Commit a5daeb29 authored by Blaise Li's avatar Blaise Li
Browse files

Switch to newer rpy2.

Interface seems to have changed. There may still be missing changes.
parent e95c85b9
......@@ -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,
......@@ -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))
......
......@@ -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,
......@@ -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))
......
......@@ -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))
......@@ -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))
......
......@@ -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,
......@@ -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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