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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
metagWGS
Commits
d675114f
Commit
d675114f
authored
Oct 05, 2021
by
MARTIN Pierre
Browse files
sorted sample files to avoid random output
parent
68d095e3
Changes
2
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Inline
Side-by-side
bin/Quantification_clusters.py
View file @
d675114f
...
...
@@ -145,7 +145,7 @@ print(str(datetime.now()))
# For each count file (output of featureCounts), reading of lines one by one,
# recovery of name of gene and count number and incrementing of corresponding
# value in d_count_by_g_clstr.
for
(
count_idx
,
counts_path
)
in
enumerate
(
files_of_counts
):
for
(
count_idx
,
counts_path
)
in
enumerate
(
sorted
(
files_of_counts
)
)
:
with
open
(
counts_path
)
as
fh
:
for
f_gene_counts
in
fh
:
if
f_gene_counts
.
startswith
(
'#'
)
\
...
...
bin/merge_abundance_and_functional_annotations.py
View file @
d675114f
...
...
@@ -80,7 +80,7 @@ with open(args.list_of_file_diamond) as fdiamond_list:
concat_eggnog_mapper_files
=
pd
.
DataFrame
()
# Concatenate annotation files.
for
(
annotations_idx
,
annotations_path
)
in
enumerate
(
files_of_annotations
):
for
(
annotations_idx
,
annotations_path
)
in
enumerate
(
sorted
(
files_of_annotations
)
)
:
eggnog_mapper_file
=
pd
.
read_csv
(
annotations_path
,
delimiter
=
'
\t
'
,
decimal
=
'.'
,
skiprows
=
4
)
concat_eggnog_mapper_files
=
pd
.
concat
([
concat_eggnog_mapper_files
,
eggnog_mapper_file
])
...
...
@@ -88,7 +88,7 @@ for (annotations_idx,annotations_path) in enumerate(files_of_annotations):
concat_diamond_files
=
pd
.
DataFrame
()
# Concatenate diamond files.
for
(
diamond_idx
,
diamond_path
)
in
enumerate
(
diamond_files
):
for
(
diamond_idx
,
diamond_path
)
in
enumerate
(
sorted
(
diamond_files
)
)
:
diamond_columns
=
[
"qseqid"
,
"sseqid"
,
"pident"
,
"length"
,
"mismatch"
,
"gapopen"
,
"qstart"
,
"qend"
,
"sstart"
,
"send"
,
"evalue"
,
"bitscore"
,
"qlen"
,
"slen"
,
"stitle"
]
diamond_file
=
pd
.
read_csv
(
diamond_path
,
delimiter
=
'
\t
'
,
decimal
=
'.'
,
header
=
None
,
names
=
diamond_columns
)
diamond_file
.
loc
[:,
"sseqid"
]
=
'https://www.ncbi.nlm.nih.gov/protein/'
+
diamond_file
.
loc
[:,
"sseqid"
]
...
...
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