From 7a96d0b1b15ab28fe3a618db35364891ab5d0328 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 26 May 2020 17:30:30 -0400
Subject: Can have list of sequence labels to exclude from combined fasta

refs #68

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 .../pangenome-generate/pangenome-generate.cwl      |  2 ++
 workflows/pangenome-generate/relabel-seqs.cwl      |  5 ++++-
 workflows/pangenome-generate/relabel-seqs.py       | 22 +++++++++++++++++-----
 3 files changed, 23 insertions(+), 6 deletions(-)

(limited to 'workflows')

diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index ad8b27f..9118cf8 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -9,6 +9,7 @@ inputs:
   metadata: File[]
   metadataSchema: File
   subjects: string[]
+  exclude: File?
   bin_widths:
     type: int[]
     default: [ 1, 4, 16, 64, 256, 1000, 4000, 16000]
@@ -47,6 +48,7 @@ steps:
     in:
       readsFA: inputReads
       subjects: subjects
+      exclude: exclude
     out: [relabeledSeqs, originalLabels]
     run: relabel-seqs.cwl
   dedup:
diff --git a/workflows/pangenome-generate/relabel-seqs.cwl b/workflows/pangenome-generate/relabel-seqs.cwl
index c1f17a4..367b9bf 100644
--- a/workflows/pangenome-generate/relabel-seqs.cwl
+++ b/workflows/pangenome-generate/relabel-seqs.cwl
@@ -3,10 +3,13 @@ class: CommandLineTool
 inputs:
   readsFA: File[]
   subjects: string[]
+  exclude:
+    type: File?
+    inputBinding: {position: 2}
   script:
     type: File
     default: {class: File, location: relabel-seqs.py}
-    inputBinding: {}
+    inputBinding: {position: 1}
 outputs:
   relabeledSeqs:
     type: File
diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py
index 6b022a0..25b4a08 100644
--- a/workflows/pangenome-generate/relabel-seqs.py
+++ b/workflows/pangenome-generate/relabel-seqs.py
@@ -1,5 +1,6 @@
 import os
 import json
+import sys
 
 def readitems(stem):
     items = []
@@ -16,15 +17,26 @@ subjects = readitems("subs")
 relabeled_fasta = open("relabeledSeqs.fasta", "wt")
 original_labels = open("originalLabels.ttl", "wt")
 
+blacklist = set()
+if len(sys.argv) > 1:
+    with open(sys.argv[1]) as bl:
+        for l in bl:
+            blacklist.add(l.strip())
+
 for i, r in enumerate(reads):
     with open(r["path"], "rt") as fa:
-        label = fa.readline()
-        original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subjects[i], label[1:].strip().replace('"', '\\"')))
-        relabeled_fasta.write(">"+subjects[i]+"\n")
+        label = fa.readline().strip()
+        original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subjects[i], label[1:].replace('"', '\\"')))
+        skip = (subjects[i] in blacklist or label[1:] in blacklist)
+        if skip:
+            original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/excluded_from_graph> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean> .\n" % (subjects[i]))
+        if not skip:
+            relabeled_fasta.write(">"+subjects[i]+"\n")
         data = fa.read(8096)
         while data:
-            relabeled_fasta.write(data)
+            if not skip:
+                relabeled_fasta.write(data)
             endswithnewline = data.endswith("\n")
             data = fa.read(8096)
-        if not endswithnewline:
+        if not skip and not endswithnewline:
             relabeled_fasta.write("\n")
-- 
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