Cosmetics: removed --no-gzip and .gz for used_snps and gff files since they...

Cosmetics: removed --no-gzip and .gz for used_snps and gff files since they are not compressed actually and the option is not used https://github.com/ablab/quast/issues/111

manual.html

@@ -772,11 +772,11 @@ Do not compute GC% and do not produce GC-distribution plots (both in HTML report
 </div>
 Do not run structural variant calling and processing (make sense only if reads are specified).
 
-<div class='option'>
-<code><b>--no-gzip</b></code>
-</div>
-Do not compress large output files (files containing SNP information and predicted genes).
-    This may speed up computation, but more disk space is required.
+<!--<div class='option'>-->
+<!--<code><b>&#45;&#45;no-gzip</b></code>-->
+<!--</div>-->
+<!--Do not compress large output files (files containing SNP information and predicted genes).-->
+    <!--This may speed up computation, but more disk space is required.-->
 
 <div class='option'>
     <a name='no_read_stats'></a><code><b>--no-read-stats</b></code>

quast_libs/ca_utils/align_contigs.py

@@ -87,7 +87,7 @@ def get_aux_out_fpaths(fname):
     coords_fpath = fname + '.coords'
     coords_filtered_fpath = fname + '.coords.filtered'
     unaligned_fpath = fname + '.unaligned' if not qconfig.space_efficient else '/dev/null'
-    used_snps_fpath = fname + '.used_snps' + ('.gz' if not qconfig.no_gzip else '') if not qconfig.space_efficient else '/dev/null'
+    used_snps_fpath = fname + '.used_snps' if not qconfig.space_efficient else '/dev/null'
     return coords_fpath, coords_filtered_fpath, unaligned_fpath, used_snps_fpath
 
 

quast_libs/genemark.py

@@ -258,7 +258,7 @@ def predict_genes(index, contigs_fpath, gene_lengths, out_dirpath, tool_dirpath,
         for gene in genes:
             gene.is_full = gene.start > 1 and gene.end < contig_lengths[gene.contig]
         tool_name = "genemark"
-        out_gff_fpath = os.path.join(out_dirpath, corr_assembly_label + '_' + tool_name + '_genes.gff' + ('.gz' if not qconfig.no_gzip else ''))
+        out_gff_fpath = os.path.join(out_dirpath, corr_assembly_label + '_' + tool_name + '_genes.gff')
         add_genes_to_gff(genes, out_gff_fpath, prokaryote)
         if OUTPUT_FASTA:
             out_fasta_fpath = os.path.join(out_dirpath, corr_assembly_label + '_' + tool_name + '_genes.fasta')

quast_libs/glimmer.py

@@ -80,7 +80,7 @@ def glimmerHMM(tool_dir, tool_exec_fpath, fasta_fpath, out_fpath, gene_lengths,
     if not gffs:
         return None, None, None, None, None, None
 
-    out_gff_fpath = out_fpath + '_genes.gff' + ('.gz' if not qconfig.no_gzip else '')
+    out_gff_fpath = out_fpath + '_genes.gff'
     out_gff_path = merge_gffs(gffs, out_gff_fpath)
     unique, total = set(), 0
     genes = []

quast_libs/options_parser.py

@@ -627,14 +627,14 @@ def parse_options(logger, quast_args):
              dest='fast',
              action='callback',
              callback=set_multiple_variables,
-             callback_kwargs={'store_true_values': ['no_gc', 'no_sv', 'no_gzip', 'no_read_stats'],
+             callback_kwargs={'store_true_values': ['no_gc', 'no_sv', 'no_read_stats'],
                               'store_false_values': ['show_snps', 'draw_plots', 'html_report', 'create_icarus_html', 'analyze_gaps']},
              default=False)
          ),
-        (['--no-gzip'], dict(
-             dest='no_gzip',
-             action='store_true')
-         ),
+        # (['--no-gzip'], dict(
+        #      dest='no_gzip',
+        #      action='store_true')
+        #  ),
         (['--no-check'], dict(
              dest='no_check',
              action='store_true')

quast_libs/qconfig.py

@@ -73,7 +73,6 @@ unique_mapping = False  # for metaQUAST only
 no_gc = False
 no_sv = False
 no_read_stats = False
-no_gzip = False
 show_snps = True
 glimmer = False
 is_combined_ref = False
@@ -518,7 +517,7 @@ def usage(show_hidden=False, mode=None, short=True, stream=sys.stdout):
         stream.write("    --no-snps                         Do not report SNPs (may significantly reduce memory consumption on large genomes)\n")
         stream.write("    --no-gc                           Do not compute GC% and GC-distribution\n")
         stream.write("    --no-sv                           Do not run structural variation detection (make sense only if reads are specified)\n")
-        stream.write("    --no-gzip                         Do not compress large output files\n")
+        # stream.write("    --no-gzip                         Do not compress large output files\n")m
         stream.write("    --no-read-stats                   Do not align reads to assemblies\n"
                      "                                      Reads will be aligned to reference and used for coverage analysis,\n"
                      "                                      upper bound assembly simulation, and structural variation detection.\n"