Upcoming 0.2 - merge branch 'dev', new features:

 - hard-coded table replaced with:
   - BED fields for amplicons regions
   - YAML for signatures / variants definition
   - amplicon query tables can themselve by saved and reused
 - tool for importing signatures from PHE-Genomics
 - (preliminary) tool for evaluating quality of variants definition
   using mutation prevalences fetched from CoV-Spectum

.gitignore

@@ -0,0 +1,12 @@
+notebooks/.ipynb_checkpoints/
+notebooks/working
+notebooks/ww_plants.tsv
+notebooks/mutlist.txt
+notebooks/snv_tables/
+notebooks/tallymut_line_snv.tsv
+notebooks/tallymut_line.tsv
+notebooks/viollier_data.csv
+notebooks/data_per_city.csv
+notebooks/data_per_day_and_canton2.csv
+notebooks/ww_update_data.json
+

SARS-CoV-2.insert.V4.txt

@@ -0,0 +1,99 @@
+MN908947.3	50	408	SARS-CoV-2_INSERT_1	1	+
+MN908947.3	344	705	SARS-CoV-2_INSERT_2	2	+
+MN908947.3	666	1017	SARS-CoV-2_INSERT_3	1	+
+MN908947.3	966	1337	SARS-CoV-2_INSERT_4	2	+
+MN908947.3	1266	1623	SARS-CoV-2_INSERT_5	1	+
+MN908947.3	1562	1925	SARS-CoV-2_INSERT_6	2	+
+MN908947.3	1875	2228	SARS-CoV-2_INSERT_7	1	+
+MN908947.3	2180	2544	SARS-CoV-2_INSERT_8	2	+
+MN908947.3	2508	2861	SARS-CoV-2_INSERT_9	1	+
+MN908947.3	2850	3183	SARS-CoV-2_INSERT_10	2	+
+MN908947.3	3102	3470	SARS-CoV-2_INSERT_11	1	+
+MN908947.3	3412	3769	SARS-CoV-2_INSERT_12	2	+
+MN908947.3	3705	4067	SARS-CoV-2_INSERT_13	1	+
+MN908947.3	4018	4387	SARS-CoV-2_INSERT_14	2	+
+MN908947.3	4339	4685	SARS-CoV-2_INSERT_15	1	+
+MN908947.3	4648	4995	SARS-CoV-2_INSERT_16	2	+
+MN908947.3	4953	5302	SARS-CoV-2_INSERT_17	1	+
+MN908947.3	5259	5620	SARS-CoV-2_INSERT_18	2	+
+MN908947.3	5584	5932	SARS-CoV-2_INSERT_19	1	+
+MN908947.3	5894	6247	SARS-CoV-2_INSERT_20	2	+
+MN908947.3	6210	6553	SARS-CoV-2_INSERT_21	1	+
+MN908947.3	6507	6859	SARS-CoV-2_INSERT_22	2	+
+MN908947.3	6776	7122	SARS-CoV-2_INSERT_23	1	+
+MN908947.3	7084	7440	SARS-CoV-2_INSERT_24	2	+
+MN908947.3	7403	7747	SARS-CoV-2_INSERT_25	1	+
+MN908947.3	7695	8063	SARS-CoV-2_INSERT_26	2	+
+MN908947.3	8019	8370	SARS-CoV-2_INSERT_27	1	+
+MN908947.3	8326	8691	SARS-CoV-2_INSERT_28	2	+
+MN908947.3	8619	8990	SARS-CoV-2_INSERT_29	1	+
+MN908947.3	8944	9306	SARS-CoV-2_INSERT_30	2	+
+MN908947.3	9192	9535	SARS-CoV-2_INSERT_31	1	+
+MN908947.3	9497	9842	SARS-CoV-2_INSERT_32	2	+
+MN908947.3	9805	10150	SARS-CoV-2_INSERT_33	1	+
+MN908947.3	10099	10465	SARS-CoV-2_INSERT_34	2	+
+MN908947.3	10419	10785	SARS-CoV-2_INSERT_35	1	+
+MN908947.3	10742	11092	SARS-CoV-2_INSERT_36	2	+
+MN908947.3	11023	11388	SARS-CoV-2_INSERT_37	1	+
+MN908947.3	11330	11689	SARS-CoV-2_INSERT_38	2	+
+MN908947.3	11651	12011	SARS-CoV-2_INSERT_39	1	+
+MN908947.3	11963	12317	SARS-CoV-2_INSERT_40	2	+
+MN908947.3	12255	12618	SARS-CoV-2_INSERT_41	1	+
+MN908947.3	12546	12895	SARS-CoV-2_INSERT_42	2	+
+MN908947.3	12856	13218	SARS-CoV-2_INSERT_43	1	+
+MN908947.3	13148	13506	SARS-CoV-2_INSERT_44	2	+
+MN908947.3	13485	13833	SARS-CoV-2_INSERT_45	1	+
+MN908947.3	13775	14120	SARS-CoV-2_INSERT_46	2	+
+MN908947.3	14075	14428	SARS-CoV-2_INSERT_47	1	+
+MN908947.3	14362	14717	SARS-CoV-2_INSERT_48	2	+
+MN908947.3	14674	15023	SARS-CoV-2_INSERT_49	1	+
+MN908947.3	14983	15336	SARS-CoV-2_INSERT_50	2	+
+MN908947.3	15237	15596	SARS-CoV-2_INSERT_51	1	+
+MN908947.3	15557	15917	SARS-CoV-2_INSERT_52	2	+
+MN908947.3	15881	16239	SARS-CoV-2_INSERT_53	1	+
+MN908947.3	16137	16483	SARS-CoV-2_INSERT_54	2	+
+MN908947.3	16408	16767	SARS-CoV-2_INSERT_55	1	+
+MN908947.3	16714	17082	SARS-CoV-2_INSERT_56	2	+
+MN908947.3	17013	17381	SARS-CoV-2_INSERT_57	1	+
+MN908947.3	17345	17688	SARS-CoV-2_INSERT_58	2	+
+MN908947.3	17642	17997	SARS-CoV-2_INSERT_59	1	+
+MN908947.3	17939	18307	SARS-CoV-2_INSERT_60	2	+
+MN908947.3	18267	18624	SARS-CoV-2_INSERT_61	1	+
+MN908947.3	18578	18936	SARS-CoV-2_INSERT_62	2	+
+MN908947.3	18891	19252	SARS-CoV-2_INSERT_63	1	+
+MN908947.3	19208	19558	SARS-CoV-2_INSERT_64	2	+
+MN908947.3	19513	19877	SARS-CoV-2_INSERT_65	1	+
+MN908947.3	19836	20186	SARS-CoV-2_INSERT_66	2	+
+MN908947.3	20117	20472	SARS-CoV-2_INSERT_67	1	+
+MN908947.3	20405	20766	SARS-CoV-2_INSERT_68	2	+
+MN908947.3	20699	21050	SARS-CoV-2_INSERT_69	1	+
+MN908947.3	21013	21358	SARS-CoV-2_INSERT_70	2	+
+MN908947.3	21316	21675	SARS-CoV-2_INSERT_71	1	+
+MN908947.3	21561	21904	SARS-CoV-2_INSERT_72	2	+
+MN908947.3	21889	22247	SARS-CoV-2_INSERT_73	1	+
+MN908947.3	22113	22474	SARS-CoV-2_INSERT_74	2	+
+MN908947.3	22428	22785	SARS-CoV-2_INSERT_75	1	+
+MN908947.3	22677	23028	SARS-CoV-2_INSERT_76	2	+
+MN908947.3	22974	23327	SARS-CoV-2_INSERT_77	1	+
+MN908947.3	23246	23611	SARS-CoV-2_INSERT_78	2	+
+MN908947.3	23575	23927	SARS-CoV-2_INSERT_79	1	+
+MN908947.3	23876	24233	SARS-CoV-2_INSERT_80	2	+
+MN908947.3	24194	24545	SARS-CoV-2_INSERT_81	1	+
+MN908947.3	24448	24814	SARS-CoV-2_INSERT_82	2	+
+MN908947.3	24772	25122	SARS-CoV-2_INSERT_83	1	+
+MN908947.3	25076	25438	SARS-CoV-2_INSERT_84	2	+
+MN908947.3	25353	25711	SARS-CoV-2_INSERT_85	1	+
+MN908947.3	25672	26026	SARS-CoV-2_INSERT_86	2	+
+MN908947.3	25979	26338	SARS-CoV-2_INSERT_87	1	+
+MN908947.3	26277	26635	SARS-CoV-2_INSERT_88	2	+
+MN908947.3	26587	26956	SARS-CoV-2_INSERT_89	1	+
+MN908947.3	26895	27256	SARS-CoV-2_INSERT_90	2	+
+MN908947.3	27177	27534	SARS-CoV-2_INSERT_91	1	+
+MN908947.3	27473	27826	SARS-CoV-2_INSERT_92	2	+
+MN908947.3	27726	28082	SARS-CoV-2_INSERT_93	1	+
+MN908947.3	28021	28394	SARS-CoV-2_INSERT_94	2	+
+MN908947.3	28214	28572	SARS-CoV-2_INSERT_95	1	+
+MN908947.3	28536	28893	SARS-CoV-2_INSERT_96	2	+
+MN908947.3	28849	29206	SARS-CoV-2_INSERT_97	1	+
+MN908947.3	29161	29512	SARS-CoV-2_INSERT_98	2	+
+MN908947.3	29475	29827	SARS-CoV-2_INSERT_99	1	+

conda_cojac_env.yaml

@@ -1,11 +1,13 @@
 name: cojac
 channels:
-  - defaults
   - conda-forge
   - bioconda
+  - defaults
 dependencies:
-  - pysam
-  - python 
+  - pysam >= 0.17
+  - python
   - pandas
   - numpy
   - pyyaml
+  - strictyaml
+  - requests

cooc-colourmut

@@ -8,6 +8,8 @@ import yaml
 # parse command line
 argparser = argparse.ArgumentParser(description="print coloured pretty table on terminal",
 	epilog="see cooc-pubmut for a CSV file that can be imported into an article")
+argparser.add_argument('-a', '--amplicons', metavar='YAML', required=True,
+	type=str, dest='amp', help="list of query amplicons, from mutbamscan")
 inputgroup = argparser.add_mutually_exclusive_group(required=True)
 inputgroup.add_argument('-j', '--json', metavar='JSON',
 	type=str, dest='json', help="results generated by mutbamscan")
@@ -24,22 +26,25 @@ if args.json:
 	with open(args.json, 'rt') as jf:
 		table=json.load(fp=jf)
 elif args.yaml:
-	assert os.path.isfile(args.yaml), f"cannot find result json file {args.yaml}"
+	assert os.path.isfile(args.yaml), f"cannot find result yaml file {args.yaml}"
 	with open(args.yaml, 'rt') as yf:
 		table=yaml.safe_load(yf)
 
 assert len(table) > 0, "cannot succesfully load table"
 
-# TODO generate instead of hardcodind
+# reuse stored amplicons
+amplicon_nfo={ }
+
+assert os.path.isfile(args.amp), f"cannot find amplicon file yaml file {args.amp}"
+with open(args.amp, 'rt') as yf:
+	amp_str = yaml.safe_load(yf)
+
+amplicon_nfo = {
+		a: ','.join([
+				f"{p}{b}" if len(b) == 1 else (f"\u0394{p}-{p + len(b) - 1}" if  b == '-' * len(b) else f"{p}\u2192{b}")for p,b in aqu[4].items()
+			]) for a,aqu in amp_str.items()
+	}
 
-amplicon_nfo={
- '72_UK': '21765-21770Δ,21991-21993Δ',
- '78_UK': '23604A,23709T',
- '92_UK': '27972T,28048T,28111G',
- '93_UK': '28111G,28280-28280->CTA',
- '76_SA': '23012A,23063T',
- '77_EU': '23403G',
-}
 
 
 #
@@ -49,8 +54,8 @@ amplicon_nfo={
 l=max(len(k) for k in table)
 print(f"{'':<{l}} ", end='')
 for a in amplicon_nfo: print(f" {a :<26}", end='')
-print(f"\n{'':<{l}} ", end='')
-for a,label in amplicon_nfo.items(): print(f" {label :<26}", end='')
+print(f"\n{'':<{l}}  ", end='')
+for a,label in amplicon_nfo.items(): print(f"{label if len(label)<=27 else (label[:26]+chr(0x2026)) :<27.27}", end='')
 print(f"\n{'sample:':<{l}} ", end='')
 for a in amplicon_nfo: print(f"{'cov:' :>9}{'mut:' :>9}{'frq/%:' :>9}", end='')
 print()