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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Columns of a GTF file:
seqname - name of the chromosome or scaffold; chromosome names
without a 'chr' in Ensembl (but sometimes with a 'chr'
elsewhere)
source - name of the program that generated this feature, or
the data source (database or project name)
feature - feature type name.
Features currently in Ensembl GTFs:
gene
transcript
exon
CDS
Selenocysteine
start_codon
stop_codon
UTR
Older Ensembl releases may be missing some of these features.
start - start position of the feature, with sequence numbering
starting at 1.
end - end position of the feature, with sequence numbering
starting at 1.
score - a floating point value indiciating the score of a feature
strand - defined as + (forward) or - (reverse).
frame - one of '0', '1' or '2'. Frame indicates the number of base pairs
before you encounter a full codon. '0' indicates the feature
begins with a whole codon. '1' indicates there is an extra
base (the 3rd base of the prior codon) at the start of this feature.
'2' indicates there are two extra bases (2nd and 3rd base of the
prior exon) before the first codon. All values are given with
relation to the 5' end.
attribute - a semicolon-separated list of tag-value pairs (separated by a space),
providing additional information about each feature. A key can be
repeated multiple times.
(from ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/README)
"""
REQUIRED_COLUMNS = [
"seqname",
"source",
"feature",
"start",
"end",
"score",
"strand",
"frame",
"attribute",
]
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