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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
D-GENIES
Commits
ddf1fc73
Commit
ddf1fc73
authored
May 15, 2018
by
Floreal Cabanettes
Browse files
Fix MAF parser
parent
dae21657
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/dgenies/lib/parsers.py
View file @
ddf1fc73
...
...
@@ -39,6 +39,7 @@ def maf(in_maf, out_paf):
if
qannots
[
"strand"
]
==
-
1
:
qstart
=
qlen
-
qstart
qend
=
qlen
-
qend
strand
=
"+"
if
tannots
[
"strand"
]
==
qannots
[
"strand"
]
else
"-"
paf
.
write
(
"{qname}
\t
{qlen}
\t
{qstart}
\t
{qend}
\t
{strand}
\t
{tname}
\t
{tlen}
\t
{tstart}
\t
{tend}
\t
{matches}
\t
"
"{block_len}
\t
255
\n
"
.
format
(
tname
=
seqs
[
0
].
id
,
...
...
@@ -47,9 +48,9 @@ def maf(in_maf, out_paf):
tend
=
tend
,
qname
=
seqs
[
1
].
id
,
qlen
=
qlen
,
qstart
=
qstart
,
qend
=
qend
,
strand
=
"+"
if
tannots
[
"strand"
]
==
qannots
[
"strand"
]
else
"-"
,
qstart
=
qstart
if
strand
==
"+"
else
qend
,
qend
=
qend
if
strand
==
"+"
else
qstart
,
strand
=
strand
,
matches
=
matches
,
block_len
=
tannots
[
"size"
]
))
...
...
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