Expose --rename-regex in main annotate CLI

dammit/components/fastx.py

@@ -47,7 +47,7 @@ def rename_fasta(fasta_fn,
 
     if split_regex is None:
         counter = count()
-        header_func = lambda name: '{0}_{1}'.format(basename, next(counter))
+        header_func = lambda _: '{0}_{1}'.format(basename, next(counter))
     else:
         def header_func(header):
             results = re.search(split_regex, header).groupdict()
@@ -80,7 +80,11 @@ def rename_fasta_cmd(fasta_fn,
                      names_fn,
                      basename,
                      split_regex):
-    ''' Copy a FASTA file and rename the headers.
+    ''' Copy a FASTA file and rename the headers. If --split-regex is used,
+    it should be provided in Python `re` format and contain a named field keyed
+    as `name` that extracts the desired string. For example, providing 
+    (?P<name>^[a-zA-Z0-9]+) will match from the beginning of the sequence header
+    up to the first non-alphanumeric symbol.
     '''
 
     allowed = r'[a-zA-Z0-9_\-:|\.]+'
@@ -209,7 +213,7 @@ def generate_sequence_name(original_name, sequence, annotation_df):
     pass
 
 
-def generate_sequence_summary(original_name, sequence, annotation_df):
+def generate_sequence_summary(seqid, sequence, annotation_df):
     '''Given a FASTA sequence's original name, the sequence itself,
     and a DataFrame with its corresponding GFF3 annotations, generate
     a summary line of the annotations in key=value format.
@@ -251,12 +255,12 @@ def generate_sequence_summary(original_name, sequence, annotation_df):
                             for _, row in fgroup.iterrows()])
             annots.append('{0}={1}'.format(feature_type, collapsed))
 
-    desc = '{0} {1}'.format(original_name, ' '.join(annots))
+    desc = '{0} {1}'.format(seqid, ' '.join(annots))
 
     return desc
 
 
-def annotate_fasta(transcriptome_fn, gff3_fn, output_fn):
+def annotate_fasta(transcriptome_fn, gff3_fn, output_fn, name_map=None):
     '''Annotate the headers in a FASTA file with its corresponding GFF3 file
     and place the resulting FASTA file in output_fn.
     \f
@@ -265,13 +269,22 @@ def annotate_fasta(transcriptome_fn, gff3_fn, output_fn):
         transcriptome_fn (str): Path to the FASTA file.
         gff3_fn (str): Path to the GFF3 annotations.
         output_fn (str): Path to store the resulting annotated FASTA.
+        name_map (str): Path to CSV file with original-renamed transcripts.
     '''
 
+    if name_map is not None:
+        name_map = pd.read_csv(name_map)
+
     annotations = GFF3Parser(gff3_fn).read()
     with open(output_fn, 'w') as fp:
         for n, record in enumerate(ReadParser(transcriptome_fn)):
-            df = annotations.query('seqid == "{0}"'.format(record.name))
-            desc = generate_sequence_summary(record.name, record.sequence,
+            seqid_query = 'seqid == "{0}"'.format(record.name)
+            df = annotations.query(seqid_query)
+
+            renamed_query = 'renamed == "{0}"'.format(record.name)
+            seqid = record.name if name_map is None else name_map.query(renamed_query).original.iloc[0]
+
+            desc = generate_sequence_summary(seqid, record.sequence,
                                              df)
             fp.write('>{0}\n{1}\n'.format(desc.strip(), record.sequence))
 
@@ -280,8 +293,12 @@ def annotate_fasta(transcriptome_fn, gff3_fn, output_fn):
 @click.argument('transcriptome_fn')
 @click.argument('gff3_fn')
 @click.argument('output_fn')
-def annotate_fasta_cmd(transcriptome_fn, gff3_fn, output_fn):
+@click.option('--name-map',
+               help='CSV file with mapping of original names to renamed trascripts. '\
+                    'If provided, transcripts will be mapped back to their original names. '\
+                    'Must contain the columns "original" and "renamed".')
+def annotate_fasta_cmd(transcriptome_fn, gff3_fn, output_fn, name_map):
     '''Annotate a FASTA file from a GFF3 file.
     '''
 
-    annotate_fasta(transcriptome_fn, gff3_fn, output_fn)
+    annotate_fasta(transcriptome_fn, gff3_fn, output_fn, name_map=name_map)

dammit/components/run.py

@@ -148,7 +148,21 @@ def run_group(config,
                    ' will be of the form <name>_<X>.'\
                    ' It should not have spaces, pipes,'\
                    ' ampersands, or other characters'\
-                   ' with special meaning to BASH.')
+                   ' with special meaning to BASH.'\
+                   ' Superseded by --regex-rename.')
+@click.option('--regex-rename',
+              help='Rename transcripts using a regex pattern. The regex should follow '
+                   ' Python `re` format and contain a named field keyed'\
+                   ' as `name` that extracts the desired string. For example, providing'\
+                   ' "(?P<name>^[a-zA-Z0-9\.]+)" will match from the beginning of the sequence header'\
+                   ' up to the first symbol that is not alphanumeric or a period.'\
+                   ' Supersedes --base-name.')
+@click.option('--rename/--no-rename', default=None,
+               help='If --no-rename, original transcript names are preserved'\
+                    ' in the final annotated FASTA. --base-name is'\
+                    ' still used in intermediate files. If --rename (the default '\
+                    ' behavior), the renamed transcript names are used in the final '\
+                    ' annotated FASTA.')
 @click.option('-e', '--global-evalue',
               type=float,
               help='global e-value cutoff for similarity searches.')
@@ -165,14 +179,16 @@ def run_group(config,
 def annotate_cmd(config,
                  transcriptome,
                  base_name,
+                 regex_rename,
+                 rename,
                  global_evalue,
                  output_dir,
                  user_database,
                  dry_run,
                  extra_snakemake_args):
     ''' The main annotation pipeline. Calculates assembly stats;
     runs BUSCO; runs LAST against OrthoDB (and optionally uniref90),
-    HMMER against Pfam, Inferal against Rfam, and Conditional Reciprocal
+    HMMER against Pfam, Infernal against Rfam, and Conditional Reciprocal
     Best-hit Blast against user databases; and aggregates all results in
     a properly formatted GFF3 file.'''
 
@@ -199,6 +215,12 @@ def annotate_cmd(config,
     if base_name:
         config.core['basename'] = base_name
 
+    if regex_rename:
+        config.core['regex_rename'] = regex_rename
+
+    if rename is not None:
+        config.core['rename'] = rename
+
     # the default global_evalue is null 
     if global_evalue:
         config.core['global_evalue'] = global_evalue

dammit/config.yml

@@ -9,6 +9,8 @@ global_evalue: null
 pipeline: default
 
 basename: Transcript
+rename: true
+regex_rename: null
 
 # n_threads: total threads to pass to snakemake -j
 n_threads: 0