From 7daa9ff2cdba742a811db00c924ccde25fa2c9b6 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 22 Jun 2020 15:06:10 +0000
Subject: Handle upload & assembly of gzipped, paired-end fastq

---
 bh20sequploader/main.py | 58 +++++++++++++++++++++++++++++++------------------
 1 file changed, 37 insertions(+), 21 deletions(-)

(limited to 'bh20sequploader/main.py')

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index a2e62fa..c442af0 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,18 +22,10 @@ ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
 UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
 
-def main():
-    parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
-    parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ')
-    parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json')
-    parser.add_argument("--validate", action="store_true", help="Dry run, validate only")
-    args = parser.parse_args()
-
-    api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
-
+def qa_stuff(metadata, sequence_p1, sequence_p2):
     try:
         log.debug("Checking metadata")
-        if not qc_metadata(args.metadata.name):
+        if not qc_metadata(metadata.name):
             log.warning("Failed metadata qc")
             exit(1)
     except ValueError as e:
@@ -42,29 +34,52 @@ def main():
         print(e)
         exit(1)
 
+    target = []
     try:
-        log.debug("Checking FASTA QC")
-        target = qc_fasta(args.sequence)
+        log.debug("Checking FASTA/FASTQ QC")
+        target.append(qc_fasta(sequence_p1))
+        if sequence_p2:
+            target.append(qc_fasta(sequence_p2))
+            target[0] = ("reads_1."+target[0][0][6:], target[0][1])
+            target[1] = ("reads_2."+target[1][0][6:], target[0][1])
     except ValueError as e:
         log.debug(e)
         log.debug("Failed FASTA qc")
         print(e)
         exit(1)
 
+    return target
+
+def upload_sequence(col, target, sequence):
+    with col.open(target[0], "wb") as f:
+        r = sequence.read(65536)
+        while r:
+            f.write(r)
+            r = sequence.read(65536)
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
+    parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json')
+    parser.add_argument('sequence_p1', type=argparse.FileType('rb'), help='sequence FASTA/FASTQ')
+    parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, help='sequence FASTQ pair')
+    parser.add_argument("--validate", action="store_true", help="Dry run, validate only")
+    args = parser.parse_args()
+
+    api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
+
+    target = qa_stuff(args.metadata, args.sequence_p1, args.sequence_p2)
+    seqlabel = target[0][1]
+
     if args.validate:
         print("Valid")
         exit(0)
 
     col = arvados.collection.Collection(api_client=api)
 
-    with col.open(target, "w") as f:
-        r = args.sequence.read(65536)
-        seqlabel = r[1:r.index("\n")]
-        print(seqlabel)
-        while r:
-            f.write(r)
-            r = args.sequence.read(65536)
-    args.sequence.close()
+    upload_sequence(col, target[0], args.sequence_p1)
+    if args.sequence_p2:
+        upload_sequence(col, target[1], args.sequence_p2)
 
     print("Reading metadata")
     with col.open("metadata.yaml", "w") as f:
@@ -73,7 +88,6 @@ def main():
         while r:
             f.write(r)
             r = args.metadata.read(65536)
-    args.metadata.close()
 
     external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
 
@@ -93,6 +107,8 @@ def main():
                  (seqlabel, properties['upload_user'], properties['upload_ip']),
                  properties=properties, ensure_unique_name=True)
 
+    print("Saved to %s" % col.manifest_locator())
+
     print("Done")
 
 if __name__ == "__main__":
-- 
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