Merge pull request #64 from bedapub/dev

Dev

datasets/GSE182150/samples.tab

@@ -1,38 +1,38 @@
 # note that this is a TAB delimited file (use TAB characters to separate values)
 sample_id	readout_id	treatment_id	individual
-GSM5519243	SRR15462283	DMSO	Kasumi-1
-GSM5519244	SRR15462284	DMSO	Kasumi-1
-GSM5519245	SRR15462285	DMSO	Kasumi-1
-GSM5519246	SRR15462286	DMSO	Kasumi-1
-GSM5519247	SRR15462287	DMSO	Kasumi-1
-GSM5519248	SRR15462288	DMSO	Kasumi-1
-GSM5519249	SRR15462289	Ava_12nM	Kasumi-1
-GSM5519250	SRR15462290	Ava_12nM	Kasumi-1
-GSM5519251	SRR15462291	GSK_12nM	Kasumi-1
-GSM5519252	SRR15462292	GSK_12nM	Kasumi-1
-GSM5519253	SRR15462293	Ava_12nM_AND_GSK_12nM	Kasumi-1
-GSM5519254	SRR15462294	Ava_12nM_AND_GSK_12nM	Kasumi-1
-GSM5519315	SRR15462355	DMSO	Kasumi-1
-GSM5519316	SRR15462356	DMSO	Kasumi-1
-GSM5519317	SRR15462357	DMSO	Kasumi-1
-GSM5519318	SRR15462358	Ava_50nM	Kasumi-1
-GSM5519319	SRR15462359	Ava_50nM	Kasumi-1
-GSM5519320	SRR15462360	Ava_50nM	Kasumi-1
-GSM5519321	SRR15462361	Dox_1ugml	Kasumi-1
-GSM5519322	SRR15462362	Dox_1ugml	Kasumi-1
-GSM5519323	SRR15462363	Dox_1ugml	Kasumi-1
-GSM5519324	SRR15462364	Ava_50nM_AND_Dox_1ugml	Kasumi-1
-GSM5519325	SRR15462365	Ava_50nM_AND_Dox_1ugml	Kasumi-1
-GSM5519326	SRR15462366	Ava_50nM_AND_Dox_1ugml	Kasumi-1
-GSM5519343	SRR15462383	DMSO	14-00613
-GSM5519344	SRR15462384	DMSO	14-00613
-GSM5519345	SRR15462385	DMSO	14-00613
-GSM5519346	SRR15462386	Ava_350nM	14-00613
-GSM5519347	SRR15462387	Ava_350nM	14-00613
-GSM5519348	SRR15462388	Ava_350nM	14-00613
-GSM5519349	SRR15462389	ORY_12nM	14-00613
-GSM5519350	SRR15462390	ORY_12nM	14-00613
-GSM5519351	SRR15462391	ORY_12nM	14-00613
-GSM5519352	SRR15462392	Ava_350nM_AND_ORY_12nM	14-00613
-GSM5519353	SRR15462393	Ava_350nM_AND_ORY_12nM	14-00613
-GSM5519354	SRR15462394	Ava_350nM_AND_ORY_12nM	14-00613
+GSM5519243	SRR15462283	DMSO	Kasumi_1
+GSM5519244	SRR15462284	DMSO	Kasumi_1
+GSM5519245	SRR15462285	DMSO	Kasumi_1
+GSM5519246	SRR15462286	DMSO	Kasumi_1
+GSM5519247	SRR15462287	DMSO	Kasumi_1
+GSM5519248	SRR15462288	DMSO	Kasumi_1
+GSM5519249	SRR15462289	Ava_12nM	Kasumi_1
+GSM5519250	SRR15462290	Ava_12nM	Kasumi_1
+GSM5519251	SRR15462291	GSK_12nM	Kasumi_1
+GSM5519252	SRR15462292	GSK_12nM	Kasumi_1
+GSM5519253	SRR15462293	Ava_12nM_AND_GSK_12nM	Kasumi_1
+GSM5519254	SRR15462294	Ava_12nM_AND_GSK_12nM	Kasumi_1
+GSM5519315	SRR15462355	DMSO	Kasumi_1
+GSM5519316	SRR15462356	DMSO	Kasumi_1
+GSM5519317	SRR15462357	DMSO	Kasumi_1
+GSM5519318	SRR15462358	Ava_50nM	Kasumi_1
+GSM5519319	SRR15462359	Ava_50nM	Kasumi_1
+GSM5519320	SRR15462360	Ava_50nM	Kasumi_1
+GSM5519321	SRR15462361	Dox_1ugml	Kasumi_1
+GSM5519322	SRR15462362	Dox_1ugml	Kasumi_1
+GSM5519323	SRR15462363	Dox_1ugml	Kasumi_1
+GSM5519324	SRR15462364	Ava_50nM_AND_Dox_1ugml	Kasumi_1
+GSM5519325	SRR15462365	Ava_50nM_AND_Dox_1ugml	Kasumi_1
+GSM5519326	SRR15462366	Ava_50nM_AND_Dox_1ugml	Kasumi_1
+GSM5519343	SRR15462383	DMSO	14_00613
+GSM5519344	SRR15462384	DMSO	14_00613
+GSM5519345	SRR15462385	DMSO	14_00613
+GSM5519346	SRR15462386	Ava_350nM	14_00613
+GSM5519347	SRR15462387	Ava_350nM	14_00613
+GSM5519348	SRR15462388	Ava_350nM	14_00613
+GSM5519349	SRR15462389	ORY_12nM	14_00613
+GSM5519350	SRR15462390	ORY_12nM	14_00613
+GSM5519351	SRR15462391	ORY_12nM	14_00613
+GSM5519352	SRR15462392	Ava_350nM_AND_ORY_12nM	14_00613
+GSM5519353	SRR15462393	Ava_350nM_AND_ORY_12nM	14_00613
+GSM5519354	SRR15462394	Ava_350nM_AND_ORY_12nM	14_00613

splicekit/__init__.py

@@ -280,5 +280,6 @@ def process(force=False):
     motifs()
     promisc()
     clusterlogfc_process()
+    june_process()
     splicekit.report.process()
     jbrowse2_process(force_samples=force, force_annotation=force)

splicekit/core/annotation.py

@@ -74,7 +74,10 @@ def make_comparisons():
     annotation.treatments = {}
     samples = set()
     f = open("samples.tab")
-    header = f.readline().replace("\r", "").replace("\n", "").split("\t")
+    r = f.readline()
+    while r.startswith("#"):
+        r = f.readline()
+    header = r.replace("\r", "").replace("\n", "").split("\t")
     r = f.readline()
     separates = set()
     while r:

splicekit/core/report.py

@@ -45,7 +45,10 @@ def edgeR_feature(feature_name, version=""):
 
     samples = []
     f = open("samples.tab", "rt")
-    header = f.readline().replace("\r", "").replace("\n", "").split("\t")
+    r = f.readline()
+    while r.startswith("#"):
+        r = f.readline()
+    header = r.replace("\r", "").replace("\n", "").split("\t")
     r = f.readline()
     while r:
         r = r.replace("\r", "").replace("\n", "").split("\t")