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Blaise LI
bioinfo_utils
Commits
a5daeb29
Commit
a5daeb29
authored
May 17, 2019
by
Blaise Li
Browse files
Switch to newer rpy2.
Interface seems to have changed. There may still be missing changes.
parent
e95c85b9
Changes
4
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PRO-seq/PRO-seq.snakefile
View file @
a5daeb29
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@@ -1198,7 +1198,7 @@ rule merge_bigwig_reps:
from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError
#
from rpy2.rinterface import RRuntimeError
rule differential_expression:
input:
counts_table = source_counts,
...
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@@ -1227,7 +1227,8 @@ rule differential_expression:
contrast = StrVector(["lib", cond, ref])
formula = Formula("~ lib")
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast)
except RRuntimeError as e:
#except RRuntimeError as e:
except RuntimeError as e:
warnings.warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % (
str(e), wildcards.contrast, wildcards.orientation, wildcards.biotype))
...
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RNA_Seq_Cecere/RNA-seq.snakefile
View file @
a5daeb29
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@@ -1733,7 +1733,7 @@ rule compute_RPM_folds:
from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError
#
from rpy2.rinterface import RRuntimeError
rule differential_expression:
input:
counts_table = source_counts,
...
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@@ -1769,7 +1769,8 @@ rule differential_expression:
contrast = StrVector(["lib", cond, ref])
try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast)
except RRuntimeError as e:
#except RRuntimeError as e:
except RuntimeError as e:
warnings.warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % (
str(e), wildcards.contrast, wildcards.orientation, wildcards.biotype))
...
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Ribo-seq/Ribo-seq.snakefile
View file @
a5daeb29
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@@ -1052,7 +1052,7 @@ rule gather_read_counts_summaries:
from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError
#
from rpy2.rinterface import RRuntimeError
rule differential_expression:
input:
counts_table = source_counts,
...
...
@@ -1092,7 +1092,8 @@ rule differential_expression:
contrast = StrVector(["lib", cond, ref])
try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast)
except RRuntimeError as e:
#except RRuntimeError as e:
except RuntimeError as e:
warnings.warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s_%s" % (
str(e), wildcards.read_type, wildcards.contrast, wildcards.orientation, wildcards.biotype))
...
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@@ -2575,7 +2576,7 @@ def plot_counts_scatters(counts_and_res, cols):
###################################################
from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError
#
from rpy2.rinterface import RRuntimeError
rule small_RNA_differential_expression:
input:
counts_table = source_counts,
...
...
@@ -2611,7 +2612,8 @@ rule small_RNA_differential_expression:
# raise NotImplementedError("Unknown contrast: %s" % wildcards.contrast)
try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast)
except RRuntimeError as e:
#except RRuntimeError as e:
except RuntimeError as e:
warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % (
str(e), wildcards.contrast, wildcards.orientation, wildcards.small_type))
...
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small_RNA-seq/small_RNA-seq.snakefile
View file @
a5daeb29
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@@ -3636,7 +3636,7 @@ def plot_counts_scatters(counts_and_res, cols):
###################################################
from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError
#
from rpy2.rinterface import RRuntimeError
rule small_RNA_differential_expression:
input:
counts_table = source_small_RNA_counts,
...
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@@ -3668,7 +3668,8 @@ rule small_RNA_differential_expression:
contrast = StrVector(["lib", cond, ref])
try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast)
except RRuntimeError as e:
#except RRuntimeError as e:
except RuntimeError as e:
warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % (
str(e), wildcards.contrast, wildcards.orientation, wildcards.small_type))
...
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