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genotoul-bioinfo
jflow
Commits
77b80492
Commit
77b80492
authored
Apr 27, 2017
by
cnoirot
Browse files
# WARNING: head commit changed in the meantime
Debug call exception when testing file format Debug print output element.
parent
fd99b07a
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/jflow/component.py
View file @
77b80492
...
...
@@ -635,9 +635,9 @@ class Component(object):
if
isinstance
(
element
[
0
],
list
):
for
i
in
range
(
len
(
element
))
:
to_write
+=
"List"
+
str
(
i
+
1
)
+
":
\n
"
to_write
+=
"
\n
"
.
join
(
element
[
i
])
+
"
\n
"
to_write
+=
"
\n
"
.
join
(
str
(
element
[
i
])
)
+
"
\n
"
else
:
to_write
+=
"
\n
"
.
join
(
element
)
+
"
\n
"
to_write
+=
"
\n
"
.
join
(
str
(
element
)
)
+
"
\n
"
else
:
to_write
+=
element
+
"
\n
"
if
to_write
!=
""
:
...
...
workflows/formats.py
View file @
77b80492
...
...
@@ -33,7 +33,7 @@ def fastq(ifile):
# only check the first 10 sequences
if
nb_seq
==
10
:
break
except
:
raise
jflow
.
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a fastq file!"
)
raise
jflow
.
exceptions
.
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a fastq file!"
)
def
fasta
(
ifile
):
try
:
...
...
@@ -44,7 +44,7 @@ def fasta(ifile):
# only check the first 10 sequences
if
nb_seq
==
10
:
break
except
:
raise
jflow
.
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a fasta file!"
)
raise
jflow
.
exceptions
.
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a fasta file!"
)
def
sff
(
ifile
):
try
:
...
...
@@ -55,5 +55,5 @@ def sff(ifile):
# only check the first 10 sequences
if
nb_seq
==
10
:
break
except
:
raise
jflow
.
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a sff file!"
)
raise
jflow
.
exceptions
.
InvalidFormatError
(
"The provided file '"
+
ifile
+
"' is not a sff file!"
)
\ No newline at end of file
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