',
'34': '#87CEFA',
'35': '#87CEFA',
'36': '#87CEFA',
'37': '#87CEFA',
'38': '#87CEFA',
'39': '#87CEFA',
'40': '#FF00FF',
'41': '#FF00FF',
'42': '#71BC78',
'43': '#71BC78',
},
'Abp1': {
'20': '#FFFF00',
'23': '#FFFF00',
'24': '#FFFF00',
'25': '#FFFF00',
'26': '#FFFF00',
'29': '#FFFF00',
'30': '#FFFF00',
'34': '#FFA500',
'37': '#87CEFA',
'39': '#87CEFA',
'42': '#87CEFA',
'43': '#87CEFA',
'46': '#87CEFA',
'52': '#71BC78',
},
'phiAB1': {
'15': '#FFFF00',
'16': '#FFFF00',
'17': '#FFFF00',
'18': '#FFFF00',
'19': '#FFFF00',
'20': '#FFFF00',
'21': '#FFFF00',
'23': '#FFFF00',
'24': '#FFFF00',
'27': '#FFA500',
'28': '#FFA500',
'30': '#87CEFA',
'31': '#87CEFA',
'32': '#87CEFA',
'33': '#87CEFA',
'36': '#87CEFA',
'37': '#87CEFA',
'38': '#87CEFA',
'39': '#87CEFA',
'40': '#87CEFA',
'41': '#87CEFA',
'42': '#FF00FF',
'43': '#FF00FF',
'44': '#71BC78',
'45': '#71BC78',
},
'Acibel007': {
'16': '#FFFF00',
'18': '#FFFF00',
'20': '#FFFF00',
'22': '#FFFF00',
'26': '#FFFF00',
'28': '#FFFF00',
'31': '#FFA500',
'32': '#FFA500',
'3': '#87CEFA',
'4': '#87CEFA',
'5': '#87CEFA',
'24': '#87CEFA',
'35': '#87CEFA',
'36': '#87CEFA',
'37': '#87CEFA',
'38': '#87CEFA',
'41': '#87CEFA',
'42': '#87CEFA',
'43': '#87CEFA',
'44': '#87CEFA',
'45': '#87CEFA',
'46': '#87CEFA',
'47': '#FF00FF',
'48': '#FF00FF',
'50': '#71BC78',
'51': '#71BC78',
},
'Fri1': {
'17': '#FFFF00',
'21': '#FFFF00',
'23': '#FFFF00',
'24': '#FFFF00',
'25': '#FFFF00',
'26': '#FFFF00',
'30': '#FFFF00',
'31': '#FFFF00',
'32': '#FFFF00',
'33': '#FFA500',
'35': '#FFA500',
'36': '#FFA500',
'39': '#87CEFA',
'40': '#87CEFA',
'41': '#87CEFA',
'44': '#87CEFA',
'45': '#87CEFA',
'46': '#87CEFA',
'47': '#87CEFA',
'48': '#87CEFA',
'49': '#87CEFA',
'50': '#FF00FF',
'51': '#FF00FF',
'52': '#71BC78',
'53': '#71BC78',
},
'phiAB6': {
'12': '#FFFF00',
'13': '#FFFF00',
'16': '#FFFF00',
'17': '#FFFF00',
'19': '#FFFF00',
'20': '#FFFF00',
'22': '#FFFF00',
'23': '#FFFF00',
'24': '#FFFF00',
'26': '#FFA500',
'27': '#FFA500',
'29': '#87CEFA',
'30': '#87CEFA',
'31': '#87CEFA',
'32': '#87CEFA',
'35': '#87CEFA',
'36': '#87CEFA',
'37': '#87CEFA',
'38': '#87CEFA',
'39': '#87CEFA',
'40': '#87CEFA',
'41': '#FF00FF',
'42': '#FF00FF',
'43': '#71BC78',
'44': '#71BC78',
}
}
def color(gff3):
for rec in GFF.parse(gff3):
genes = list(feature_lambda(rec.features, feature_test_type, {'type': 'gene'}, subfeatures=True))
cdss_sorted = []
for gene in genes:
cdss = sorted(list(feature_lambda(gene.sub_features, feature_test_type, {'type': 'CDS'}, subfeatures=True)), key=lambda x: x.location.start)
for cds in cdss:
cdss_sorted.append(cds)
for num, c in enumerate(sorted(cdss_sorted, key=lambda x: x.location.start), 1):
color = "black"
if str(num) in coloring[rec.id]:
color = coloring[rec.id][str(num)]
c.qualifiers.update({'color': [color]})
c.qualifiers.update({'num': [num]})
GFF.write([rec], sys.stdout)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='add color to CDSs')
parser.add_argument('gff3', type=argparse.FileType("r"), help='GFF3 annotations')
args = parser.parse_args()
color(**vars(args))