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Merge pull request #20 from bioinform/fix_diff
Fix diff
2 parents 4c8a60f + a958a9b commit 9a4ddee

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‎docker/Dockerfile‎

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@@ -1,7 +1,7 @@
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FROM ubuntu:18.04
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ENV RNACOCKTAIL_VERSION 0.3.1
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ENV RNACOCKTAIL_VERSION 0.3.2
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ENV R_VERSION 3.6.1-3bionic
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ENV DEBIAN_FRONTEND noninteractive
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ENV DEBCONF_NONINTERACTIVE_SEEN true

‎index.html‎

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@@ -168,8 +168,8 @@ <h2>Publication</h2>
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<h2>Download RNACocktail</h2>
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<p>Latest version: <a href="https://github.com/bioinform/RNACocktail/archive/v0.3.1.tar.gz"
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onclick="trackOutboundLink('https://github.com/bioinform/RNACocktail/archive/v0.3.1.tar.gz'); return false;">https://github.com/bioinform/RNACocktail/archive/v0.3.1.tar.gz</a></p>
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<p>Latest version: <a href="https://github.com/bioinform/RNACocktail/archive/v0.3.2.tar.gz"
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onclick="trackOutboundLink('https://github.com/bioinform/RNACocktail/archive/v0.3.2.tar.gz'); return false;">https://github.com/bioinform/RNACocktail/archive/v0.3.2.tar.gz</a></p>
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<p>For other versions, see "releases". <a href="https://github.com/bioinform/RNACocktail/releases"
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onclick="trackOutboundLink('https://github.com/bioinform/RNACocktail/releases'); return false;">https://github.com/bioinform/RNACocktail/releases</a></p>
@@ -386,8 +386,8 @@ <h2>System Requirements</h2>
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</p>
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<h2>Installing RNACocktail</h2>
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<p>RNACocktail is a Python 2.7 package and can be installed using <code>pip</code>. To install type <code>pip install https://github.com/bioinform/RNACocktail/archive/v0.3.1.tar.gz</code> (using Python 2.7). The current version
390-
of RNACocktail is v0.3.1. In general, the install source would be https://github.com/bioinform/RNACocktail/archive/version.tar.gz</p>
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<p>RNACocktail is a Python 2.7 package and can be installed using <code>pip</code>. To install type <code>pip install https://github.com/bioinform/RNACocktail/archive/v0.3.2.tar.gz</code> (using Python 2.7). The current version
390+
of RNACocktail is v0.3.2. In general, the install source would be https://github.com/bioinform/RNACocktail/archive/version.tar.gz</p>
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<h2>Running RNACocktail</h2>

‎src/_version.py‎

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@@ -1 +1 @@
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__version__ = "0.3.1"
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__version__ = "0.3.2"

‎src/run_diff.py‎

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@@ -3,6 +3,7 @@
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from defaults import *
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from utils import *
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import csv
6+
import glob
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78
FORMAT = '%(levelname)s %(asctime)-15s %(name)-20s %(message)s'
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logFormatter = logging.Formatter(FORMAT)
@@ -182,6 +183,7 @@ def run_deseq2(quant_files="", alignments="",
182183
if start<=step:
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logger.info("--------------------------STEP %s--------------------------"%step)
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command = "%s -e \"library('DESeq2'); load('%s/txi.rda'); \
186+
samples <- c(%s); \
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condition <- factor(c(%s)); \
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(colData <- data.frame(row.names=colnames(txi$count), condition));\
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counts <- round(txi$counts); mode(counts) <- 'integer'; \
@@ -193,12 +195,24 @@ def run_deseq2(quant_files="", alignments="",
193195
lengths <- txi$length; dimnames(lengths) <- dimnames(dds);\
194196
assays(dds)[['avgTxLength']] <- lengths; }; \
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dds <- dds[ rowSums(counts(dds)) >= %d, ]; \
196-
dds$condition <- relevel(dds$condition, ref='C1'); \
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dds <- DESeq(dds); res <- results(dds, alpha=%f); \
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(summary(res)); save(txi,colData,condition,dds,res, \
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file='%s/deseq2.rda'); write.table(res, file = '%s/deseq2_res.tab', \
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quote = FALSE, sep='\\t');\""%(
201-
R, work_deseq2, ",".join(map(lambda i:"rep('C%d', %d)"%(i,n_replicates[i]),range(len(samples)))),
198+
dds <- DESeq(dds); \
199+
for (i in seq_along(samples)){ \
200+
for (j in seq_along(samples)){ \
201+
if (i < j){\
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sample1 <- samples[i]; \
203+
sample2 <- samples[j]; \
204+
res <- results(dds, contrast=c('condition',sample1,sample2), alpha=%f); \
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(summary(res)); \
206+
res_file= sprintf('%s/deseq2_res_%%s_vs_%%s.tab',sample1,sample2);\
207+
write.table(res, file = res_file, \
208+
quote = FALSE, sep='\\t'); \
209+
} \
210+
} \
211+
}; \
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save(txi,colData,condition,dds,res, \
213+
file='%s/deseq2.rda');\""%(
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R, work_deseq2, ",".join(map(lambda i:"'sample%d'"%(i),range(len(samples)))),
215+
",".join(map(lambda i:"rep('sample%d', %d)"%(i,n_replicates[i]),range(len(samples)))),
202216
mincount, alpha, work_deseq2, work_deseq2)
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cmd = TimedExternalCmd(command, logger, raise_exception=True)
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retcode = cmd.run(cmd_log_fd_out=deseq2_log_fd, cmd_log=deseq2_log, msg=msg, timeout=timeout)
@@ -233,17 +247,29 @@ def run_deseq2(quant_files="", alignments="",
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command = "%s -e \"library('DESeq2'); countData <- read.table('%s/featureCounts.txt', \
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header=TRUE, row.names=1); countData <- countData[ ,6:ncol(countData)]; \
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countData <- as.matrix(countData); \
250+
samples <- c(%s); \
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condition <- factor(c(%s)); \
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(colData <- data.frame(row.names=colnames(countData), condition));\
238253
dds <- DESeqDataSetFromMatrix(countData=countData, colData=colData, design=~ condition);\
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dds <- dds[ rowSums(counts(dds)) >= %d, ]; \
240-
dds$condition <- relevel(dds$condition, ref='C1'); \
241-
dds <- DESeq(dds); res <- results(dds, alpha=%f); \
242-
(summary(res)); save(countData,colData,condition,dds,res, \
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file='%s/deseq2.rda'); write.table(res, file = '%s/deseq2_res.tab', \
244-
quote = FALSE, sep='\\t');\""%(
245-
R, work_deseq2, ",".join(map(lambda i:"rep('C%d', %d)"%(i,n_replicates[i]),
246-
range(len(samples)))),
255+
dds <- DESeq(dds); \
256+
for (i in seq_along(samples)){ \
257+
for (j in seq_along(samples)){ \
258+
if (i < j){\
259+
sample1 <- samples[i]; \
260+
sample2 <- samples[j]; \
261+
res <- results(dds, contrast=c('condition',sample1,sample2), alpha=%f); \
262+
(summary(res)); \
263+
res_file= sprintf('%s/deseq2_res_%%s_vs_%%s.tab',sample1,sample2);\
264+
write.table(res, file = res_file, \
265+
quote = FALSE, sep='\\t'); \
266+
} \
267+
} \
268+
}; \
269+
save(countData,colData,condition,dds,res, \
270+
file='%s/deseq2.rda');\""%(
271+
R, work_deseq2, ",".join(map(lambda i:"'sample%d'"%(i),range(len(samples)))),
272+
",".join(map(lambda i:"rep('sample%d', %d)"%(i,n_replicates[i]),range(len(samples)))),
247273
mincount, alpha, work_deseq2, work_deseq2)
248274
cmd = TimedExternalCmd(command, logger, raise_exception=True)
249275
retcode = cmd.run(cmd_log_fd_out=deseq2_log_fd, cmd_log=deseq2_log, msg=msg, timeout=timeout)
@@ -299,17 +325,29 @@ def run_deseq2(quant_files="", alignments="",
299325
command = "%s -e \"library('DESeq2'); countData <- read.table('%s/featureCounts.txt', \
300326
header=TRUE, row.names=1); countData <- countData[ ,6:ncol(countData)]; \
301327
countData <- as.matrix(countData); \
328+
samples <- c(%s); \
302329
condition <- factor(c(%s)); \
303330
(colData <- data.frame(row.names=colnames(countData), condition));\
304331
dds <- DESeqDataSetFromMatrix(countData=countData, colData=colData, design=~ condition);\
305332
dds <- dds[ rowSums(counts(dds)) >= %d, ]; \
306-
dds$condition <- relevel(dds$condition, ref='C1'); \
307-
dds <- DESeq(dds); res <- results(dds, alpha=%f); \
308-
(summary(res)); save(countData,colData,condition,dds,res, \
309-
file='%s/deseq2.rda'); write.table(res, file = '%s/deseq2_res.tab', \
310-
quote = FALSE, sep='\\t');\""%(
311-
R, work_deseq2, ",".join(map(lambda i:"rep('C%d', %d)"%(i,n_replicates[i]),
312-
range(len(samples)))),
333+
dds <- DESeq(dds); \
334+
for (i in seq_along(samples)){ \
335+
for (j in seq_along(samples)){ \
336+
if (i < j){\
337+
sample1 <- samples[i]; \
338+
sample2 <- samples[j]; \
339+
res <- results(dds, contrast=c('condition',sample1,sample2), alpha=%f); \
340+
(summary(res)); \
341+
res_file= sprintf('%s/deseq2_res_%%s_vs_%%s.tab',sample1,sample2);\
342+
write.table(res, file = res_file, \
343+
quote = FALSE, sep='\\t'); \
344+
} \
345+
} \
346+
}; \
347+
save(countData,colData,condition,dds, \
348+
file='%s/deseq2.rda');\""%(
349+
R, work_deseq2, ",".join(map(lambda i:"'sample%d'"%(i),range(len(samples)))),
350+
",".join(map(lambda i:"rep('sample%d', %d)"%(i,n_replicates[i]),range(len(samples)))),
313351
mincount, alpha, work_deseq2, work_deseq2)
314352
cmd = TimedExternalCmd(command, logger, raise_exception=True)
315353
retcode = cmd.run(cmd_log_fd_out=deseq2_log_fd, cmd_log=deseq2_log, msg=msg, timeout=timeout)
@@ -322,20 +360,21 @@ def run_deseq2(quant_files="", alignments="",
322360
msg="Copy predictions to output directory for %s."%samples_txt
323361
if start<=step:
324362
logger.info("--------------------------STEP %s--------------------------"%step)
325-
if os.path.exists("%s/deseq2_res.tab"%work_deseq2):
326-
command = "cp %s/deseq2_res.tab %s/deseq2_res.tab"%(
327-
work_deseq2, out_deseq2)
328-
cmd = TimedExternalCmd(command, logger, raise_exception=True)
329-
retcode = cmd.run(cmd_log_fd_out=deseq2_log_fd, cmd_log=deseq2_log, msg=msg, timeout=timeout)
363+
if len(glob.glob("%s/deseq2_res*.tab"%work_deseq2))>0:
364+
for out_file in glob.glob("%s/deseq2_res*.tab"%work_deseq2):
365+
command = "cp %s %s/"%(
366+
out_file, out_deseq2)
367+
cmd = TimedExternalCmd(command, logger, raise_exception=True)
368+
retcode = cmd.run(cmd_log_fd_out=deseq2_log_fd, cmd_log=deseq2_log, msg=msg, timeout=timeout)
330369
else:
331370
logger.info("Skipping step %d: %s"%(step,msg))
332371
step+=1
333372

334373
diff = ""
335-
if os.path.exists("%s/deseq2_res.tab"%out_deseq2):
374+
if len(glob.glob("%s/deseq2_res*.tab"%out_deseq2))>0:
336375
logger.info("DESeq2 was successfull!")
337-
logger.info("Output differential expressions: %s/deseq2_res.tab"%out_deseq2)
338-
diff = "%s/deseq2_res.tab"%out_deseq2
376+
logger.info("Output differential expressions: %s"%(glob.glob("%s/deseq2_res*.tab"%out_deseq2)))
377+
diff = glob.glob("%s/deseq2_res*.tab"%out_deseq2)
339378
else:
340379
logger.info("DESeq2 failed!")
341380
return diff

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