PyPI - geoseeq - Versions diffs - 0.6.14.dev6__tar.gz → 0.6.14.dev7__tar.gz - Mend

@@ -118,7 +118,7 @@ def _is_fastq(path, fq_exts=['.fastq', '.fq'], compression_exts=['.gz', '.bz2',
     return False
-def _is_fasta(path, fa_exts=['.fasta', '.fa'], compression_exts=['.gz', '.bz2', '']):
+def _is_fasta(path, fa_exts=['.fasta', '.fa', '.fna', '.faa'], compression_exts=['.gz', '.bz2', '']):
     for fa_ext in fa_exts:
         for compression_ext in compression_exts:
             if path.endswith(fa_ext + compression_ext):
@@ -289,9 +289,9 @@ def cli_upload_reads_wizard(state, cores, overwrite, yes, regex, private, link_t
     [FILES...] can be paths to BAM files or a file containing a list of paths, or a mix of both.
     Example: "path/to/bam/files
     """
-    knex = state.get_knex()
-    proj = handle_project_id(knex, project_id, yes, private)
-    filepaths = {basename(line): line for line in flatten_list_of_bams(files)}
-    click.echo(f'Found {len(filepaths)} files to upload.', err=True)
-    groups = _group_files(knex, filepaths, 'bam::bam', regex, yes)
-    _do_upload(groups, 'bam::bam', link_type, proj, filepaths, overwrite, no_new_versions, cores, state)
+    # knex = state.get_knex()
+    # proj = handle_project_id(knex, project_id, yes, private)
+    # filepaths = {basename(line): line for line in flatten_list_of_bams(files)}
+    # click.echo(f'Found {len(filepaths)} files to upload.', err=True)
+    # groups = _group_files(knex, filepaths, 'bam::bam', regex, yes)
+    # _do_upload(groups, 'bam::bam', link_type, proj, filepaths, overwrite, no_new_versions, cores, state)

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev6
+Version: 0.6.14.dev7
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

@@ -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('0.6.14dev6')  # remember to update pyproject.toml
+    click.echo('0.6.14dev7')  # remember to update pyproject.toml
 @main.group('advanced')

@@ -6,7 +6,7 @@ from .upload_reads import (
     _make_in_process_logger,
     _get_regex,
     _group_files,
-    flatten_list_of_fastqs,
+    flatten_list_of_fastxs,
 )
 from multiprocessing import Pool, current_process
@@ -84,7 +84,7 @@ def cli_find_urls_for_reads(state, cores, overwrite, yes, regex, private, module
     """
     knex = state.get_knex()
     proj = handle_project_id(knex, project_id, yes, private)
-    filepaths = {basename(line): line for line in flatten_list_of_fastqs(fastq_files)}
+    filepaths = {basename(line): line for line in flatten_list_of_fastxs(fastq_files)}
     click.echo(f'Found {len(filepaths)} files to upload.', err=True)
     regex = _get_regex(knex, filepaths, module_name, proj, regex)
     groups = _group_files(knex, filepaths, module_name, regex, yes)

@@ -2,7 +2,13 @@ from os import environ
 from os.path import join
 FIVE_MB = 5 * (1024 ** 2)
-FASTQ_MODULE_NAMES = ['short_read::paired_end', 'short_read::single_end', 'long_read::nanopore', 'raw::raw_reads']
+FASTQ_MODULE_NAMES = [
+    'short_read::paired_end',
+    'short_read::single_end',
+    'long_read::nanopore',
+    'raw::raw_reads',
+    'genome::fasta',
+]
 DEFAULT_ENDPOINT = "https://backend.geoseeq.com"
 CONFIG_FOLDER = environ.get("XDG_CONFIG_HOME", join(environ["HOME"], ".config"))

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev6
+Version: 0.6.14.dev7
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "geoseeq"
-version = "0.6.14dev6"
+version = "0.6.14dev7"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]

geoseeq 0.6.14.dev6__tar.gz → 0.6.14.dev7__tar.gz

geoseeq 0.6.14.dev6tar.gz → 0.6.14.dev7tar.gz