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>

1 files changed, 17 insertions, 5 deletions

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")