Merge branch 'master' into patch-3

1 files changed, 30 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py
new file mode 100644
index 0000000..6b022a0
--- /dev/null
+++ b/workflows/pangenome-generate/relabel-seqs.py
@@ -0,0 +1,30 @@
+import os
+import json
+
+def readitems(stem):
+    items = []
+    b = 1
+    while os.path.exists("%s%i" % (stem, b)):
+        with open("%s%i" % (stem, b)) as f:
+            items.extend(json.load(f))
+        b += 1
+    return items
+
+reads = readitems("block")
+subjects = readitems("subs")
+
+relabeled_fasta = open("relabeledSeqs.fasta", "wt")
+original_labels = open("originalLabels.ttl", "wt")
+
+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")
+        data = fa.read(8096)
+        while data:
+            relabeled_fasta.write(data)
+            endswithnewline = data.endswith("\n")
+            data = fa.read(8096)
+        if not endswithnewline:
+            relabeled_fasta.write("\n")