Repository: biocore/deblur

Issue:
Support "left trimming" on sequences
It would be useful if in addition to the normal trimming (at the end of the sequence), there was a parameter to trim initial bases of a sequence.

Comments:

Patch:
diff --git a/ChangeLog.md b/ChangeLog.md
index ea3e5aa..a8981f9 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -4,6 +4,8 @@
 
 ### Features
 
+* Added `--left-trim-length` to allow for trimming nucleotides on the 5' end of each sequence. Please see [issue #154](https://github.com/biocore/deblur/issues/154) for more information.
+
 ### Backward-incompatible changes [stable]
 
 ### Performance enhancements
diff --git a/deblur/workflow.py b/deblur/workflow.py
index 6eb21f7..0f7d55a 100644
--- a/deblur/workflow.py
+++ b/deblur/workflow.py
@@ -100,7 +100,7 @@ def sequence_generator(input_fp):
         yield (record.metadata['id'], str(record))
 
 
-def trim_seqs(input_seqs, trim_len):
+def trim_seqs(input_seqs, trim_len, left_trim_len):
     """Trim FASTA sequences to specified length.
 
     Parameters
@@ -109,6 +109,9 @@ def trim_seqs(input_seqs, trim_len):
         The list of input sequences in (label, sequence) format
     trim_len : int
         Sequence trimming length. Specify a value of -1 to disable trimming.
+    left_trim_len : int
+        Sequence trimming from the 5' end. A value of 0 will disable this trim.
+
 
     Returns
     -------
@@ -132,7 +135,7 @@ def trim_seqs(input_seqs, trim_len):
             yield label, seq
         elif len(seq) >= trim_len:
             okseqs += 1
-            yield label, seq[:trim_len]
+            yield label, seq[left_trim_len:trim_len]
 
     if okseqs < 0.01*totseqs:
         logger = logging.getLogger(__name__)
@@ -771,8 +774,8 @@ def create_otu_table(output_fp, deblurred_list,
 
 
 def launch_workflow(seqs_fp, working_dir, mean_error, error_dist,
-                    indel_prob, indel_max, trim_length, min_size, ref_fp,
-                    ref_db_fp, threads_per_sample=1,
+                    indel_prob, indel_max, trim_length, left_trim_length,
+                    min_size, ref_fp, ref_db_fp, threads_per_sample=1,
                     sim_thresh=None, coverage_thresh=None):
     """Launch full deblur workflow for a single post split-libraries fasta file
 
@@ -792,6 +795,8 @@ def launch_workflow(seqs_fp, working_dir, mean_error, error_dist,
         maximal indel number
     trim_length: integer
         sequence trim length
+    left_trim_length: integer
+        trim the first n reads
     min_size: integer
         upper limit on sequence abundance (discard sequences below limit)
     ref_fp: tuple
@@ -823,7 +828,8 @@ def launch_workflow(seqs_fp, working_dir, mean_error, error_dist,
     with open(output_trim_fp, 'w') as out_f:
         for label, seq in trim_seqs(
                 input_seqs=sequence_generator(seqs_fp),
-                trim_len=trim_length):
+                trim_len=trim_length,
+                left_trim_len=left_trim_length):
             out_f.write(">%s\n%s\n" % (label, seq))
     # Step 2: Dereplicate sequences
     output_derep_fp = join(working_dir,
diff --git a/scripts/deblur b/scripts/deblur
index bd9704d..f5d9dcc 100755
--- a/scripts/deblur
+++ b/scripts/deblur
@@ -420,6 +420,10 @@ def build_biom_table(seqs_fp, output_biom_fp, min_reads, file_type, log_level,
                     "trim-length will be discarded. A value of -1 can be "
                     "specified to skip trimming; this assumes all sequences "
                     "have an identical length."))
+@click.option('--left-trim-length', required=False, type=int,
+              show_default=True, default=0,
+              help=("Trim the first N bases from every sequence. A value of 0 "
+                    "disables this trim."))
 @click.option('--pos-ref-fp', required=False, multiple=True,
               default=[], show_default=False,
               type=click.Path(resolve_path=True, readable=True, exists=True,
@@ -518,9 +522,9 @@ def build_biom_table(seqs_fp, output_biom_fp, min_reads, file_type, log_level,
 def workflow(seqs_fp, output_dir, pos_ref_fp, pos_ref_db_fp,
              neg_ref_fp, neg_ref_db_fp, overwrite,
              mean_error, error_dist, indel_prob, indel_max,
-             trim_length, min_reads, min_size, threads_per_sample,
-             keep_tmp_files, log_level, log_file, jobs_to_start,
-             is_worker_thread):
+             trim_length, left_trim_length, min_reads, min_size,
+             threads_per_sample, keep_tmp_files, log_level, log_file,
+             jobs_to_start, is_worker_thread):
     """Launch deblur workflow"""
     start_log(level=log_level * 10, filename=log_file)
     logger = logging.getLogger(__name__)
@@ -623,6 +627,7 @@ def workflow(seqs_fp, output_dir, pos_ref_fp, pos_ref_db_fp,
                     mean_error=mean_error,
                     error_dist=error_dist, indel_prob=indel_prob,
                     indel_max=indel_max, trim_length=trim_length,
+                    left_trim_length=left_trim_length,
                     min_size=min_size, ref_fp=ref_fp, ref_db_fp=ref_db_fp,
                     threads_per_sample=threads_per_sample)
                 if deblurred_file_name is None:
@@ -651,7 +656,8 @@ def workflow(seqs_fp, output_dir, pos_ref_fp, pos_ref_db_fp,
 
     # also create biom tables with
     # only sequences matching the pos_ref_fp sequences (reference-hit.biom)
-    # and only sequences not matching the pos_ref_fp sequences (reference-non-hit.biom)
+    # and only sequences not matching the pos_ref_fp sequences
+    # (reference-non-hit.biom)
     tmp_files = remove_artifacts_from_biom_table(output_fp, outputfasta_fp,
                                                  pos_ref_fp, output_dir,
                                                  pos_ref_db_fp,


Test patch:
diff --git a/deblur/test/test_workflow.py b/deblur/test/test_workflow.py
index 0ea7174..b9bc8c6 100644
--- a/deblur/test/test_workflow.py
+++ b/deblur/test/test_workflow.py
@@ -128,7 +128,7 @@ class workflowTests(TestCase):
                 ("seq5", "gagtgcgagatgcgtggtgagg"),
                 ("seq6", "ggatgcgagatgcgtggtgatt"),
                 ("seq7", "agggcgagattcctagtgga--")]
-        obs = trim_seqs(seqs, -1)
+        obs = trim_seqs(seqs, -1, 0)
         self.assertEqual(list(obs), seqs)
 
     def test_trim_seqs_notrim_outofbounds(self):
@@ -140,7 +140,7 @@ class workflowTests(TestCase):
                 ("seq6", "ggatgcgagatgcgtggtgatt"),
                 ("seq7", "agggcgagattcctagtgga--")]
         with self.assertRaises(ValueError):
-            list(trim_seqs(seqs, -2))
+            list(trim_seqs(seqs, -2, 0))
 
     def test_trim_seqs(self):
         seqs = [("seq1", "tagggcaagactccatggtatga"),
@@ -150,7 +150,7 @@ class workflowTests(TestCase):
                 ("seq5", "gagtgcgagatgcgtggtgagg"),
                 ("seq6", "ggatgcgagatgcgtggtgatt"),
                 ("seq7", "agggcgagattcctagtgga--")]
-        obs = trim_seqs(seqs, 20)
+        obs = trim_seqs(seqs, 20, 0)
 
         self.assertTrue(isinstance(obs, GeneratorType))
 
@@ -162,6 +162,26 @@ class workflowTests(TestCase):
                ("seq7", "agggcgagattcctagtgga")]
         self.assertEqual(list(obs), exp)
 
+    def test_trim_seqs_left(self):
+        seqs = [("seq1", "tagggcaagactccatggtatga"),
+                ("seq2", "cggaggcgagatgcgtggta"),
+                ("seq3", "tactagcaagattcctggtaaagga"),
+                ("seq4", "aggatgcgagatgcgtg"),
+                ("seq5", "gagtgcgagatgcgtggtgagg"),
+                ("seq6", "ggatgcgagatgcgtggtgatt"),
+                ("seq7", "agggcgagattcctagtgga--")]
+        obs = trim_seqs(seqs, 20, 5)
+
+        self.assertTrue(isinstance(obs, GeneratorType))
+
+        exp = [("seq1", "caagactccatggta"),
+               ("seq2", "gcgagatgcgtggta"),
+               ("seq3", "gcaagattcctggta"),
+               ("seq5", "cgagatgcgtggtga"),
+               ("seq6", "cgagatgcgtggtga"),
+               ("seq7", "gagattcctagtgga")]
+        self.assertEqual(list(obs), exp)
+
     def test_dereplicate_seqs_remove_singletons(self):
         """ Test dereplicate_seqs() method functionality with
             removing singletons
@@ -622,12 +642,14 @@ class workflowTests(TestCase):
         indel_prob = 0.01
         indel_max = 3
         min_size = 2
+        left_trim_length = 0
         nochimera = launch_workflow(seqs_fp=seqs_fp, working_dir=output_fp,
                                     mean_error=mean_error,
                                     error_dist=error_dist,
                                     indel_prob=indel_prob,
                                     indel_max=indel_max,
                                     trim_length=trim_length,
+                                    left_trim_length=left_trim_length,
                                     min_size=min_size,
                                     ref_fp=(ref_fp,),
                                     ref_db_fp=ref_db_fp,
@@ -789,6 +811,7 @@ class workflowTests(TestCase):
         min_size = 2
         # trim length longer than sequences
         trim_length = -1
+        left_trim_length = 0
         threads = 1
 
         output_fp = launch_workflow(seqs_fp=seqs_fp,
@@ -798,6 +821,7 @@ class workflowTests(TestCase):
                                     indel_prob=indel_prob,
                                     indel_max=indel_max,
                                     trim_length=trim_length,
+                                    left_trim_length=left_trim_length,
                                     min_size=min_size,
                                     ref_fp=(ref_fp,),
                                     ref_db_fp=ref_db_fp,
@@ -826,6 +850,7 @@ class workflowTests(TestCase):
         min_size = 2
         # trim length longer than sequences
         trim_length = 151
+        left_trim_length = 0
         threads = 1
         with self.assertWarns(UserWarning):
             launch_workflow(seqs_fp=seqs_fp, working_dir=output_fp,
@@ -834,6 +859,7 @@ class workflowTests(TestCase):
                             indel_prob=indel_prob,
                             indel_max=indel_max,
                             trim_length=trim_length,
+                            left_trim_length=left_trim_length,
                             min_size=min_size,
                             ref_fp=(ref_fp,),
                             ref_db_fp=ref_db_fp,