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: ...@@ -1198,7 +1198,7 @@ rule merge_bigwig_reps:
from rpy2.robjects import Formula, StrVector from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError #from rpy2.rinterface import RRuntimeError
rule differential_expression: rule differential_expression:
input: input:
counts_table = source_counts, counts_table = source_counts,
...@@ -1227,7 +1227,8 @@ rule differential_expression: ...@@ -1227,7 +1227,8 @@ rule differential_expression:
contrast = StrVector(["lib", cond, ref]) contrast = StrVector(["lib", cond, ref])
formula = Formula("~ lib") formula = Formula("~ lib")
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast) 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( warnings.warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % ( "Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % (
str(e), wildcards.contrast, wildcards.orientation, wildcards.biotype)) str(e), wildcards.contrast, wildcards.orientation, wildcards.biotype))
......
...@@ -1733,7 +1733,7 @@ rule compute_RPM_folds: ...@@ -1733,7 +1733,7 @@ rule compute_RPM_folds:
from rpy2.robjects import Formula, StrVector from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError #from rpy2.rinterface import RRuntimeError
rule differential_expression: rule differential_expression:
input: input:
counts_table = source_counts, counts_table = source_counts,
...@@ -1769,7 +1769,8 @@ rule differential_expression: ...@@ -1769,7 +1769,8 @@ rule differential_expression:
contrast = StrVector(["lib", cond, ref]) contrast = StrVector(["lib", cond, ref])
try: try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast) 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( warnings.warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % ( "Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % (
str(e), wildcards.contrast, wildcards.orientation, wildcards.biotype)) str(e), wildcards.contrast, wildcards.orientation, wildcards.biotype))
......
...@@ -1052,7 +1052,7 @@ rule gather_read_counts_summaries: ...@@ -1052,7 +1052,7 @@ rule gather_read_counts_summaries:
from rpy2.robjects import Formula, StrVector from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError #from rpy2.rinterface import RRuntimeError
rule differential_expression: rule differential_expression:
input: input:
counts_table = source_counts, counts_table = source_counts,
...@@ -1092,7 +1092,8 @@ rule differential_expression: ...@@ -1092,7 +1092,8 @@ rule differential_expression:
contrast = StrVector(["lib", cond, ref]) contrast = StrVector(["lib", cond, ref])
try: try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast) 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( warnings.warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s_%s" % ( "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)) str(e), wildcards.read_type, wildcards.contrast, wildcards.orientation, wildcards.biotype))
...@@ -2575,7 +2576,7 @@ def plot_counts_scatters(counts_and_res, cols): ...@@ -2575,7 +2576,7 @@ def plot_counts_scatters(counts_and_res, cols):
################################################### ###################################################
from rpy2.robjects import Formula, StrVector from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError #from rpy2.rinterface import RRuntimeError
rule small_RNA_differential_expression: rule small_RNA_differential_expression:
input: input:
counts_table = source_counts, counts_table = source_counts,
...@@ -2611,7 +2612,8 @@ rule small_RNA_differential_expression: ...@@ -2611,7 +2612,8 @@ rule small_RNA_differential_expression:
# raise NotImplementedError("Unknown contrast: %s" % wildcards.contrast) # raise NotImplementedError("Unknown contrast: %s" % wildcards.contrast)
try: try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast) 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( warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % ( "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)) str(e), wildcards.contrast, wildcards.orientation, wildcards.small_type))
......
...@@ -3636,7 +3636,7 @@ def plot_counts_scatters(counts_and_res, cols): ...@@ -3636,7 +3636,7 @@ def plot_counts_scatters(counts_and_res, cols):
################################################### ###################################################
from rpy2.robjects import Formula, StrVector from rpy2.robjects import Formula, StrVector
from rpy2.rinterface import RRuntimeError #from rpy2.rinterface import RRuntimeError
rule small_RNA_differential_expression: rule small_RNA_differential_expression:
input: input:
counts_table = source_small_RNA_counts, counts_table = source_small_RNA_counts,
...@@ -3668,7 +3668,8 @@ rule small_RNA_differential_expression: ...@@ -3668,7 +3668,8 @@ rule small_RNA_differential_expression:
contrast = StrVector(["lib", cond, ref]) contrast = StrVector(["lib", cond, ref])
try: try:
res, size_factors = do_deseq2(COND_NAMES, CONDITIONS, counts_data, formula=formula, contrast=contrast) 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( warn(
"Probably not enough usable data points to perform DESeq2 analyses:\n%s\nSkipping %s_%s_%s" % ( "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)) str(e), wildcards.contrast, wildcards.orientation, wildcards.small_type))
......
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