From 329a1a7e122eda41016185d1b1e8d50d97f8857b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 7 Jan 2021 03:17:47 -0600
Subject: Allow for xml and xml.gz files

---
 workflows/pull-data/genbank/genbank.py             |  3 +-
 .../genbank/transform-genbank-xml2yamlfa.py        | 78 ++++++++++++----------
 2 files changed, 43 insertions(+), 38 deletions(-)

(limited to 'workflows')

diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py
index 85d615c..026c03f 100644
--- a/workflows/pull-data/genbank/genbank.py
+++ b/workflows/pull-data/genbank/genbank.py
@@ -111,7 +111,8 @@ def get_metadata(id, gbseq):
         # print(n,file=sys.stderr)
         if n != 'Unpublished':
             institute,address = n.split(',',1)
-            submitter.submitter_name = institute.split(') ')[1]
+            if ")" in institute:
+                submitter.submitter_name = institute.split(')')[1]
             submitter.submitter_address = address.strip()
     except AttributeError:
         pass
diff --git a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
index 9414864..1a8035d 100755
--- a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
+++ b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
@@ -33,43 +33,47 @@ states = {}
 
 for xmlfn in args.files:
     print(f"--- Reading {xmlfn}")
-    with gzip.open(xmlfn, 'r') as f:
-        xml = f.read().decode()
-        tree = ET.fromstring(xml)
-        for gb in tree.findall('./GBSeq'):
-            valid = None
-            error = None
-            meta = {}
-            id = gb.find("GBSeq_locus").text
-            basename = dir+"/"+id
-            print(f"    parsing {id}")
-            try:
-                valid,meta = genbank.get_metadata(id,gb)
-                if valid:
-                    # --- write JSON
-                    jsonfn = basename + ".json"
-                    with open(jsonfn, 'w') as outfile:
-                        print(f"    writing {jsonfn}")
-                        json.dump(meta, outfile, indent=4)
-                    # --- write FASTA
-                    fa = basename+".fa"
-                    seq = genbank.get_sequence(id,gb)
-                    print(f"    writing {fa}")
-                    with open(fa,"w") as f2:
-                        f2.write(f"> {id}\n")
-                        f2.write(seq)
-                    # print(seq)
-            except genbank.GBError as e:
-                error = f"{e} for {id}"
-                print(error,file=sys.stderr)
-                valid = False
-            state = {}
-            state['valid'] = valid
-            if error:
-                state['error'] = error
-            if meta['warnings']:
-                state['warnings'] = meta['warnings']
-            states[id] = state
+    try:
+        with gzip.open(xmlfn, 'r') as f:
+            xml = f.read().decode()
+    except Exception:
+        with open(xmlfn, 'r') as f:
+            xml = f.read()
+    tree = ET.fromstring(xml)
+    for gb in tree.findall('./GBSeq'):
+        valid = None
+        error = None
+        meta = {}
+        id = gb.find("GBSeq_locus").text
+        basename = dir+"/"+id
+        print(f"    parsing {id}")
+        try:
+            valid,meta = genbank.get_metadata(id,gb)
+            if valid:
+                # --- write JSON
+                jsonfn = basename + ".json"
+                with open(jsonfn, 'w') as outfile:
+                    print(f"    writing {jsonfn}")
+                    json.dump(meta, outfile, indent=4)
+                # --- write FASTA
+                fa = basename+".fa"
+                seq = genbank.get_sequence(id,gb)
+                print(f"    writing {fa}")
+                with open(fa,"w") as f2:
+                    f2.write(f"> {id}\n")
+                    f2.write(seq)
+                # print(seq)
+        except genbank.GBError as e:
+            error = f"{e} for {id}"
+            print(error,file=sys.stderr)
+            valid = False
+        state = {}
+        state['valid'] = valid
+        if error:
+            state['error'] = error
+        if meta['warnings']:
+            state['warnings'] = meta['warnings']
+        states[id] = state
 
 statefn = dir + '/state.json'
 with open(statefn, 'w') as outfile:
-- 
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