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genotoul-bioinfo
jflow
Commits
3c722634
Commit
3c722634
authored
May 30, 2017
by
cnoirot
Browse files
Add gff3 format
parent
d111eba7
Changes
1
Hide whitespace changes
Inline
Side-by-side
workflows/formats.py
View file @
3c722634
...
...
@@ -17,6 +17,7 @@
import
jflow
from
jflow
import
seqio
from
jflow.featureiolib.gff3
import
GFF3IO
from
jflow.exceptions
import
InvalidFormatError
import
os
import
sys
...
...
@@ -57,4 +58,14 @@ def sff(ifile):
if
nb_seq
==
10
:
break
except
:
raise
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a sff file!"
)
\ No newline at end of file
def
gff3
(
ifile
):
#try:
reader
=
GFF3IO
(
ifile
,
"r"
)
nb_line
=
0
for
record
in
reader
:
nb_line
+=
1
# only check the first 10 sequences
if
nb_line
==
10
:
break
#except:
# raise InvalidFormatError("The provided file '" + ifile + "' is not a gff3 file!")
\ No newline at end of file
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