rdrpcatch 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

rdrpcatch/rdrpcatch_scripts/format_pyhmmer_out.py

@@ -68,7 +68,7 @@ class hmmsearch_formatter:
         # Check if the dataframe is empty
         if data_df.is_empty():
             title_line= ['Contig_name', 'Translated_contig_name (frame)', 'Sequence_length(AA)', 'Profile_name',
-                         'Profile_length', 'E-value', 'score', 'acc', 'norm_bitscore_profile',
+                         'Profile_length', 'E-value', 'score','norm_bitscore_profile',
                          'norm_bitscore_contig', 'ID_score', 'RdRp_from(AA)', 'RdRp_to(AA)', 'profile_coverage',
                          'contig_coverage']
             data_df = pl.DataFrame({col: [] for col in title_line})

rdrpcatch/rdrpcatch_wrapper.py

@@ -111,7 +111,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
     if not os.path.exists(outputs.output_dir):
         os.makedirs(outputs.output_dir)
     else:
-        raise FileExistsError(f"Output directory already exists: {outputs.output_dir}, please choose a different directory.")
+        raise FileExistsError(f"Output directory already exists: {outputs.output_dir}, Please choose a different directory.")
     if not os.path.exists(outputs.log_dir):
         os.makedirs(outputs.log_dir)
 
@@ -363,7 +363,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
 
 
         # Combine all the dataframes in the list
-        combined_df = pl.concat(df_list, how='vertical')
+        combined_df = pl.concat(df_list, how='vertical_relaxed')
         # Write the combined dataframe to a tsv file
         for col in ['E-value', 'score', 'norm_bitscore_profile', 'norm_bitscore_contig',
                     'ID_score', 'profile_coverage', 'contig_coverage']:
@@ -526,9 +526,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             outputs.tsv_outdir.mkdir(parents=True)
 
 
-
         # Combine all the dataframes in the list
-        combined_df = pl.concat(df_list, how='vertical')
+        combined_df = pl.concat(df_list, how='vertical_relaxed')
         # Write the combined dataframe to a tsv file
         for col in ['E-value', 'score', 'norm_bitscore_profile', 'norm_bitscore_contig',
                     'ID_score', 'profile_coverage', 'contig_coverage']:

{rdrpcatch-0.0.4.dist-info → rdrpcatch-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdrpcatch
-Version: 0.0.4
+Version: 0.0.5
 Dynamic: Summary
 Project-URL: Home, https://github.com/dimitris-karapliafis/RdRpCATCH
 Project-URL: Source, https://github.com/dimitris-karapliafis/RdRpCATCH
@@ -81,7 +81,7 @@ The dependencies can be installed using conda or mamba. Follow these steps:
 
 Create a new conda environment and install the dependencies:
 ```bash
-conda create -n rdrpcatch python=3.12
+conda env create -n rdrpcatch python=3.12
 conda activate rdrpcatch
 conda install -c bioconda mmseqs2==17.b804f seqkit==2.10.0
 ```

{rdrpcatch-0.0.4.dist-info → rdrpcatch-0.0.5.dist-info}/RECORD

@@ -1,10 +1,10 @@
 rdrpcatch/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rdrpcatch/rdrpcatch_wrapper.py,sha256=PUMzQ3tIU0VuBY6XrRXupo-NruszwHreyxWXzEARjM4,30550
+rdrpcatch/rdrpcatch_wrapper.py,sha256=bZ5w4NuTlCSUsCx9baEtJSk7jGiyp-6XthO80IKaMXI,30564
 rdrpcatch/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdrpcatch/cli/args.py,sha256=2E2gXY42hNasUP94HmPxpgVCA1glk_oN7D5ftbu6W2c,15805
 rdrpcatch/rdrpcatch_scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdrpcatch/rdrpcatch_scripts/fetch_dbs.py,sha256=e9ShColfLgBvWSZpGOvY3zKhEgIg3rw1IIV__KX7N-g,11054
-rdrpcatch/rdrpcatch_scripts/format_pyhmmer_out.py,sha256=uah2XPrGNkkeptCv_WWBz_qTn5AtDTfVm6XjbCmNO00,25033
+rdrpcatch/rdrpcatch_scripts/format_pyhmmer_out.py,sha256=2_ERXFQK2lpVReWl0jwQdnKIObv_zq07uFJOzGsTHlo,25025
 rdrpcatch/rdrpcatch_scripts/gui.py,sha256=he8kx_4VJWB7SVv9XSQPk0DmkOjEFIg-uGMAtDp3t-w,10576
 rdrpcatch/rdrpcatch_scripts/mmseqs_tax.py,sha256=bwzuCxu8nHQ5OC0Yr5Lyvhcyk9OWjuamInqe0T0lc38,3809
 rdrpcatch/rdrpcatch_scripts/paths.py,sha256=roTZ2QPF4Fii7jtHkS9I6INJg1Vu78Dc_ieQGKjOCP4,4710
@@ -12,8 +12,8 @@ rdrpcatch/rdrpcatch_scripts/plot.py,sha256=Y1mZL7rkKHFKEs2D7T2Qj2kpfiORmFwRLq1LY
 rdrpcatch/rdrpcatch_scripts/run_pyhmmer.py,sha256=9zcMzaIwQ4_-NgYzG9kejxOBaDi-gbzaqpvZti8ZXA4,9008
 rdrpcatch/rdrpcatch_scripts/run_seqkit.py,sha256=5y7DtJ6NLa4sRoBQOcjBfczKlqG_LibNrEqNmKLrHu0,4361
 rdrpcatch/rdrpcatch_scripts/utils.py,sha256=jvpyPxchAMn6BeLV7HOFECSY_a3nbkxDBBL8tunmM8A,16938
-rdrpcatch-0.0.4.dist-info/METADATA,sha256=rhb3kvfpy5zj9dUgIB1MbRfv9NNPZeQlOS1YDB7ZkrA,14000
-rdrpcatch-0.0.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rdrpcatch-0.0.4.dist-info/entry_points.txt,sha256=uiyoPO41jNz_KVOt2JdPak9NbVei-D8WQ6saMeMBFpE,53
-rdrpcatch-0.0.4.dist-info/licenses/LICENSE,sha256=3jm5vKRMIaiETEFfNN34-oyWUShxZtmDmL38PNAwlUI,1120
-rdrpcatch-0.0.4.dist-info/RECORD,,
+rdrpcatch-0.0.5.dist-info/METADATA,sha256=X3wolDh_nUrk7caPG4jFMvsF7FHZCvYuGzjPLZnC4VA,14004
+rdrpcatch-0.0.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rdrpcatch-0.0.5.dist-info/entry_points.txt,sha256=uiyoPO41jNz_KVOt2JdPak9NbVei-D8WQ6saMeMBFpE,53
+rdrpcatch-0.0.5.dist-info/licenses/LICENSE,sha256=3jm5vKRMIaiETEFfNN34-oyWUShxZtmDmL38PNAwlUI,1120
+rdrpcatch-0.0.5.dist-info/RECORD,,