# HG changeset patch
# User iuc
# Date 1519582097 18000
# Node ID 475ee31c61d97303521bc8304eeb0bb5dc620601
# Parent d1015c2516b7ae09bcdd440f54f887a86c54cf13
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_paired.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_paired.html Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,1 @@
+ Cell and Count Metrics
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_paired.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_paired.log Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,40 @@
+# output generated by whitelist --bc-pattern=CCCNNNNNNNNXXXXX --subset-reads=0 --stdin=/tmp/tmpibtvD6/files/000/dataset_5.dat --read2-in=/tmp/tmpibtvD6/files/000/dataset_6.dat --expect-cells=5 --error-correct-threshold=3 --method=reads --plot-prefix=OUT --log=/tmp/tmpibtvD6/files/000/dataset_8.dat
+# job started at Sun Feb 25 10:50:16 2018 on bag -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18
+# pid: 2385, system: Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64
+# blacklist_tsv : None
+# cell_number : False
+# compresslevel : 6
+# error_correct_threshold : 3
+# expect_cells : 5
+# extract_method : string
+# filter_cell_barcodes : False
+# log2stderr : False
+# loglevel : 1
+# method : reads
+# pattern : CCCNNNNNNNNXXXXX
+# pattern2 : None
+# plot_prefix : OUT
+# prime3 : None
+# random_seed : None
+# read2_in : /tmp/tmpibtvD6/files/000/dataset_6.dat
+# short_help : None
+# stderr : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'>
+# stdin : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_5.dat' mode='r' encoding='UTF-8'>
+# stdlog : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_8.dat' mode='a' encoding='UTF-8'>
+# stdout : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'>
+# subset_reads : 0
+# timeit_file : None
+# timeit_header : None
+# timeit_name : all
+# whitelist_tsv : None
+2018-02-25 10:50:16,016 INFO Starting barcode extraction
+2018-02-25 10:50:16,017 INFO Parsed 0 reads
+2018-02-25 10:50:16,019 INFO Starting - whitelist determination
+2018-02-25 10:50:17,208 INFO Finished - whitelist determination
+2018-02-25 10:50:17,208 INFO Starting - finding putative error cell barcodes
+2018-02-25 10:50:17,208 INFO Finished - finding putative error cell barcodes
+2018-02-25 10:50:17,208 INFO Writing out whitelist
+2018-02-25 10:50:17,208 INFO Parsed 100 reads
+2018-02-25 10:50:17,208 INFO 100 reads matched the barcode pattern
+2018-02-25 10:50:17,208 INFO Found 23 unique cell barcodes
+# job finished in 1 seconds at Sun Feb 25 10:50:17 2018 -- 2.35 0.08 0.00 0.00 -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_paired.tresh.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_paired.tresh.tab Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,7 @@
+count action
+1 Selected
+5 Rejected
+8 Rejected
+11 Rejected
+14 Rejected
+20 Rejected
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_paired.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_paired.txt Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,1 @@
+TTT AAA,AAG,AAT,AGA,AGG,AGT,ATA,ATT,GAG,GGT,GTA,GTG,GTT,TAA,TAG,TAT,TCT,TGA,TGG,TGT,TTA,TTG 15 2,4,1,6,3,4,6,8,3,2,2,2,8,2,3,6,1,1,2,4,8,7
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_single.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_single.html Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,1 @@
+ Cell and Count Metrics
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_single.tresh.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_single.tresh.tab Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,3 @@
+count action
+1 Rejected
+4 Selected
diff -r d1015c2516b7 -r 475ee31c61d9 test-data/out_wl_single.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_wl_single.txt Sun Feb 25 13:08:17 2018 -0500
@@ -0,0 +1,44 @@
+# output generated by whitelist --bc-pattern=CCCCCCCCNNNNNNNN --subset-reads=0 --stdin=/tmp/tmpibtvD6/files/000/dataset_1.dat --method=reads --plot-prefix=OUT --3prime
+# job started at Sun Feb 25 10:49:56 2018 on bag -- cb0db520-8a4e-4040-aa88-93efc0718fa8
+# pid: 2217, system: Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64
+# blacklist_tsv : None
+# cell_number : False
+# compresslevel : 6
+# error_correct_threshold : 1
+# expect_cells : False
+# extract_method : string
+# filter_cell_barcodes : False
+# log2stderr : False
+# loglevel : 1
+# method : reads
+# pattern : CCCCCCCCNNNNNNNN
+# pattern2 : None
+# plot_prefix : OUT
+# prime3 : True
+# random_seed : None
+# read2_in : None
+# short_help : None
+# stderr : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'>
+# stdin : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_1.dat' mode='r' encoding='UTF-8'>
+# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'>
+# stdout : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'>
+# subset_reads : 0
+# timeit_file : None
+# timeit_header : None
+# timeit_name : all
+# whitelist_tsv : None
+## 2018-02-25 10:49:56,061 INFO Starting barcode extraction
+## 2018-02-25 10:49:56,061 INFO Parsed 0 reads
+## 2018-02-25 10:49:56,062 INFO Starting - whitelist determination
+## 2018-02-25 10:49:57,383 INFO Finished - whitelist determination
+## 2018-02-25 10:49:57,383 INFO Starting - finding putative error cell barcodes
+## 2018-02-25 10:49:57,383 INFO Finished - finding putative error cell barcodes
+## 2018-02-25 10:49:57,383 INFO Writing out whitelist
+AAAAAAAA AAAAAACA,AAACAAAA,AATAAAAA 3 1,1,1
+ACAAAAAC 2
+ACAACAAA 2
+TTACTTAA TTACTAAA 2 1
+## 2018-02-25 10:49:57,383 INFO Parsed 100 reads
+## 2018-02-25 10:49:57,383 INFO 100 reads matched the barcode pattern
+## 2018-02-25 10:49:57,383 INFO Found 95 unique cell barcodes
+# job finished in 1 seconds at Sun Feb 25 10:49:57 2018 -- 2.25 0.06 0.00 0.00 -- cb0db520-8a4e-4040-aa88-93efc0718fa8