RFCT Move uncompressing FASTA closer to use site

SemiBin/main.py

@@ -989,17 +989,6 @@ def training(logger, contig_fasta, num_process,
         is_combined = False
 
     if training_mode == 'semi':
-        contig_fasta_unzip = []
-        for fasta_index,temp_fasta in enumerate(contig_fasta):
-            if temp_fasta.endswith('.gz') or temp_fasta.endswith('.bz2') or temp_fasta.endswith('.xz'):
-                temp_fasta_unzip = os.path.join(output, 'unzip_contig_{}.fa'.format(fasta_index))
-                with open(temp_fasta_unzip, 'wt') as out:
-                    for h,seq in fasta_iter(temp_fasta):
-                            out.write(f'>{h}\n{seq}\n')
-                contig_fasta_unzip.append(temp_fasta_unzip)
-            else:
-                contig_fasta_unzip.append(temp_fasta)
-
         if mode == 'single':
             binned_lengths.append(
                     utils.compute_min_length(min_length, contig_fasta[0], ratio))
@@ -1010,7 +999,7 @@ def training(logger, contig_fasta, num_process,
 
         model = train(
             output,
-            contig_fasta_unzip,
+            contig_fasta,
             binned_lengths,
             logger,
             data,

SemiBin/utils.py

@@ -383,6 +383,17 @@ def extract_seeds(vs, sel):
             counts = data.groupby('gene')['orf'].count()
             return extract_seeds(counts, data)
 
+def maybe_uncompress(fafile, tdir):
+    if fafile.endswith('.gz') or \
+            fafile.endswith('.bz2') or \
+            fafile.endswith('.xz'):
+        oname = f'{tdir}/expanded.fa'
+        with open(oname, 'wt') as out:
+            for header, seq in fasta_iter(fafile):
+                    out.write(f'>{header}\n{seq}\n')
+        return oname
+    return fafile
+
 
 def cal_num_bins(fasta_path, binned_length, num_process, multi_mode=False, output = None, orf_finder = 'prodigal', prodigal_output_faa=None):
     '''Estimate number of bins from a FASTA file
@@ -395,6 +406,7 @@ def cal_num_bins(fasta_path, binned_length, num_process, multi_mode=False, outpu
     '''
     from .orffinding import run_orffinder
     with tempfile.TemporaryDirectory() as tdir:
+        fasta_path = maybe_uncompress(fasta_path, tdir)
         if output is not None:
             if os.path.exists(os.path.join(output, 'markers.hmmout')):
                 return get_marker(os.path.join(output, 'markers.hmmout'), fasta_path, binned_length, multi_mode, orf_finder=orf_finder)