Merge pull request #12 from NBISweden/develop

Version 0.5.10

.github/workflows/python-package.yml

@@ -35,7 +35,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
         os: [ubuntu-latest, macos-latest]
     needs: download_taxonomy
     steps:

contigtax/assign.py

@@ -172,6 +172,33 @@ def propagate_lower(x, taxid, ranks):
                     right_index=True)
 
 
+def unique_cols(x):
+    """
+    Checks the columns for a taxid entry and only returns unique indices
+    This is meant to fix the problem of some taxids having multiple entries
+    for the same taxonomic rank.
+
+    Example: Alouatta palliata mexicana (Howler monkey)
+    taxid = 182248
+            superkingdom phylum order genus species  class  family    class
+            2759         7711   9443  9499  30589    40674  378855    1338369
+
+    This function would return indices for columns to use with 'iloc' in order
+    to get:
+            superkingdom phylum order genus species  class  family
+            2759         7711   9443  9499  30589    40674  378855
+    :param x:
+    :return:
+    """
+    col_index = []
+    cols = []
+    for i, c in enumerate(x.columns):
+        if c not in cols:
+            cols.append(c)
+            col_index.append(i)
+    return col_index
+
+
 def get_lca(r, assignranks, reportranks):
     """
     Assign lowest common ancestor from a set of taxids.
@@ -508,6 +535,8 @@ def process_lineages(items):
     x.columns = x.loc["rank"]
     x.drop("rank", inplace=True)
     x.index = [taxid]
+    # Only select unique columns
+    x = x.iloc[:, unique_cols(x)]
     # Add taxids for lower ranks in the hierarchy
     x = propagate_lower(x, taxid, ranks)
     # Add names for taxids
@@ -543,6 +572,15 @@ def make_name_dict(df, ranks):
     return name_dict
 
 
+def exit_no_info(taxdir):
+    sys.exit(f"""
+ERROR: No taxonomic information found in the database at {taxdir} 
+This may be caused by an out-of-date or incomplete taxonomy database.
+Try running:
+contigtax download taxonomy -f -t {taxdir}
+to force an update.
+            """)
+
 def make_lineage_df(taxids, taxdir, dbname, ranks, cpus=1):
     """
     Creates a lineage dataframe with full taxonomic information for a list of
@@ -583,6 +621,8 @@ def make_lineage_df(taxids, taxdir, dbname, ranks, cpus=1):
     rename = {y: x for x, y in translate_dict.items()}
     # Update lineages with missing taxids
     lineages.update(ncbi_taxa.get_lineage_translator(translate_dict.values()))
+    if len(lineages.keys()) == 0:
+        exit_no_info(taxdir)
     items = [[taxid, ranks, taxdir, dbname, lineages[taxid]] for taxid in
              list(lineages.keys())]
     with Pool(processes=cpus) as pool:

environment.yaml

@@ -4,10 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python
+  - python>=3.6
   - diamond>=0.8.37, <=0.9.24
   - ete3
   - biopython
   - pandas
-  - tqdm
+  - tqdm>4.7.2
   - numpy

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="contigtax",
-    version="0.5.9",
+    version="0.5.10",
     author="John Sundh",
     author_email="john.sundh@scilifelab.se",
     description="A package to assign taxonomy to metagenomic contigs",

tests/data/shreds.fasta

@@ -1,3 +1,14 @@
+>182248|contig1001
+CCCCGCAAAACTCACCCACTAGCAAAAATCATCAACAATTCATTCATTGACCTCCCTACAC
+CATCCAACATCTCCGCCTGGTGAAATTTCGGCTCACTCCTAGGTATTTGCCTAATTATTCAAATCACTAC
+AGGTCTATTCTTAGCCATACACTATACACCAGACACTTCAACCGCCTTCTCCTCAGTCGCCCACATCACC
+CGAGACGTCAACTATGGCTGAATAATCCGCTATCTACATGCCAACGGCGCCTCCATATTCTTTATCTGCC
+TCTTTCTCCACATTGGCCGAGGCTTATATTACGGATCATTCCTTTTTCTGGAGACCTGGAACGTCGGTAT
+TATCCTCCTACTCACAACCATAGCCACAGCATTCATAGGCTATGTCCTCCCATGAGGCCAAATATCATTC
+TGAGGGGCCACAGTAATTACAAACCTTCTGTCAGCCATTCCATATATCGGGTCTGACCTCGTACAATGAA
+TCTGAGGTGGCTTCTCAGTAGATAAAGCCACCCTCACACGATTTTTCACCTTTCACTTTATCTTGCCATT
+TATTATCGCTGCCCTAGCAACCATCCACCTCTTGTTTCTGCATGAAACAGGATCAAGTAACCCATCAGGA
+GTAGCATCGGACCTCGACAAAATTACATTTCACCCCTACT
 >1097667|contig0
 CCCGGGTCGCCCGGCGCGTCGACCTGCAGGACCAGATCGGCGTCGGCGGCCCACGAGCGGCCGGCGACCGCGGCCGGCAGATCGAGGATCCGCAGCCACAGCGCGTCGCCCTGCTGGATCGTCCGCATGGCCCGCGGATCGGCCGGCGCCAGCTCCAGCTCGTCGTCGAGCGGTCGCTCGTGGAGCTCGACCCGGGTCGCCAGGTCGATGCTCGTCAGGAAGGCGAGCAGGGCCCGGCCGGCCTCCGGCGTGGCCGCGATCAGCTCCTGGACCTCGACGGTGGTCTGGCCGATCCCGCCGACCGGACCGCCGGCCACGTCCTCGTGGACGCGGTAGAGCGCGTAGCCGTCCTCGCCGCACGCGACGAGCCGCTTGGGCGCCCCGTCGGCCGGTCGCTCGTCCTGTGCGTCGCTGAGGATCCGGGTCGTCCACCAGGCCGGCGGGCGCGACATGATCCCCGCGCGCTGCCGGCGGGCGCGGTCGAAGATCGCCGCGGTCAGCGGCGCCGCCCCGGCCAGATCGACGAGCCGCAGCGACGGATCGGCGACCGGCGACCGCAGCGGCACCCCGCCCGCCAGGTCGATCCGACTGCGGCGCGTCCAGCTGGCCGGCCCGAAGCCGAACCGCCCGTAGATCCGGCCCTCGGACGCCCACAGCGCCGCCAGCGGCTCCCCCCGCTCGCGCGCGTCGGCGACCAGCGCCTTCATCATCCGCCGCAGGATCCCGCGCCGGCGGTGGGTCGGCAGGACGGTGACGAGCGTGATCGCGGCGCACGGCAGCTCCCCGCCGGGGACCGTCAGCCGCCAGCCCCACGCCGACGAGGTGCCGACGACCTGGCCGTCGTCGAGCGCGATCCGACTGCGGTCGAGCTCGAACCGGTCCCGCAGCCGCAGCCGGGACGCATCGCTGCGATCGCCGTGGAAGGCGATCGCAGCGGCGTCCAGCAGCGCGCCGAACTCGTCCTCGGTGGCCGCACGCACGGCCAGGCGATCGCTCATCGCTCGACCCTATCGCCCGCCGGACGGCTGCCGGCCGCGACGCGAAATCACCGTCCGCACGGGGCCCGCGGCGCCCGCCTTCTACGCTGACGCGATGGCCGAGACCGCCCCGCCCACCCGACCGACGCAGGTGCTCGTCGTCCTGGACGCCTACTGCGGCTGGTGCCACGGGTTCCGCGACGCGTTGCTCGGCTTCTGGGAGCGCCATCGCGAGGACCACGAGTTCGTCGTCCTCGCCGGCGGCCTGGTCACCGGCGATCGGGTCGCGCCGATCGCGAGCTTCGACTTCATCCCCGACGGCAACCGGCGGATCGCCGAGCTGACCGGGGCCCGCTTCGGCGAGCCCTACCTGGAGCTGCTGGCCGACGGCTCGCTGGTGATCGACTCGACCGACGCCGCCCGCGGATTCACCGCGCTGCGCGCCCAGGCCCCCGAGCGCTCGGTCCCGCTGGCGGTCGCGATCGCCGACGCCTTCTTCCACGACGGGCGGTCGCTGTCGGACGTCGCGACCTTCCGCGCCGTCGCCGTCGACCAGGGGCTCGATCCCGACGCCGTCGAGGCGGCCTTCGAGGACCCCGCGACCGCCGCCCAGGTGGCCGAGGAGTTCGCCGCCGTCTCGCGGATCGGCGTCAGCGGCTTCCCGACGGTCGCCGTCAGCCACGGCGACCACCTGCACGCGATCGCCGTCGGCTACGCGACCGGCGAAGAGCTGGAGCAGCGCCTGGCCGCGGCGGCCCAGGCCCACTGATCGCGTCGTCGGTCGGGGCGATCCCCGACCGCGGACGGCGCCGGATCCTCCTCTCGGCGGAGGCCGCCCGCTGCCCGGCGCGTCAGACTGGGGACGATGGCTGACGCGCGCCCGGCTGCGGGTACCACCCTCGCCCGCCTGCTGGTGGCCGCCGGCGTCGCGCTGGCCCTCGCCGACGCGTCGGTGGTGACCCTGGCGCTGCCCCAGATCCTGACCCGGCTCGACACGTCGATCGACGGCGTCGCCGCGGTGATCGGCGTCTACACGGTGGTCCTCGCGGCGGCCGTGCTGGTGGCCGTGCCGCTGCGCCGGCGGCTCGGCAGCGCGGCGCTGGGAGCGGCCGGGATGCTGCTGTTCGCGCTGGCCGGCGCCGCCTGCGGGCTGGCGGAGTCGCTGGAGCTGCTGCTGGCCGCCCGCGCCGCCCAGGCGATCGGGGCCGGGGCCGGCCTGGTCGCCGGCTACTCGCTGCTGCACCGGACGCGCCAGATCGGCCAGCGGGCGGACGCGCTCTGGATCGCCGGCGCGGTCTTCGGCACGGCCGTCGGGCCGGCGCTCGGCGGGGCGCTGACGGAGCTCTT
 >1097667|contig1

tests/data/shreds.taxids.tsv

@@ -1,3 +1,4 @@
+182248|contig1001	182248
 1097667|contig0	1097667
 1097667|contig1	1097667
 1097667|contig10	1097667

tests/data/uniref100.fasta

@@ -1,3 +1,9 @@
+>UniRef100_Q8HFX4 Complex III subunit 3 (Fragment) OS=Alouatta palliata palliata OX=182250 GN=cytb PE=4 SV=1 TaxID=182248
+MTTPRKTHPLAKIINNSFIDLPTPSNISAWWNFGSLLGICLIIQITTGLFLAMHYTPDTS
+TAFSSVAHITRDVNYGWMIRYLHANGASMFFICLFLHIGRGLYYGSFLFLETWNVGIILL
+LTTMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGSDLVQWIWGGFSVDKATLTRFFT
+FHFILPFIIAALATIHLLFLHETGSSNPSGVASDLDKITFHPYYTTKDILGLIILLLCLM
+SLTLFLPDLLTDPDNYTLANPLNTPP
 >UniRef100_T0LMY7 Bifunctional NAD(P)H-hydrate repair enzyme n=1 Tax=Thermoplasmatales archaeon I-plasma TaxID=667138 RepID=T0LMY7_9EURY
 MHTILDSRILDANAEAAGVNMEELMNNAGNAVAKLVMSLEPKRVLVACGSGNNGGDGYVA
 ATTLKREGISVTCYPVSPPATYLSKKKYAAYLKNKGRVVHSMKEGSYDVIIDALLGVGIS