updated mge report writer

phac-nml · Aug 15, 2023 · e807129 · e807129
1 parent afd22d8
commit e807129
Showing 1 changed file with 0 additions and 64 deletions.
diff --git a/mob_suite/utils.py b/mob_suite/utils.py
@@ -1299,70 +1299,6 @@ def blast_mge(contig_fasta, mge_fasta,tmp_dir, min_length, logging, min_rpp_iden
 
     return results
 
-def writeMGEresults(contig_membership,mge_results,outfile):
-    out_string = ["\t".join(MGE_INFO_HEADER)]
-    for contig_id in contig_membership['chromosome']:
-        if not contig_id in mge_results:
-            continue
-
-        for i in range(0, len(mge_results[contig_id])):
-            row = {}
-            for field in MGE_INFO_HEADER:
-                row[field] = ''
-                if field in mge_results[contig_id]:
-                    row[field] = mge_results[contig_id][field]
-
-            id = mge_results[contig_id][i]['qseqid'].split('|')
-            row['mge_id'] = id[0]
-            row['mge_acs'] = id[1]
-            row['mge_type'] = id[2]
-            row['mge_subtype'] = id[3]
-            row['mge_length'] = mge_results[contig_id][i]['qlen']
-            row['mge_start'] = mge_results[contig_id][i]['qstart']
-            row['mge_end'] = mge_results[contig_id][i]['qend']
-            row['contig_start'] = mge_results[contig_id][i]['sstart']
-            row['contig_end'] = mge_results[contig_id][i]['send']
-
-            for field in contig_membership['chromosome'][contig_id]:
-                if field in row:
-                    row[field] = contig_membership['chromosome'][contig_id][field]
-
-            out_string.append("\t".join([str(x) for x in list(row.values())]))
-
-    for mobcluster in contig_membership['plasmid']:
-        for contig_id in contig_membership['plasmid'][mobcluster]:
-            if not contig_id in mge_results:
-                continue
-
-            for i in range(0, len(mge_results[contig_id])):
-                row = {}
-                for field in MGE_INFO_HEADER:
-                    row[field] = ''
-                    if field in mge_results[contig_id][i]:
-                        row[field] = mge_results[contig_id][i][field]
-                id = mge_results[contig_id][i]['qseqid'].split('|')
-                row['mge_id'] = id[0]
-                row['mge_acs'] = id[1]
-                row['mge_type'] = id[2]
-                row['mge_subtype'] = id[3]
-                row['mge_length'] =  mge_results[contig_id][i]['qlen']
-                row['mge_start'] = mge_results[contig_id][i]['qstart']
-                row['mge_end'] = mge_results[contig_id][i]['qend']
-                row['contig_start'] = mge_results[contig_id][i]['sstart']
-                row['contig_end'] = mge_results[contig_id][i]['send']
-
-                for field in contig_membership['plasmid'][mobcluster][contig_id]:
-                    if field in row:
-                        row[field] = contig_membership['plasmid'][mobcluster][contig_id][field]
-
-                out_string.append("\t".join([str(x) for x in list(row.values())]))
-
-
-    fh = open(outfile,'w')
-    fh.write("\n".join(out_string))
-    fh.close()
-
-
 def writeMGEresults(contig_membership,mge_results,outfile):
     if len(mge_results) == 0:
         return