file rapidrun

README.md

 # snakemake_rapidrun_swarm
 
-OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
\ No newline at end of file
+OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
+
+
+# Prerequisites
+
+
+
+pip3 install pymysql
+
+pip install pandas
\ No newline at end of file

infos/Chond.rrr

+P1_A1	180430_SN234_A_L001_AIMI-9	SPY173250	Guadeloupe	chond
+P1_B1	180430_SN234_A_L001_AIMI-9	SPY173251	Guadeloupe	chond
+P1_C1	180430_SN234_A_L001_AIMI-9	SPY173252	Guadeloupe	chond
+P1_D1	180430_SN234_A_L001_AIMI-9	SPY173253	Guadeloupe	chond
+P1_E1	180430_SN234_A_L001_AIMI-9	SPY173254	Guadeloupe	chond
+P1_F1	180430_SN234_A_L001_AIMI-9	SPY173255	Guadeloupe	chond
+P1_G1	180430_SN234_A_L001_AIMI-9	SPY173256	Guadeloupe	chond
+P1_H1	180430_SN234_A_L001_AIMI-9	SPY173257	Guadeloupe	chond
+P1_A3	180430_SN234_A_L001_AIMI-9	SPY173258	Guadeloupe	chond
+P1_B3	180430_SN234_A_L001_AIMI-9	SPY173259	Guadeloupe	chond
+P1_A1	180504_SND405_A_L001_AIMI-10	SPY173260	Guadeloupe	chond
+P1_B1	180504_SND405_A_L001_AIMI-10	SPY173261	Guadeloupe	chond
+P1_C1	180504_SND405_A_L001_AIMI-10	SPY173262	Guadeloupe	chond
+P1_D1	180504_SND405_A_L001_AIMI-10	SPY173263	Guadeloupe	chond
+P1_E1	180504_SND405_A_L001_AIMI-10	SPY173264	Guadeloupe	chond
+P1_F1	180504_SND405_A_L001_AIMI-10	SPY173265	Guadeloupe	chond
+P1_G1	180504_SND405_A_L001_AIMI-10	SPY173266	Guadeloupe	chond
+P1_H1	180504_SND405_A_L001_AIMI-10	SPY173267	Guadeloupe	chond
+P1_A3	180504_SND405_A_L001_AIMI-10	SPY173268	Guadeloupe	chond
+P1_B3	180504_SND405_A_L001_AIMI-10	SPY173269	Guadeloupe	chond
+P1_C3	180504_SND405_A_L001_AIMI-10	SPY173270	Guadeloupe	chond
+P1_D3	180504_SND405_A_L001_AIMI-10	SPY173271	Guadeloupe	chond
+P1_H3	180504_SND405_A_L002_AIMI-11	SPY173272	Guadeloupe	chond
+P1_A5	180504_SND405_A_L002_AIMI-11	SPY180501	Guadeloupe	chond
+P1_B5	180504_SND405_A_L002_AIMI-11	SPY173273	Guadeloupe	chond
+P1_C5	180504_SND405_A_L002_AIMI-11	SPY173274	Guadeloupe	chond
+P1_D5	180504_SND405_A_L002_AIMI-11	SPY173275	Guadeloupe	chond
+P1_E5	180504_SND405_A_L002_AIMI-11	SPY173276	Guadeloupe	chond
+P1_F5	180504_SND405_A_L002_AIMI-11	SPY173278	Guadeloupe	chond
+P1_G5	180504_SND405_A_L002_AIMI-11	SPY173279	Guadeloupe	chond
+P1_H5	180504_SND405_A_L002_AIMI-11	SPY173280	Guadeloupe	chond
+P1_A7	180504_SND405_A_L002_AIMI-11	SPY173281	Guadeloupe	chond
+P1_B7	180504_SND405_A_L002_AIMI-11	SPY173282	Guadeloupe	chond
+P1_C7	180504_SND405_A_L002_AIMI-11	SPY173283	Guadeloupe	chond
+P1_A1	181102_SND405_A_L001_AIMI-48	SPY181533	Fakarava	chond
+P1_B1	181102_SND405_A_L001_AIMI-48	SPY181536	Fakarava	chond
+P1_C1	181102_SND405_A_L001_AIMI-48	SPY181541	Fakarava	chond
+P1_D1	181102_SND405_A_L001_AIMI-48	SPY181831	Fakarava	chond
+P1_E1	181102_SND405_A_L001_AIMI-48	SPY181832	Fakarava	chond
+P1_F1	181102_SND405_A_L001_AIMI-48	SPY181885	Fakarava	chond
+P1_G1	181102_SND405_A_L001_AIMI-48	SPY181886	Fakarava	chond
+P1_H1	181102_SND405_A_L001_AIMI-48	SPY181887	Fakarava	chond
+P1_A3	181102_SND405_A_L001_AIMI-48	SPY181888	Fakarava	chond
+P1_B3	181102_SND405_A_L001_AIMI-48	SPY181892	Fakarava	chond
+P1_D3	181102_SND405_A_L001_AIMI-48	SPY181895	Fakarava	chond
+P1_E3	181102_SND405_A_L001_AIMI-48	SPY181896	Fakarava	chond
+P1_F3	181102_SND405_A_L001_AIMI-48	SPY181899	Fakarava	chond
+P1_G3	181102_SND405_A_L001_AIMI-48	SPY181900	Fakarava	chond
+P1_H3	181102_SND405_A_L001_AIMI-48	SPY181902	Fakarava	chond
+P1_A5	181102_SND405_A_L001_AIMI-48	SPY181905	Fakarava	chond
+P1_B5	181102_SND405_A_L001_AIMI-48	SPY181906	Fakarava	chond
+P1_C5	181102_SND405_A_L001_AIMI-48	SPY181907	Fakarava	chond
+P1_D5	181102_SND405_A_L001_AIMI-48	SPY181909	Fakarava	chond
+P1_E5	181102_SND405_A_L001_AIMI-48	SPY181911	Fakarava	chond
+P1_F5	181102_SND405_A_L001_AIMI-48	SPY181912	Fakarava	chond
+P1_G5	181102_SND405_A_L001_AIMI-48	SPY181914	Fakarava	chond
+P1_H5	181102_SND405_A_L001_AIMI-48	SPY181915	Fakarava	chond
+P1_A7	181102_SND405_A_L001_AIMI-48	SPY181917	Fakarava	chond
+P1_B7	181102_SND405_A_L001_AIMI-48	SPY181918	Fakarava	chond
+P1_C7	181102_SND405_A_L001_AIMI-48	SPY181919	Fakarava	chond
+P1_D7	181102_SND405_A_L001_AIMI-48	SPY181920	Fakarava	chond
+P1_E7	181102_SND405_A_L001_AIMI-48	SPY181922	Fakarava	chond
+P1_D1	181102_SND405_A_L002_AIMI-49	SPY180581	Malpelo	chond
+P1_E1	181102_SND405_A_L002_AIMI-49	SPY180582	Malpelo	chond
+P1_F1	181102_SND405_A_L002_AIMI-49	SPY180583	Malpelo	chond
+P1_G1	181102_SND405_A_L002_AIMI-49	SPY180584	Malpelo	chond
+P1_H1	181102_SND405_A_L002_AIMI-49	SPY180585	Malpelo	chond
+P1_A3	181102_SND405_A_L002_AIMI-49	SPY180586	Malpelo	chond
+P1_B3	181102_SND405_A_L002_AIMI-49	SPY180587	Malpelo	chond
+P1_C3	181102_SND405_A_L002_AIMI-49	SPY180588	Malpelo	chond
+P1_D3	181102_SND405_A_L002_AIMI-49	SPY180589	Malpelo	chond
+P1_E3	181102_SND405_A_L002_AIMI-49	SPY180590	Malpelo	chond
+P1_F3	181102_SND405_A_L002_AIMI-49	SPY180591	Malpelo	chond
+P1_G3	181102_SND405_A_L002_AIMI-49	SPY180592	Malpelo	chond
+P1_H3	181102_SND405_A_L002_AIMI-49	SPY180593	Malpelo	chond
+P1_A5	181102_SND405_A_L002_AIMI-49	SPY180594	Malpelo	chond
+P1_B5	181102_SND405_A_L002_AIMI-49	SPY180595	Malpelo	chond
+P1_C5	181102_SND405_A_L002_AIMI-49	SPY180596	Malpelo	chond
+P1_D5	181102_SND405_A_L002_AIMI-49	SPY180597	Malpelo	chond
+P1_E5	181102_SND405_A_L002_AIMI-49	SPY180598	Malpelo	chond
+P1_G5	181102_SND405_A_L002_AIMI-49	SPY180599	Malpelo	chond
+P1_H5	181102_SND405_A_L002_AIMI-49	SPY180600	Malpelo	chond
+P1_A7	181102_SND405_A_L002_AIMI-49	SPY180601	Malpelo	chond
+P1_B7	181102_SND405_A_L002_AIMI-49	SPY180602	Malpelo	chond
+P1_C7	181102_SND405_A_L002_AIMI-49	SPY180603	Malpelo	chond
+P1_D7	181102_SND405_A_L002_AIMI-49	SPY180604	Malpelo	chond
+P1_E7	181102_SND405_A_L002_AIMI-49	SPY180605	Malpelo	chond
+P1_F7	181102_SND405_A_L002_AIMI-49	SPY180768	Malpelo	chond
+P1_A1	181116_SND405_A_L001_AIMI-50	SPY180769	Malpelo	chond
+P1_B1	181116_SND405_A_L001_AIMI-50	SPY180773	Malpelo	chond
+P1_C1	181116_SND405_A_L001_AIMI-50	SPY180775	Malpelo	chond
+P1_D1	181116_SND405_A_L001_AIMI-50	SPY180776	Malpelo	chond
+P1_E1	181116_SND405_A_L001_AIMI-50	SPY180777	Malpelo	chond
+P1_F1	181116_SND405_A_L001_AIMI-50	SPY180778	Malpelo	chond
+P1_G1	181116_SND405_A_L001_AIMI-50	SPY180779	Malpelo	chond
+P1_H1	181116_SND405_A_L001_AIMI-50	SPY180780	Malpelo	chond
+P1_A3	181116_SND405_A_L001_AIMI-50	SPY180781	Malpelo	chond
+P1_B3	181116_SND405_A_L001_AIMI-50	SPY180782	Malpelo	chond

infos/Mamm.rrr

+P1_A1	181102_SND405_A_L001_AIMI-48	SPY181533	Fakarava	mamm
+P1_B1	181102_SND405_A_L001_AIMI-48	SPY181536	Fakarava	mamm
+P1_C1	181102_SND405_A_L001_AIMI-48	SPY181541	Fakarava	mamm
+P1_D1	181102_SND405_A_L001_AIMI-48	SPY181831	Fakarava	mamm
+P1_E1	181102_SND405_A_L001_AIMI-48	SPY181832	Fakarava	mamm
+P1_F1	181102_SND405_A_L001_AIMI-48	SPY181885	Fakarava	mamm
+P1_G1	181102_SND405_A_L001_AIMI-48	SPY181886	Fakarava	mamm
+P1_H1	181102_SND405_A_L001_AIMI-48	SPY181887	Fakarava	mamm
+P1_A3	181102_SND405_A_L001_AIMI-48	SPY181888	Fakarava	mamm
+P1_B3	181102_SND405_A_L001_AIMI-48	SPY181892	Fakarava	mamm
+P1_D3	181102_SND405_A_L001_AIMI-48	SPY181895	Fakarava	mamm
+P1_E3	181102_SND405_A_L001_AIMI-48	SPY181896	Fakarava	mamm
+P1_F3	181102_SND405_A_L001_AIMI-48	SPY181899	Fakarava	mamm
+P1_G3	181102_SND405_A_L001_AIMI-48	SPY181900	Fakarava	mamm
+P1_H3	181102_SND405_A_L001_AIMI-48	SPY181902	Fakarava	mamm
+P1_A5	181102_SND405_A_L001_AIMI-48	SPY181905	Fakarava	mamm
+P1_B5	181102_SND405_A_L001_AIMI-48	SPY181906	Fakarava	mamm
+P1_C5	181102_SND405_A_L001_AIMI-48	SPY181907	Fakarava	mamm
+P1_D5	181102_SND405_A_L001_AIMI-48	SPY181909	Fakarava	mamm
+P1_E5	181102_SND405_A_L001_AIMI-48	SPY181911	Fakarava	mamm
+P1_F5	181102_SND405_A_L001_AIMI-48	SPY181912	Fakarava	mamm
+P1_G5	181102_SND405_A_L001_AIMI-48	SPY181914	Fakarava	mamm
+P1_H5	181102_SND405_A_L001_AIMI-48	SPY181915	Fakarava	mamm
+P1_B7	181102_SND405_A_L001_AIMI-48	SPY181917	Fakarava	mamm
+P1_C7	181102_SND405_A_L001_AIMI-48	SPY181918	Fakarava	mamm
+P1_D7	181102_SND405_A_L001_AIMI-48	SPY181919	Fakarava	mamm
+P1_E7	181102_SND405_A_L001_AIMI-48	SPY181920	Fakarava	mamm
+P1_F7	181102_SND405_A_L001_AIMI-48	SPY181922	Fakarava	mamm
+P1_A1	181102_SND405_A_L002_AIMI-49	SPY180581	Malpelo	mamm
+P1_B1	181102_SND405_A_L002_AIMI-49	SPY180582	Malpelo	mamm
+P1_C1	181102_SND405_A_L002_AIMI-49	SPY180583	Malpelo	mamm
+P1_D1	181102_SND405_A_L002_AIMI-49	SPY180584	Malpelo	mamm
+P1_E1	181102_SND405_A_L002_AIMI-49	SPY180585	Malpelo	mamm
+P1_F1	181102_SND405_A_L002_AIMI-49	SPY180586	Malpelo	mamm
+P1_G1	181102_SND405_A_L002_AIMI-49	SPY180587	Malpelo	mamm
+P1_H1	181102_SND405_A_L002_AIMI-49	SPY180588	Malpelo	mamm
+P1_A3	181102_SND405_A_L002_AIMI-49	SPY180589	Malpelo	mamm
+P1_B3	181102_SND405_A_L002_AIMI-49	SPY180590	Malpelo	mamm
+P1_C3	181102_SND405_A_L002_AIMI-49	SPY180591	Malpelo	mamm
+P1_D3	181102_SND405_A_L002_AIMI-49	SPY180592	Malpelo	mamm
+P1_E3	181102_SND405_A_L002_AIMI-49	SPY180593	Malpelo	mamm
+P1_F3	181102_SND405_A_L002_AIMI-49	SPY180594	Malpelo	mamm
+P1_G3	181102_SND405_A_L002_AIMI-49	SPY180595	Malpelo	mamm
+P1_H3	181102_SND405_A_L002_AIMI-49	SPY180596	Malpelo	mamm
+P1_A5	181102_SND405_A_L002_AIMI-49	SPY180597	Malpelo	mamm
+P1_B5	181102_SND405_A_L002_AIMI-49	SPY180598	Malpelo	mamm
+P1_D5	181102_SND405_A_L002_AIMI-49	SPY180599	Malpelo	mamm
+P1_E5	181102_SND405_A_L002_AIMI-49	SPY180600	Malpelo	mamm
+P1_F5	181102_SND405_A_L002_AIMI-49	SPY180601	Malpelo	mamm
+P1_G5	181102_SND405_A_L002_AIMI-49	SPY180602	Malpelo	mamm
+P1_A7	181102_SND405_A_L002_AIMI-49	SPY180603	Malpelo	mamm
+P1_B7	181102_SND405_A_L002_AIMI-49	SPY180604	Malpelo	mamm
+P1_C7	181102_SND405_A_L002_AIMI-49	SPY180605	Malpelo	mamm
+P1_D7	181102_SND405_A_L002_AIMI-49	SPY180768	Malpelo	mamm
+P1_E7	181102_SND405_A_L002_AIMI-49	SPY180769	Malpelo	mamm
+P1_F7	181102_SND405_A_L002_AIMI-49	SPY180773	Malpelo	mamm
+P1_G7	181102_SND405_A_L002_AIMI-49	SPY180775	Malpelo	mamm
+P1_H7	181102_SND405_A_L002_AIMI-49	SPY180776	Malpelo	mamm
+P1_A9	181102_SND405_A_L002_AIMI-49	SPY180777	Malpelo	mamm
+P1_B9	181102_SND405_A_L002_AIMI-49	SPY180778	Malpelo	mamm
+P1_C9	181102_SND405_A_L002_AIMI-49	SPY180779	Malpelo	mamm
+P1_D9	181102_SND405_A_L002_AIMI-49	SPY180780	Malpelo	mamm
+P1_E9	181102_SND405_A_L002_AIMI-49	SPY180781	Malpelo	mamm
+P1_F9	181102_SND405_A_L002_AIMI-49	SPY180782	Malpelo	mamm

infos/Vert.rrr

+P1_A1	181102_SND405_A_L001_AIMI-48	SPY181533	Fakarava	vert
+P1_B1	181102_SND405_A_L001_AIMI-48	SPY181536	Fakarava	vert
+P1_C1	181102_SND405_A_L001_AIMI-48	SPY181541	Fakarava	vert
+P1_D1	181102_SND405_A_L001_AIMI-48	SPY181831	Fakarava	vert
+P1_E1	181102_SND405_A_L001_AIMI-48	SPY181832	Fakarava	vert
+P1_F1	181102_SND405_A_L001_AIMI-48	SPY181885	Fakarava	vert
+P1_G1	181102_SND405_A_L001_AIMI-48	SPY181886	Fakarava	vert
+P1_H1	181102_SND405_A_L001_AIMI-48	SPY181887	Fakarava	vert
+P1_A3	181102_SND405_A_L001_AIMI-48	SPY181888	Fakarava	vert
+P1_B3	181102_SND405_A_L001_AIMI-48	SPY181892	Fakarava	vert
+P1_D3	181102_SND405_A_L001_AIMI-48	SPY181895	Fakarava	vert
+P1_E3	181102_SND405_A_L001_AIMI-48	SPY181896	Fakarava	vert
+P1_F3	181102_SND405_A_L001_AIMI-48	SPY181899	Fakarava	vert
+P1_G3	181102_SND405_A_L001_AIMI-48	SPY181900	Fakarava	vert
+P1_H3	181102_SND405_A_L001_AIMI-48	SPY181902	Fakarava	vert
+P1_A5	181102_SND405_A_L001_AIMI-48	SPY181905	Fakarava	vert
+P1_B5	181102_SND405_A_L001_AIMI-48	SPY181906	Fakarava	vert
+P1_C5	181102_SND405_A_L001_AIMI-48	SPY181907	Fakarava	vert
+P1_D5	181102_SND405_A_L001_AIMI-48	SPY181909	Fakarava	vert
+P1_E5	181102_SND405_A_L001_AIMI-48	SPY181911	Fakarava	vert
+P1_F5	181102_SND405_A_L001_AIMI-48	SPY181912	Fakarava	vert
+P1_G5	181102_SND405_A_L001_AIMI-48	SPY181914	Fakarava	vert
+P1_H5	181102_SND405_A_L001_AIMI-48	SPY181915	Fakarava	vert
+P1_A7	181102_SND405_A_L001_AIMI-48	SPY181917	Fakarava	vert
+P1_B7	181102_SND405_A_L001_AIMI-48	SPY181918	Fakarava	vert
+P1_C7	181102_SND405_A_L001_AIMI-48	SPY181919	Fakarava	vert
+P1_D7	181102_SND405_A_L001_AIMI-48	SPY181920	Fakarava	vert
+P1_E7	181102_SND405_A_L001_AIMI-48	SPY181922	Fakarava	vert
+P1_A3	181116_SND405_A_L001_AIMI-50	SPY180581	Malpelo	vert
+P1_B3	181116_SND405_A_L001_AIMI-50	SPY180582	Malpelo	vert
+P1_C3	181116_SND405_A_L001_AIMI-50	SPY180583	Malpelo	vert
+P1_D3	181116_SND405_A_L001_AIMI-50	SPY180584	Malpelo	vert
+P1_E3	181116_SND405_A_L001_AIMI-50	SPY180585	Malpelo	vert
+P1_F3	181116_SND405_A_L001_AIMI-50	SPY180586	Malpelo	vert
+P1_G3	181116_SND405_A_L001_AIMI-50	SPY180587	Malpelo	vert
+P1_H3	181116_SND405_A_L001_AIMI-50	SPY180588	Malpelo	vert
+P1_A5	181116_SND405_A_L001_AIMI-50	SPY180589	Malpelo	vert
+P1_B5	181116_SND405_A_L001_AIMI-50	SPY180590	Malpelo	vert
+P1_C5	181116_SND405_A_L001_AIMI-50	SPY180591	Malpelo	vert
+P1_D5	181116_SND405_A_L001_AIMI-50	SPY180592	Malpelo	vert
+P1_E5	181116_SND405_A_L001_AIMI-50	SPY180593	Malpelo	vert
+P1_F5	181116_SND405_A_L001_AIMI-50	SPY180594	Malpelo	vert
+P1_G5	181116_SND405_A_L001_AIMI-50	SPY180595	Malpelo	vert
+P1_H5	181116_SND405_A_L001_AIMI-50	SPY180596	Malpelo	vert
+P1_A7	181116_SND405_A_L001_AIMI-50	SPY180597	Malpelo	vert
+P1_B7	181116_SND405_A_L001_AIMI-50	SPY180598	Malpelo	vert
+P1_A1	181116_SND405_A_L002_AIMI-51	SPY180599	Malpelo	vert
+P1_B1	181116_SND405_A_L002_AIMI-51	SPY180600	Malpelo	vert
+P1_C1	181116_SND405_A_L002_AIMI-51	SPY180601	Malpelo	vert
+P1_D1	181116_SND405_A_L002_AIMI-51	SPY180602	Malpelo	vert
+P1_E1	181116_SND405_A_L002_AIMI-51	SPY180603	Malpelo	vert
+P1_F1	181116_SND405_A_L002_AIMI-51	SPY180604	Malpelo	vert
+P1_G1	181116_SND405_A_L002_AIMI-51	SPY180605	Malpelo	vert
+P1_H1	181116_SND405_A_L002_AIMI-51	SPY180768	Malpelo	vert
+P1_A3	181116_SND405_A_L002_AIMI-51	SPY180769	Malpelo	vert
+P1_B3	181116_SND405_A_L002_AIMI-51	SPY180773	Malpelo	vert
+P1_C3	181116_SND405_A_L002_AIMI-51	SPY180775	Malpelo	vert
+P1_D3	181116_SND405_A_L002_AIMI-51	SPY180776	Malpelo	vert
+P1_E3	181116_SND405_A_L002_AIMI-51	SPY180777	Malpelo	vert
+P1_F3	181116_SND405_A_L002_AIMI-51	SPY180778	Malpelo	vert
+P1_G3	181116_SND405_A_L002_AIMI-51	SPY180779	Malpelo	vert
+P1_H3	181116_SND405_A_L002_AIMI-51	SPY180780	Malpelo	vert
+P1_A5	181116_SND405_A_L002_AIMI-51	SPY180781	Malpelo	vert
+P1_B5	181116_SND405_A_L002_AIMI-51	SPY180782	Malpelo	vert

infos/markers.csv

+teleo,ACACCGCCCGTCACTCT,CTTCCGGTACACTTACCATG
+vert,TAGAACAGGCTCCTCTAG,TTAGATACCCCACTATGC
+chond,ACACCGCCCGTCACTCTC,CATGTTACGACTTGCCTCCTC
+mamm,CCGCCCGTCACYCTCCT,GTAYRCTTACCWTGTTACGAC