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Blaise LI
bioinfo_utils
Commits
9154ba5c
Commit
9154ba5c
authored
2 years ago
by
Blaise Li
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Script extracting gtf info switched to python3.
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Genome_preparation/extract_info_from_gtf.py
+53
-31
53 additions, 31 deletions
Genome_preparation/extract_info_from_gtf.py
with
53 additions
and
31 deletions
Genome_preparation/extract_info_from_gtf.py
+
53
−
31
View file @
9154ba5c
#!/usr/bin/env python
2
#!/usr/bin/env python
3
# vim: set fileencoding=<utf-8> :
"""
"""
This script extracts various information from an Ensembl gtf annotation file.
This script extracts various information from an Ensembl gtf annotation file.
It generates separate gtf files for the different transcript types.
It generates separate gtf files for the different transcript types.
It pickles a python dictionary converting from gene_id to gene_name.
"""
It pickles a python dictionary converting from gene_id to gene_name.
"""
# TODO: convert to python3
from
__future__
import
print_function
from
os.path
import
splitext
from
os.path
import
splitext
import
sys
import
sys
from
collections
import
defaultdict
from
collections
import
defaultdict
from
contextlib
import
ExitStack
# To store dictionaries
# To store dictionaries
from
cPickle
import
dump
,
HIGHEST_PROTOCOL
from
pickle
import
dump
,
HIGHEST_PROTOCOL
def
default_gene_name_getter
(
annots
,
*
_
):
return
annots
[
"
gene_name
"
]
def
mir_name_getter
(
annots
,
gene_id
):
if
gene_id
[
-
1
]
==
"
a
"
:
return
annots
[
"
gene_name
"
]
+
"
-5p
"
if
gene_id
[
-
1
]
==
"
b
"
:
return
annots
[
"
gene_name
"
]
+
"
-3p
"
raise
ValueError
(
"
miRNA transcript id should end with either
'
a
'
or
'
b
'"
)
in_gtf
=
sys
.
argv
[
1
]
in_gtf
=
sys
.
argv
[
1
]
base
,
ext
=
splitext
(
in_gtf
)
base
,
ext
=
splitext
(
in_gtf
)
biotype_counter
=
defaultdict
(
int
)
biotype_counter
=
defaultdict
(
int
)
# TODO: Use ExitStack to have a context manager.
biotypes2id
=
{
# Open gtf files
"
rRNA
"
:
"
gene_id
"
,
biotypes
=
{
"
rRNA
"
:
open
(
"
%s_rRNA%s
"
%
(
base
,
ext
),
"
w
"
),
# TODO: use "transcript_id" to have distinct 3p and 5p entries
"
miRNA
"
:
open
(
"
%s_miRNA%s
"
%
(
base
,
ext
),
"
w
"
),
# "miRNA": "transcript_id",
"
piRNA
"
:
open
(
"
%s_piRNA%s
"
%
(
base
,
ext
),
"
w
"
),
"
miRNA
"
:
"
gene_id
"
,
"
snRNA
"
:
open
(
"
%s_snRNA%s
"
%
(
base
,
ext
),
"
w
"
),
"
piRNA
"
:
"
gene_id
"
,
"
lincRNA
"
:
open
(
"
%s_lincRNA%s
"
%
(
base
,
ext
),
"
w
"
),
"
snRNA
"
:
"
gene_id
"
,
"
tRNA
"
:
open
(
"
%s_tRNA%s
"
%
(
base
,
ext
),
"
w
"
),
"
lincRNA
"
:
"
gene_id
"
,
"
snoRNA
"
:
open
(
"
%s_snoRNA%s
"
%
(
base
,
ext
),
"
w
"
),
"
tRNA
"
:
"
gene_id
"
,
"
protein_coding
"
:
open
(
"
%s_protein_coding%s
"
%
(
base
,
ext
),
"
w
"
),
"
snoRNA
"
:
"
gene_id
"
,
"
antisense
"
:
open
(
"
%s_antisense%s
"
%
(
base
,
ext
),
"
w
"
),
"
protein_coding
"
:
"
gene_id
"
,
"
ncRNA
"
:
open
(
"
%s_ncRNA%s
"
%
(
base
,
ext
),
"
w
"
),
"
antisense
"
:
"
gene_id
"
,
"
pseudogene
"
:
open
(
"
%s_pseudogene%s
"
%
(
base
,
ext
),
"
w
"
)}
"
ncRNA
"
:
"
gene_id
"
,
"
pseudogene
"
:
"
gene_id
"
}
gene_name_getters
=
{
# TODO: use this
# "miRNA": mir_name_getter
}
# Mapping gene_id to gene_name
# Mapping gene_id to gene_name
id2name
=
{}
id2name
=
{}
...
@@ -39,7 +54,11 @@ max_lengths = defaultdict(int)
...
@@ -39,7 +54,11 @@ max_lengths = defaultdict(int)
# To check that it is sorted
# To check that it is sorted
chromosomes
=
[
None
]
chromosomes
=
[
None
]
start
=
0
start
=
0
with
open
(
in_gtf
,
"
r
"
)
as
gtf
:
with
ExitStack
()
as
stack
,
open
(
in_gtf
,
"
r
"
)
as
gtf
:
dest_files
=
{
biotype
:
stack
.
enter_context
(
open
(
f
"
{
base
}
_
{
biotype
}{
ext
}
"
,
"
w
"
))
for
biotype
in
biotypes2id
.
keys
()
}
for
line
in
gtf
:
for
line
in
gtf
:
fields
=
line
.
strip
().
split
(
"
\t
"
)
fields
=
line
.
strip
().
split
(
"
\t
"
)
chrom
=
fields
[
0
]
chrom
=
fields
[
0
]
...
@@ -52,27 +71,30 @@ with open(in_gtf, "r") as gtf:
...
@@ -52,27 +71,30 @@ with open(in_gtf, "r") as gtf:
start
=
int
(
fields
[
3
])
start
=
int
(
fields
[
3
])
# We only use "transcript" annotation.
# We only use "transcript" annotation.
if
fields
[
2
]
==
"
transcript
"
:
if
fields
[
2
]
==
"
transcript
"
:
annots
=
dict
([(
k
,
v
.
strip
(
'"'
))
for
(
k
,
v
)
in
[
f
.
split
(
"
"
)
for
f
in
fields
[
8
].
split
(
"
;
"
)[:
-
1
]]])
annots
=
dict
([
(
k
,
v
.
strip
(
'"'
))
for
(
k
,
v
)
in
[
f
.
split
(
"
"
)
for
f
in
fields
[
8
].
split
(
"
;
"
)[:
-
1
]]])
if
"
exon_number
"
not
in
annots
:
if
"
exon_number
"
not
in
annots
:
biotype
=
annots
[
"
gene_biotype
"
]
biotype
=
annots
[
"
gene_biotype
"
]
biotyp
es
[
biotype
].
write
(
line
)
dest_fil
es
[
biotype
].
write
(
line
)
biotype_counter
[
biotype
]
+=
1
biotype_counter
[
biotype
]
+=
1
end
=
int
(
fields
[
4
])
end
=
int
(
fields
[
4
])
length
=
end
+
1
-
start
length
=
end
+
1
-
start
max_lengths
[
biotype
]
=
max
(
length
,
max_lengths
[
biotype
])
max_lengths
[
biotype
]
=
max
(
length
,
max_lengths
[
biotype
])
gene_id
=
annots
[
"
gene_id
"
]
gene_id
=
annots
[
biotypes2id
[
biotype
]
]
if
gene_id
in
id2name
:
if
gene_id
in
id2name
:
assert
annots
[
"
gene_name
"
]
==
id2name
[
gene_id
],
"
Gene %s already registered with another name.
"
%
gene_id
assert
annots
[
"
gene_name
"
]
==
id2name
[
gene_id
],
"
Gene %s already registered with another name.
"
%
gene_id
else
:
else
:
id2name
[
gene_id
]
=
annots
[
"
gene_name
"
]
post_process_name
=
gene_name_getters
.
get
(
biotype
,
default_gene_name_getter
)
id2name
[
gene_id
]
=
post_process_name
(
annots
,
gene_id
)
with
open
(
"
%s
_id2name.pickle
"
%
base
,
"
w
"
)
as
pickle_file
:
with
open
(
f
"
{
base
}
_id2name.pickle
"
,
"
w
b
"
)
as
pickle_file
:
print
(
"
Storing id2name in
%s
"
%
pickle_file
.
name
)
print
(
f
"
Storing id2name in
{
pickle_file
.
name
}
"
)
dump
(
id2name
,
pickle_file
,
HIGHEST_PROTOCOL
)
dump
(
id2name
,
pickle_file
,
HIGHEST_PROTOCOL
)
#
Close gtf files and i
nform user about number of entries.
#
I
nform user about number of entries.
for
(
biotype
,
count
)
in
biotype_counter
.
items
():
for
(
biotype
,
count
)
in
biotype_counter
.
items
():
print
(
biotype
,
count
,
"
(max length = %d)
"
%
max_lengths
[
biotype
],
sep
=
"
\t
"
)
print
(
biotype
,
count
,
f
"
(max length =
{
max_lengths
[
biotype
]
}
)
"
,
sep
=
"
\t
"
)
biotypes
[
biotype
].
close
()
sys
.
exit
(
0
)
sys
.
exit
(
0
)
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