| Previous changeset 2:d1015c2516b7 (2018-01-10) Next changeset 4:e73a22ff585c (2018-04-16) |
|
Commit message:
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a |
|
added:
test-data/out_wl_paired.html test-data/out_wl_paired.log test-data/out_wl_paired.tresh.tab test-data/out_wl_paired.txt test-data/out_wl_single.html test-data/out_wl_single.tresh.tab test-data/out_wl_single.txt |
| b |
| 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 |
| b |
| @@ -0,0 +1,1 @@ +<html> <head></head><body> <h1>Cell and Count Metrics</h1> <img src="OUT_cell_barcode_count_density.png" ><br /> <img src="OUT_cell_barcode_knee.png" ><br /> <img src="OUT_cell_barcode_counts.png" ><br /> </body></html> |
| b |
| 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 |
| b |
| @@ -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='<stderr>' 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='<stdout>' 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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,7 @@ +count action +1 Selected +5 Rejected +8 Rejected +11 Rejected +14 Rejected +20 Rejected |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,1 @@ +<html> <head></head><body> <h1>Cell and Count Metrics</h1> <img src="OUT_cell_barcode_count_density.png" ><br /> <img src="OUT_cell_barcode_knee.png" ><br /> <img src="OUT_cell_barcode_counts.png" ><br /> </body></html> |
| b |
| 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 |
| b |
| @@ -0,0 +1,3 @@ +count action +1 Rejected +4 Selected |
| b |
| 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 |
| b |
| @@ -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='<stderr>' 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='<stdout>' mode='w' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='<stdout>' 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 |