geoseeq 0.7.6__py3-none-any.whl → 0.7.8__py3-none-any.whl

geoseeq/cli/download.py

@@ -458,11 +458,15 @@ def _make_read_configs(download_results, config_dir="."):
         else:
             config_blobs[sample.name]["reads_2"].append(local_path)
 
+    # make config dir
+    makedirs(config_dir, exist_ok=True)
+
     for sample_name, config_blob in config_blobs.items():
         config_path = join(config_dir, f"{sample_name}.config.json")
         with open(config_path, "w") as f:
             json.dump(config_blob, f, indent=4)
 
+
 def _open_maybe_gzip(local_path):
     """Open a file that may be gzipped. Do not rely on file extension."""
     with open(local_path, "rb") as f:
@@ -474,7 +478,7 @@ def _open_maybe_gzip(local_path):
 
 
 def _trim_fastq_to_complete_reads(key, local_path):
-    """Trim a fastq file to the nearest complete read boundary under head_bytes.
+    """Trim a fastq file to the nearest complete read boundary.
     
     Write the output as a gzipped file regardless of input compression.
     """
@@ -484,14 +488,15 @@ def _trim_fastq_to_complete_reads(key, local_path):
         while True:
             read_lines = []
             for _ in range(4):
-                line = infile.readline()
+                try:
+                    line = infile.readline()
+                except Exception:  # ignore errors reading line, assume end of file
+                    break
                 if not line:
                     break
                 read_lines.append(line)
             if len(read_lines) < 4:
                 break  # end of file
-            if infile.tell() > key[4]:  # key[4] is head_bytes
-                break  # reached head limit
             for line in read_lines:
                 outfile.write(line)
             lines_written += 4

geoseeq/cli/main.py

@@ -55,7 +55,7 @@ def version():
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo("0.7.6")  # remember to update pyproject.toml
+    click.echo("0.7.8")  # remember to update pyproject.toml
 
 
 @main.group("advanced")

{geoseeq-0.7.6.dist-info → geoseeq-0.7.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geoseeq
-Version: 0.7.6
+Version: 0.7.8
 Summary: GeoSeeq command line tools and python API
 Project-URL: Homepage, https://github.com/biotia/geoseeq_api_client
 Project-URL: Issues, https://github.com/biotia/geoseeq_api_client/issues

{geoseeq-0.7.6.dist-info → geoseeq-0.7.8.dist-info}/RECORD

@@ -21,11 +21,11 @@ geoseeq/cli/__init__.py,sha256=4WnK87K5seRK3SGJAxNWnQTqyg5uBhdhrOrzB1D4b3M,24
 geoseeq/cli/constants.py,sha256=NtRSNBuna42605LE0sVywTPfmzYQnG-3yrT_M7Ml5B0,213
 geoseeq/cli/copy.py,sha256=02U9kdrAIbbM8MlRMLL6p-LMYFSuRObE3h5jyvcL__M,2275
 geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
-geoseeq/cli/download.py,sha256=JHKd4VKAgJmvd3fVpSNlxJJT2goLB7eYkWY5UkfXESI,25347
+geoseeq/cli/download.py,sha256=RZolqwaIVRa7fkaN9AZxswJ7BSaAg6Itk0SKs_dCjVs,25422
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/find_grn.py,sha256=oMDxkzGQBQb2_cCuvmwoeHOsFHqyO9RLeJzrB6bAe5M,439
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=mDfD0R7d-FJJyKFMnsMIZDGprVoslE6Ts5QbJTTIBFY,4133
+geoseeq/cli/main.py,sha256=s6iWmXFp7a3C_If5NxTo_mBuRhPqp3VWeN5iXf60fzk,4133
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/project.py,sha256=V5SdXm2Hwo2lxrkpwRDedw-mAE4XnM2uwT-Gj1D90VQ,3030
@@ -92,8 +92,8 @@ geoseeq/vc/vc_cache.py,sha256=P4LXTbq2zOIv1OhP7Iw5MmypR2vXuy29Pq5K6gRvi-M,730
 geoseeq/vc/vc_dir.py,sha256=A9CLTh2wWCRzZjiLyqXD1vhtsWZGD3OjaMT5KqlfAXI,457
 geoseeq/vc/vc_sample.py,sha256=qZeioWydXvfu4rGMs20nICfNcp46y_XkND-bHdV6P5M,3850
 geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
-geoseeq-0.7.6.dist-info/METADATA,sha256=yTvBpyBSN4eelbfdHrL3jxWYG38vN7uOL7fSUlFp5ok,5652
-geoseeq-0.7.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-geoseeq-0.7.6.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.7.6.dist-info/licenses/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.7.6.dist-info/RECORD,,
+geoseeq-0.7.8.dist-info/METADATA,sha256=Z-HVBUxxGG8YGY3JSw5PHjkujPgsso9b5vUzfRbrG28,5652
+geoseeq-0.7.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+geoseeq-0.7.8.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.7.8.dist-info/licenses/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.7.8.dist-info/RECORD,,