Merge pull request #163 from PediatricOpenTargets/pedc-names

PedCBio formatted sample ID column

analyses/pedcbio-sample-name/README.md

@@ -0,0 +1,41 @@
+## Add formatted sample id column for PedCBio upload
+
+**Module author:** Run Jin ([@runjin326](https://github.com/runjin326))
+
+Currently, for some of the samples, when multiple DNA or RNA specimens are associated with the same sample, there 
+is no column that would distinguish between different aliquots while still tying DNA and RNA together.
+This module adds a column called `formatted_sample_id` where the base name is the sample id and additional `tiebreaks` were added when multiple RNA or DNA samples are associated with the same participant.
+
+For PBTA samples, `sample_id` column is used as the basename
+- Using `sample_id` column, we can tie all DNA and RNA samples together
+- Using `formatted_sample_id` column, we can distinguish amongst multiple DNA or RNA samples 
+  - Multiple DNA samples associated with the same sample would use `aliquot_id` as the tie breaker
+  - Multiple RNA samples associated with the same sample would use `RNA_library` as the tie breaker 
+
+For TARGET, TCGA, and GTEx samples, `Kids_First_Participant_ID` column is used as the basename
+- Using `Kids_First_Participant_ID` column, we can tie all DNA and RNA samples together
+- Using `formatted_sample_id` column, we can distinguish amongst multiple DNA or RNA samples 
+  - For TARGET, `Kids_First_Participant_ID` + last 7 digits from the `Kids_First_Specimen_ID` is used as formatted sample ID
+  - For TCGA, `Kids_First_Participant_ID` + `sample_id` + `aliquot_id` is used as formatted sample ID
+  - For GTEx, `Kids_First_Participant_ID` + `aliquot_id` is used as formatted sample ID
+
+Usage:
+  ```
+Rscript -e "rmarkdown::render('pedcbio_sample_name_col.Rmd', clean = TRUE)"
+
+```
+or
+```
+bash run_add_name.sh
+```
+
+Input:
+- `input/cbtn_cbio_sample.csv`
+- `input/oligo_nation_cbio_sample.csv`
+- `input/dgd_cbio_sample.csv`
+- `input/x01_fy16_nbl_maris_cbio_sample.csv`
+
+Output:
+- `results/histologies-formatted-id-added.tsv`
+
+The output files are directly uploaded to S3 buckets for loading into PedCBio.

analyses/pedcbio-sample-name/input/oligo_nation_cbio_sample.csv

@@ -0,0 +1,62 @@
+"participant_id","sequencing_center_ids","collection_event_id","formatted_sample_id","specimen_id","analyte_types","normal_bs_id","normal_sample_id"
+"PT_BSR2P67X","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-1","16510-1","{BS_6EH1T1S8,BS_PQY28YXA}","{DNA,RNA}","BS_BMYBS3EX","16510-1"
+"PT_NKGQYCKZ","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-10","16510-10","{BS_E4VCDN6S,BS_JAT12TX2}","{DNA,RNA}","BS_XZMQZMY9","16510-10"
+"PT_3B27053H","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-11","16510-11","{BS_AQYC2SXT,BS_17SAB1QN}","{DNA,RNA}","BS_WSS7TGJX","16510-11"
+"PT_VK94C42M","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-12","16510-12","{BS_ZK7DMJQS,BS_XFWH05PB}","{DNA,RNA}","BS_NAKGZ1F0","16510-12"
+"PT_4VYW4AAZ","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-13","16510-13","{BS_S1RSJCAM,BS_9M84M36J}","{DNA,RNA}","BS_K33VBFJV","16510-13"
+"PT_D7GN92VR","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-14","16510-14","{BS_T7PQR658,BS_AS4K2YQW}","{DNA,RNA}","BS_FRY5QDDQ","16510-14"
+"PT_1PVVBG1B","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-15","16510-15","{BS_P867VK77,BS_M8A8KHD8}","{DNA,RNA}","BS_1VKXE4H5","16510-15"
+"PT_74Y53WN8","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-16","16510-16","{BS_7S2CDYVX,BS_AYAMBZHS}","{DNA,RNA}","BS_E6AVH26R","16510-16"
+"PT_F2CG3ZZB","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-17","16510-17","{BS_91P6RMCF,BS_QV09SGSJ}","{DNA,RNA}","BS_FATPVK66","16510-17"
+"PT_G24FN04H","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-18","16510-18","{BS_V90NNZ0D,BS_JT5BXPHZ}","{DNA,RNA}","BS_YZDD793H","16510-18"
+"PT_PMFS3A49","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-19","16510-19","{BS_0J57HJ1S,BS_ZYPMR035}","{DNA,RNA}","BS_HP0BWRY0","16510-19"
+"PT_DN84REQ3","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-2","16510-2","{BS_ZK8DW7Y1,BS_8ZTEXH90}","{DNA,RNA}","BS_X9GKMCXV","16510-2"
+"PT_28A07ZDV","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-20","16510-20","{BS_FHJP8HE0,BS_WTVQNPE4}","{DNA,RNA}","BS_5A11TKW2","16510-20"
+"PT_JBCAXNK2","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-21","16510-21","{BS_K6BDQS4D,BS_M9CH91QV}","{DNA,RNA}","BS_1B8B622B","16510-21"
+"PT_F1MDWB5W","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-22","16510-22","{BS_1SV5KG4Y,BS_2K3FVT86}","{DNA,RNA}","BS_6CXJKHG6","16510-22"
+"PT_4X7VW8WT","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-24","16510-24","{BS_PPAGQPMZ,BS_SRD8TFGV}","{DNA,RNA}","BS_AXJ00JPW","16510-24"
+"PT_MKWZC1QY","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-25","16510-25","{BS_QBPZQF73,BS_D5MT05YK}","{DNA,RNA}","BS_F3K6K7R6","16510-25"
+"PT_STE26Y8Z","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-26","16510-26","{BS_YRNJ7Z3E,BS_NGMQF1B5}","{DNA,RNA}","BS_1HQACYRD","16510-26"
+"PT_XQ001FC5","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-3","16510-3","{BS_5PTCMTJ0,BS_A8V685RR}","{DNA,RNA}","BS_VRHRMEW1","16510-3"
+"PT_VN63HHEN","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-4","16510-4","{BS_Z45QE3VE,BS_6NJRE82B}","{DNA,RNA}","BS_E758QJDD","16510-4"
+"PT_TG2YJS5J","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-5","16510-5","{BS_C4WJZS6W,BS_WQNXWJXE}","{DNA,RNA}","BS_T5QB3H8B","16510-5"
+"PT_G9D39RG0","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-6","16510-6","{BS_14PEVAHC,BS_V0JFAS12}","{DNA,RNA}","BS_M9J949F5","16510-6"
+"PT_B694AQYE","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-7","16510-7","{BS_FEX3A4SE,BS_1739JAKK}","{DNA,RNA}","BS_9DKCQN5E","16510-7"
+"PT_401GQ0VV","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-8","16510-8","{BS_A8P99605,BS_1HHS9AFK}","{DNA,RNA}","BS_KPVPQYD0","16510-8"
+"PT_R4JE89YX","{SC_2ZBAMKK0,SC_2ZBAMKK0}","16510-9","16510-9","{BS_EYFC3E6B,BS_BGTPAACY}","{DNA,RNA}","BS_QJ8EE8WP","16510-9"
+"PT_88F5PD21","{SC_2ZBAMKK0}","7316-6188","7316-6188","{BS_P1AZ9H9A}","{RNA}","",""
+"PT_9CSACR9N","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-1136","7316UP-1136","{BS_NV67MSZN,BS_GKWT3J9X}","{DNA,RNA}","BS_54HFWZ7Q","7316UP-1136"
+"PT_TC4ZC42Z","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-1333","7316UP-1333","{BS_AX1ACH6G,BS_28CTRAS5}","{DNA,RNA}","BS_YEEKXSJD","7316UP-1333"
+"PT_P40S0HQK","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-1641","7316UP-1641","{BS_WH6C5Z6S,BS_YF44RR88}","{DNA,RNA}","BS_CNHA65ED","7316UP-1641"
+"PT_GKSTR4C1","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-1975","7316UP-1975","{BS_5AZW4DKB,BS_5FRQVRRE}","{DNA,RNA}","BS_M5R9Q04Z","7316UP-1975"
+"PT_7Y81E8DQ","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2013","7316UP-2013","{BS_5ARWRQ8E,BS_TYQ0N4YP}","{DNA,RNA}","BS_CN4VY1RE","7316UP-2013"
+"PT_TYWS8PXY","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2064","7316UP-2064","{BS_HTXZA5CH,BS_D432YMV4}","{DNA,RNA}","BS_PQTX4827","7316UP-2064"
+"PT_KCDPF85V","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2066","7316UP-2066","{BS_EPX4DZN8,BS_8SQARNQW}","{DNA,RNA}","BS_Q16PX3HA","7316UP-2066"
+"PT_FAZEJ3VR","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2238","7316UP-2238","{BS_GF83ZWD3,BS_CV9QNWN7}","{DNA,RNA}","BS_8K1Y6NE6","7316UP-2238"
+"PT_6QCSWBBQ","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2243","7316UP-2243","{BS_S8M4XW3Z,BS_NW3NGVR8}","{DNA,RNA}","BS_VFK2ACZ4","7316UP-2243"
+"PT_8YS7JD5V","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2398","7316UP-2398","{BS_P2377HHG,BS_4Q3NRFBD}","{DNA,RNA}","BS_16KWXER9","7316UP-2398"
+"PT_3NQ55S57","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2413","7316UP-2413","{BS_6FZTHTXK,BS_2QGRF15R}","{DNA,RNA}","BS_5HPHMEF3","7316UP-2413"
+"PT_SNTWW5V0","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2448","7316UP-2448","{BS_77XZNGVC,BS_ZD6XFSVJ}","{DNA,RNA}","BS_MT98YTT4","7316UP-2448"
+"PT_DF9T1B5G","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2477","7316UP-2477","{BS_NKSZBDY8,BS_MKGP8P5A}","{DNA,RNA}","BS_4C6204BS","7316UP-2477"
+"PT_JE9RX5DR","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2508","7316UP-2508","{BS_6AFWGT6Z,BS_ZMA11A2B}","{DNA,RNA}","BS_96TGJVMN","7316UP-2508"
+"PT_Q9VRRAR8","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2515","7316UP-2515","{BS_0Q7HKPD2,BS_R98ZGVVW}","{DNA,RNA}","BS_CFYBAG3K","7316UP-2515"
+"PT_3FH27J1X","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2620","7316UP-2620","{BS_FZPNPDQQ,BS_FA3JYABA}","{DNA,RNA}","BS_60BP98YA","7316UP-2620"
+"PT_5SPSW3YF","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2722","7316UP-2722","{BS_3R4N22YY,BS_TPTEE9Y9}","{RNA,DNA}","BS_29AM0104","7316UP-2722"
+"PT_6SYP6A7X","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2838","7316UP-2838","{BS_SATYBH1F,BS_B47WQMHK}","{DNA,RNA}","BS_B77EHCCP","7316UP-2838"
+"PT_FFSCZ7CA","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2877","7316UP-2877","{BS_J5R6HX4M,BS_74GHJS7N}","{DNA,RNA}","BS_8X5V1WPA","7316UP-2877"
+"PT_3G8J8D4M","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2900","7316UP-2900","{BS_XKCDEJZ2,BS_TQJDGF04}","{DNA,RNA}","BS_HSPX2BV8","7316UP-2900"
+"PT_GWBKEDF7","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-2960","7316UP-2960","{BS_4KHK5ZVS,BS_B3516CQJ}","{DNA,RNA}","BS_GQ8X5D7D","7316UP-2960"
+"PT_JVZ4T317","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-3083","7316UP-3083","{BS_KHF6DPKN,BS_3XVSTN5S}","{DNA,RNA}","BS_42XKWTEF","7316UP-3083"
+"PT_7G7G1B27","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-3249","7316UP-3249","{BS_D4844MVS,BS_SQ6ZN982}","{DNA,RNA}","BS_SHEX782D","7316UP-3249"
+"PT_N0KJ1CR2","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-3296","7316UP-3296","{BS_G753Z42N,BS_8AA254XK}","{DNA,RNA}","BS_3QM87V4D","7316UP-3296"
+"PT_C9647EKZ","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-3675","7316UP-3675","{BS_HED4167A,BS_7PXAWDC9}","{DNA,RNA}","BS_31NJR956","7316UP-3675"
+"PT_XMYN334C","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-3705","7316UP-3705","{BS_A4G7F9CH,BS_0Y1BP5A4}","{DNA,RNA}","BS_331NCNGJ","7316UP-3705"
+"PT_33EK2MN8","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-474","7316UP-474","{BS_8EMJ3PZY,BS_CF5HC0PR}","{DNA,RNA}","BS_X70XT4GF","7316UP-474"
+"PT_9BJWHYZP","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-528","7316UP-528","{BS_6AYC4A6W,BS_73GEX9CY}","{DNA,RNA}","BS_F48CQZ0E","7316UP-528"
+"PT_TJ74G94K","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-580","7316UP-580","{BS_2Y7H85D0,BS_RDBNX7YJ}","{DNA,RNA}","BS_9ZM2J7V4","7316UP-580"
+"PT_DRVY2FQQ","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-584","7316UP-584","{BS_0KP6JYPD,BS_QNE4NG2X}","{DNA,RNA}","BS_NFHNG4MV","7316UP-584"
+"PT_V469B27Z","{SC_2ZBAMKK0}","7316UP-646","7316UP-646","{BS_NDX7BHNT}","{RNA}","",""
+"PT_A8YXZ42Q","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-716","7316UP-716","{BS_M9RTNS4X,BS_CSXE7SXN}","{DNA,RNA}","BS_MNF5CN7X","7316UP-716"
+"PT_5JCY0JFD","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-756","7316UP-756","{BS_2EVAFHE0,BS_MJMZZ1EY}","{DNA,RNA}","BS_ZFNG7X82","7316UP-756"
+"PT_D75EGJWB","{SC_2ZBAMKK0,SC_2ZBAMKK0}","7316UP-857","7316UP-857","{BS_3A8D4FXB,BS_BSNW9PTR}","{DNA,RNA}","BS_HVY3C919","7316UP-857"
+"PT_7S81MVTV","{SC_2ZBAMKK0}","7316UP-903","7316UP-903","{BS_0JCEEVZT}","{RNA}","",""