tservice-plugins
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quartet-rnaseq-report
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tags/v0.1.0
YJC 3 years ago
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  4. +29
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      src/tservice/plugins/quartet_rnaseq_report.clj
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      src/tservice/plugins/quartet_rnaseq_report/exp2qcdt.clj
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      src/tservice/plugins/quartet_rnaseq_report/merge_exp.clj

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.gitignore View File

/target
/classes
/checkouts
pom.xml
pom.xml.asc
*.jar
*.class
/.lein-*
/.nrepl-port
.hgignore
.hg/

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LICENSE.md View File

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README.md View File

# quartet-rnaseq-report

FIXME: description

## Installation

Download from http://example.com/FIXME.

## Usage

FIXME: explanation

## Options

FIXME: listing of options this app accepts.

## Examples

...

### Bugs

...

### Any Other Sections
### That You Think
### Might be Useful

## License

Copyright © 2021 FIXME

This program and the accompanying materials are made available under the
terms of the Eclipse Public License 2.0 which is available at
http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary
Licenses when the conditions for such availability set forth in the Eclipse
Public License, v. 2.0 are satisfied: GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or (at your
option) any later version, with the GNU Classpath Exception which is available
at https://www.gnu.org/software/classpath/license.html.

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project.clj View File

(defproject tservice/quartet-rnaseq-report "v0.1.0"
:description "FIXME: write description"
:url "http://example.com/FIXME"
:license {:name "Eclipse Public License"
:url "http://www.eclipse.org/legal/epl-v10.html"}
:min-lein-version "2.5.0"
:deployable false

:dependencies
[[org.clojure/data.csv "1.0.0"]
[me.raynes/fs "1.4.6"]
[org.clojure/tools.logging "1.1.0"]
[org.clojure/core.async "0.4.500"
:exclusions [org.clojure/tools.reader]]]

:profiles
{:provided
{:dependencies
[[org.clojure/clojure "1.10.1"]
[tservice "0.3.1"]]}

:uberjar
{:auto-clean true
:aot :all
:omit-source true
:javac-options ["-target" "1.8", "-source" "1.8"]
:target-path "target/%s"
:resource-paths ["resources"]
:uberjar-name "quartet-rnaseq-report.tservice-plugin.jar"}})

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resources/quartet_rnaseq_report.yaml View File

run_modules:
- rnaseq_data_generation_information
- rnaseq_performance_assessment
- rnaseq_raw_qc
- rnaseq_post_alignment_qc
- rnaseq_quantification_qc
- rnaseq_supplementary

skip_generalstats: true

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resources/tservice-plugin.yaml View File

info:
name: FIXME: write name
version: v0.1.0
description: FIXME: write description
plugin:
name: quartet-rnaseq-report
display-name: FIXME: write display name
lazy-load: false
init:
- step: load-namespace
namespace: tservice.plugins.quartet-rnaseq-report
- step: register-plugin
entrypoint: tservice.plugins.quartet-rnaseq-report/metadata
- step: init-event
entrypoint: tservice.plugins.quartet-rnaseq-report/events-init

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src/tservice/plugins/quartet_rnaseq_report.clj View File

(ns tservice.plugins.quartet-rnaseq-report
(:require [clojure.core.async :as async]
[clojure.data.json :as json]
[clojure.spec.alpha :as s]
[clojure.tools.logging :as log]
[tservice.lib.commons :as comm :refer [get-path-variable]]
[tservice.plugins.quartet-rnaseq-report.exp2qcdt :as exp2qcdt]
[tservice.plugins.quartet-rnaseq-report.merge-exp :as me]
[spec-tools.core :as st]
[spec-tools.json-schema :as json-schema]
[tservice.config :refer [get-workdir env]]
[tservice.events :as events]
[tservice.lib.filter-files :as ff]
[tservice.lib.fs :as fs-lib]
[tservice.util :as u]
[tservice.util.files :as files]
[clojure.java.io :as io]
[tservice.db.handler :as db-handler]
[clojure.java.shell :as shell :refer [sh]]
[tservice.vendor.multiqc :as mq]))

;;; ------------------------------------------------ Event Specs ------------------------------------------------
(s/def ::name
(st/spec
{:spec string?
:type :string
:description "The name of the report"
:swagger/default ""
:reason "Not a valid report name"}))

(s/def ::description
(st/spec
{:spec string?
:type :string
:description "Description of the report"
:swagger/default ""
:reason "Not a valid description."}))

(s/def ::project_id
(st/spec
{:spec #(some? (re-matches #"[a-f0-9]{8}(-[a-f0-9]{4}){4}[a-f0-9]{8}" %))
:type :string
:description "project-id"
:swagger/default "40644dec-1abd-489f-a7a8-1011a86f40b0"
:reason "Not valid a project-id."}))

(s/def ::filepath
(st/spec
{:spec (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)?[a-zA-Z0-9_\/]+.*" %))
:type :string
:description "File path for covertor."
:swagger/default nil
:reason "The filepath must be string."}))

(s/def ::group
(st/spec
{:spec string?
:type :string
:description "A group name which is matched with library."
:swagger/default []
:reason "The group must a string."}))

(s/def ::library
(st/spec
{:spec string?
:type :string
:description "A library name."
:swagger/default []
:reason "The library must a string."}))

(s/def ::sample
(st/spec
{:spec string?
:type :string
:description "A sample name."
:swagger/default []
:reason "The sample name must a string."}))

(s/def ::metadat-item
(s/keys :req-un [::library
::group
::sample]))

(s/def ::metadata
(s/coll-of ::metadat-item))

(s/def ::lab
(st/spec
{:spec string?
:type :string
:description "Lab name."
:swagger/default []
:reason "The lab_name must be string."}))

(s/def ::sequencing_platform
(st/spec
{:spec string?
:type :string
:description "Sequencing Platform."
:swagger/default []
:reason "The sequencing_platform must be string."}))

(s/def ::sequencing_method
(st/spec
{:spec string?
:type :string
:description "Sequencing Method"
:swagger/default []
:reason "The sequencing_method must be string."}))

(s/def ::library_protocol
(st/spec
{:spec string?
:type :string
:description "Library protocol."
:swagger/default []
:reason "The library_protocol must be string."}))

(s/def ::library_kit
(st/spec
{:spec string?
:type :string
:description "Library kit."
:swagger/default []
:reason "The library_kit must be string."}))

(s/def ::read_length
(st/spec
{:spec string?
:type :string
:description "Read length"
:swagger/default []
:reason "The read_length must be string."}))

(s/def ::date
(st/spec
{:spec string?
:type :string
:description "Date"
:swagger/default []
:reason "The date must be string."}))

(s/def ::parameters
(s/keys :req-un [::lab
::sequencing_platform
::sequencing_method
::library_protocol
::library_kit
::read_length
::date]))

(def quartet-rna-report-params-body
"A spec for the body parameters."
(s/keys :req-un [::name ::description ::filepath ::metadata ::parameters]
:opt-un [::project_id]))

;;; ------------------------------------------------ Event Metadata ------------------------------------------------
(def metadata
{:route ["/report/quartet-rnaseq-report"
{:tags ["Report"]
:post {:summary "Parse the results of the quartet-rnaseq-qc app and generate the report."
:parameters {:body quartet-rna-report-params-body}
:responses {201 {:body {:results string? :log string? :report string? :id string?}}}
:handler (fn [{{{:keys [name description project_id filepath metadata parameters]} :body} :parameters}]
(let [workdir (get-workdir)
from-path (u/replace-path filepath workdir)
uuid (u/uuid)
relative-dir (fs-lib/join-paths "download" uuid)
to-dir (fs-lib/join-paths workdir relative-dir)
log-path (fs-lib/join-paths to-dir "log")]
(fs-lib/create-directories! to-dir)
(spit log-path (json/write-str {:status "Running" :msg ""}))
(events/publish-event! :quartet_rnaseq_report-convert
{:datadir from-path
:parameters parameters
:metadata metadata
:dest-dir to-dir})
(db-handler/create-report! {:id (u/uuid)
:report_name name
:project_id project_id
:app_name "quartet_rnaseq_report"
:description description
:report_path (fs-lib/join-paths relative-dir "multiqc.html")
:started_time (u/time->int (u/now))
:finished_time nil
:archived_time nil
:report_type "multireport"
:status "Started"
:log (fs-lib/join-paths relative-dir "log")})
{:status 201
:body {:results (fs-lib/join-paths relative-dir)
:report (fs-lib/join-paths relative-dir "multiqc_report.html")
:log (fs-lib/join-paths relative-dir "log")
:id uuid}}))}
:get {:summary "A json shema for quartet-rnaseq-report."
:parameters {}
:responses {200 {:body map?}}
:handler (fn [_]
{:status 200
:body (json-schema/transform quartet-rna-report-params-body)})}}]
:manifest {:description "Parse the results of the quartet-rna-qc app and generate the report."
:category "Report"
:home "https://github.com/clinico-omics/quartet-rnaseq-report"
:name "Quartet RNA-Seq Report"
:source "PGx"
:short_name "quartet-rnaseq-report"
:icons [{:src "", :type "image/png", :sizes "192x192"}
{:src "", :type "image/png", :sizes "192x192"}]
:author "Jun Shang"
:hidden false
:id "f65d87fd3dd2213d91bb15900ba57c11"
:app_name "shangjun/quartet-rnaseq-report"}})

(def ^:const quartet-rnaseq-report-topics
"The `Set` of event topics which are subscribed to for use in quartet-rnaseq-report tracking."
#{:quartet_rnaseq_report-convert})

(def ^:private quartet-rnaseq-report-channel
"Channel for receiving event quartet-rnaseq-report we want to subscribe to for quartet-rnaseq-report events."
(async/chan))

;;; ------------------------------------------------ Event Processing ------------------------------------------------

(defn- decompression-tar
[filepath]
(shell/with-sh-env {:PATH (get-path-variable)
:LC_ALL "en_US.utf-8"
:LANG "en_US.utf-8"}
(let [command ["bash" "-c"
(format "tar -xvf %s -C %s" filepath (fs-lib/parent-path filepath))]
result (apply sh command)
status (if (= (:exit result) 0) "Success" "Error")
msg (str (:out result) "\n" (:err result))]
{:status status
:msg msg})))

(defn- filter-mkdir-copy
[fmc-datadir fmc-patterns fmc-destdir fmc-newdir]
(let [files-keep (ff/batch-filter-files fmc-datadir fmc-patterns)
files-keep-dir (fs-lib/join-paths fmc-destdir fmc-newdir)]
(fs-lib/create-directories! files-keep-dir)
(ff/copy-files! files-keep files-keep-dir {:replace-existing true})))

(defn- extract-config-file
[filename dest-path]
(when (io/resource filename)
(files/with-open-path-to-resource [filepath filename]
(files/copy-files! filepath dest-path))))

(defn- quartet-rnaseq-report!
"Chaining Pipeline: filter-files -> copy-files -> merge_exp_file -> exp2qcdt -> multiqc."
[datadir parameters metadata dest-dir]
(log/info "Generate quartet rnaseq report: " datadir parameters metadata dest-dir)
(let [metadata-file (fs-lib/join-paths dest-dir
"results"
"metadata.csv")
parameters-file (fs-lib/join-paths dest-dir
"results"
"general-info.json")
ballgown-dir (fs-lib/join-paths dest-dir "ballgown")
count-dir (fs-lib/join-paths dest-dir "count")
exp-fpkm-filepath (fs-lib/join-paths dest-dir "fpkm.csv")
exp-count-filepath (fs-lib/join-paths dest-dir "count.csv")
result-dir (fs-lib/join-paths dest-dir "results")
log-path (fs-lib/join-paths dest-dir "log")
config-path (fs-lib/join-paths dest-dir "results", "quartet_rnaseq_report.yaml")]
(try
(fs-lib/create-directories! result-dir)
(log/info "Merge these files")
(log/info "Merge gene experiment files from ballgown directory to a experiment table: " ballgown-dir exp-fpkm-filepath)
(log/info "Merge these files")
(log/info "Merge gene experiment files from count directory to a experiment table: " count-dir exp-count-filepath)
(filter-mkdir-copy datadir [".*call-ballgown/.*.txt"] dest-dir "ballgown")
(filter-mkdir-copy datadir [".*call-count/.*gene_count_matrix.csv"] dest-dir "count")
(filter-mkdir-copy datadir [".*call-qualimapBAMqc/.*tar.gz"] dest-dir "results/post_alignment_qc/bam_qc")
(filter-mkdir-copy datadir [".*call-qualimapRNAseq/.*tar.gz"] dest-dir "results/post_alignment_qc/rnaseq_qc")
(filter-mkdir-copy datadir [".*call-fastqc/.*.zip"] dest-dir "results/rawqc/fastqc")
(filter-mkdir-copy datadir [".*call-fastqscreen/.*.txt"] dest-dir "results/rawqc/fastq_screen")
(me/merge-exp-files! (ff/list-files ballgown-dir {:mode "file"}) exp-fpkm-filepath)
(me/merge-exp-files! (ff/list-files count-dir {:mode "file"}) exp-count-filepath)
(spit parameters-file (json/write-str parameters))
(comm/write-csv! metadata-file metadata)
;;(decompression-tar files-qualimap-bam)
;;(decompression-tar files-qualimap-RNA)
(doseq [files-qualimap-bam-tar (ff/batch-filter-files (fs-lib/join-paths dest-dir "results/post_alignment_qc/bam_qc") [".*tar.gz"])]
(decompression-tar files-qualimap-bam-tar))
(doseq [files-qualimap-RNA-tar (ff/batch-filter-files (fs-lib/join-paths dest-dir "results/post_alignment_qc/rnaseq_qc") [".*tar.gz"])]
(decompression-tar files-qualimap-RNA-tar))
(extract-config-file "quartet_rnaseq_report.yaml" config-path)
(let [exp2qcdt-result (exp2qcdt/call-exp2qcdt! exp-fpkm-filepath exp-count-filepath metadata-file result-dir)
multiqc-result (if (= (:status exp2qcdt-result) "Success")
(mq/multiqc result-dir dest-dir {:config config-path :template "default" :title "Quartet RNA report"})
;;(mq/multiqc result-dir)
exp2qcdt-result)
result {:status (:status multiqc-result)
:msg (:msg multiqc-result)}
log (json/write-str result)]
(log/info "Status: " result)
(spit log-path log))
(catch Exception e
(let [log (json/write-str {:status "Error" :msg (.toString e)})]
(log/info "Status: " log)
(spit log-path log))))))

(defn- process-quartet-rnaseq-report-event!
"Handle processing for a single event notification received on the quartet-rnaseq-report-channel"
[quartet-rnaseq-report-event]
;; try/catch here to prevent individual topic processing exceptions from bubbling up. better to handle them here.
(try
(when-let [{topic :topic object :item} quartet-rnaseq-report-event]
;; TODO: only if the definition changed??
(case (events/topic->model topic)
"quartet_rnaseq_report" (quartet-rnaseq-report! (:datadir object) (:parameters object) (:metadata object) (:dest-dir object))))
(catch Throwable e
(log/warn (format "Failed to process quartet-rnaseq-report event. %s" (:topic quartet-rnaseq-report-event)) e))))

;;; --------------------------------------------------- Lifecycle ----------------------------------------------------

(defn events-init
"Automatically called during startup; start event listener for quartet-rnaseq-report events."
[]
(events/start-event-listener! quartet-rnaseq-report-topics quartet-rnaseq-report-channel process-quartet-rnaseq-report-event!))

+ 33
- 0
src/tservice/plugins/quartet_rnaseq_report/exp2qcdt.clj View File

(ns tservice.plugins.quartet-rnaseq-report.exp2qcdt
"A wrapper for exp2qcdt tool."
(:require [tservice.lib.commons :refer [get-path-variable]]
[tservice.config :refer [get-plugin-dir]]
[tservice.lib.fs :as fs]
[clojure.java.shell :as shell :refer [sh]]))

(defn add-env-to-path
"Add the path of the plugin's environment into the PATH and return the PATH"
[]
(let [env-bin-path (fs/join-paths (get-plugin-dir) "plugins" "repository" "quartet-rnaseq-report" "bin")
path (get-path-variable)]
(str env-bin-path ":" path)))

(defn call-exp2qcdt!
"Call exp2qcdt bash script.
exp-file: FPKM file , each row is the expression values of a gene and each column is a library.
cnt-file: Count file, each row is the expression values of a gene and each column is a library.
meta-file: Need to contain three columns: library, group, and sample and library names must be matched with the column names in the `exp-file`.
result-dir: A directory for result files.
"
[exp-file cnt-file meta-file result-dir]
(shell/with-sh-env {:PATH (add-env-to-path)
:LC_ALL "en_US.utf-8"
:LANG "en_US.utf-8"}
(let [command ["bash" "-c"
(format "exp2qcdt -e %s -c %s -m %s -o %s" exp-file cnt-file meta-file result-dir)]
result (apply sh command)
status (if (= (:exit result) 0) "Success" "Error")
msg (str (:out result) "\n" (:err result))]
{:status status
:msg msg})))


+ 36
- 0
src/tservice/plugins/quartet_rnaseq_report/merge_exp.clj View File

(ns tservice.plugins.quartet-rnaseq-report.merge-exp
"Merge expression files."
(:require [tservice.lib.commons :refer [read-csv write-csv! vec-remove write-csv-by-cols!]]))

(set! *warn-on-reflection* true)

(defn sort-exp-data
[coll]
(sort-by :GENE_ID coll))

(defn read-csvs
[files]
(map #(sort-exp-data (read-csv %)) files))

(defn reorder
[data]
(let [cols (vec (sort (keys (first data))))]
(cons :GENE_ID (vec-remove (.indexOf cols :GENE_ID) cols))))

(defn merge-exp
"[[{:GENE_ID 'XXX0' :YYY0 1.2} {:GENE_ID 'XXX1' :YYY1 1.3}]
[{:GENE_ID 'XXX0' :YYY2 1.2} {:GENE_ID 'XXX1' :YYY3 1.3}]]"
[all-exp-data]
(apply map merge all-exp-data))

(defn write-csv-by-ordered-cols!
[path row-data]
(let [cols (reorder row-data)]
(write-csv-by-cols! path row-data cols)))

(defn merge-exp-files!
"Assumption: all files have the same GENE_ID list, no matter what order."
[files path]
(->> (read-csvs files)
(merge-exp)
(write-csv-by-ordered-cols! path)))

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