start initial logger impl

goatools/anno/dnld_ebi_goa.py

@@ -1,61 +1,66 @@
 """Download GOA files from the Gene Ontology Annotation (GOA) resource http://www.ebi.ac.uk/GOA."""
 
-__copyright__ = "Copyright (C) 2016-present, DV Klopfenstein, H Tang. All rights reserved."
+__copyright__ = (
+    "Copyright (C) 2016-present, DV Klopfenstein, H Tang. All rights reserved."
+)
 __author__ = "DV Klopfenstein"
 
 import os
 import sys
-from goatools.base import dnld_file
+from goatools.base import download_file
+
 
 class DnldGoa:
     """Download files from the Gene Ontology Annotation (GOA) resource http://www.ebi.ac.uk/GOA."""
 
     # European Bioinformatics Institute (EMBL-EBI) ftp site
-    ftp_pub = 'ftp://ftp.ebi.ac.uk/pub/'
+    ftp_pub = "ftp://ftp.ebi.ac.uk/pub/"
 
     # Species available from ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
     # Example:             https://ftp.ebi.ac.uk/pub/databases/GO/goa/CHICKEN/
     species = [
-        'arabidopsis',
-        'chicken',
-        'cow',
-        'dicty',
-        'dog',
-        'fly',
-        'human',
-        'mouse',
+        "arabidopsis",
+        "chicken",
+        "cow",
+        "dicty",
+        "dog",
+        "fly",
+        "human",
+        "mouse",
         #'pdb',
-        'pig',
-        'rat',
-        'uniprot',
-        'worm',
-        'yeast',
-        'zebrafish',
+        "pig",
+        "rat",
+        "uniprot",
+        "worm",
+        "yeast",
+        "zebrafish",
     ]
 
-    species_items = ['complex', 'isoform', 'rna']
-    exts = ['gaf', 'gpa', 'gpi']
+    species_items = ["complex", "isoform", "rna"]
+    exts = ["gaf", "gpa", "gpi"]
 
     def __init__(self):
-        self.ftp_src_goa = os.path.join(self.ftp_pub, 'databases/GO/goa/')
+        self.ftp_src_goa = os.path.join(self.ftp_pub, "databases/GO/goa/")
 
-    def dnld_goa(self, species, ext='gaf', item=None, fileout=None):
+    def dnld_goa(self, species, ext="gaf", item=None, fileout=None):
         """Download GOA source file name on EMBL-EBI ftp server."""
         basename = self.get_basename(species, ext, item)
-        src = os.path.join(self.ftp_src_goa, species.upper(), "{F}.gz".format(F=basename))
+        src = os.path.join(
+            self.ftp_src_goa, species.upper(), "{F}.gz".format(F=basename)
+        )
         dst = os.path.join(os.getcwd(), basename) if fileout is None else fileout
-        dnld_file(src, dst, prt=sys.stdout, loading_bar=None)
+        download_file(src, dst, prt=sys.stdout, loading_bar=None)
         return dst
 
-    def get_basename(self, species, ext='gaf', item=None):
+    def get_basename(self, species, ext="gaf", item=None):
         """Get GOA basename for a specific species. Ex: goa_human.gaf"""
         assert ext in self.exts, " ".join(self.exts)
-        if species == 'uniprot':
-            species = 'uniprot_all' if item != 'gcrp' else 'uniprot_gcrp'
+        if species == "uniprot":
+            species = "uniprot_all" if item != "gcrp" else "uniprot_gcrp"
         if item is None:
-            return 'goa_{SPECIES}.{EXT}'.format(SPECIES=species, EXT=ext)
+            return "goa_{SPECIES}.{EXT}".format(SPECIES=species, EXT=ext)
         assert item in self.species_items
-        return 'goa_{SPECIES}_{ITEM}.{EXT}'.format(SPECIES=species, ITEM=item, EXT=ext)
+        return "goa_{SPECIES}_{ITEM}.{EXT}".format(SPECIES=species, ITEM=item, EXT=ext)
 
 
 # Copyright (C) 2016-present, DV Klopfenstein, H Tang. All rights reserved."

goatools/associations.py

@@ -8,7 +8,7 @@
 from collections import defaultdict
 import os
 import sys
-from goatools.base import dnld_file
+from goatools.base import download_file
 from goatools.base import ftp_get
 from goatools.anno.factory import get_objanno
 from goatools.anno.factory import get_anno_desc
@@ -19,7 +19,8 @@
 from goatools.anno.opts import AnnoOptions
 from goatools.utils import get_b2aset as utils_get_b2aset
 
-def dnld_assc(assc_name, go2obj=None, namespace='BP', prt=sys.stdout):
+
+def dnld_assc(assc_name, go2obj=None, namespace="BP", prt=sys.stdout):
     """Download association from http://geneontology.org/gene-associations."""
     # Example assc_name: "tair.gaf"
     # Download the Association
@@ -39,38 +40,48 @@ def dnld_assc(assc_name, go2obj=None, namespace='BP', prt=sys.stdout):
         assc[gene] = goids_cur.intersection(goids_dag)
     return assc
 
+
 def dnld_annotation(assc_file, prt=sys.stdout):
     """Download gaf, gpad, or gpi from http://current.geneontology.org/annotations/"""
     if not os.path.isfile(assc_file):
         # assc_http = "http://geneontology.org/gene-associations/"
         assc_http = "http://current.geneontology.org/annotations/"
         _, assc_base = os.path.split(assc_file)
         src = os.path.join(assc_http, "{ASSC}.gz".format(ASSC=assc_base))
-        dnld_file(src, assc_file, prt, loading_bar=None)
+        download_file(src, assc_file, prt, loading_bar=None)
 
-def read_associations(assoc_fn, anno_type='id2gos', namespace='BP', **kws):
+
+def read_associations(assoc_fn, anno_type="id2gos", namespace="BP", **kws):
     """Return associatinos in id2gos format"""
     # kws get_objanno: taxids hdr_only prt allow_missing_symbol
     obj = get_objanno(assoc_fn, anno_type, **kws)
     # kws get_id2gos: ev_include ev_exclude keep_ND keep_NOT b_geneid2gos go2geneids
     return obj.get_id2gos(namespace, **kws)
 
+
 def get_assoc_ncbi_taxids(taxids, force_dnld=False, loading_bar=True, **kws):
     """Download NCBI's gene2go. Return annotations for user-specified taxid(s)."""
-    print('DEPRECATED read_ncbi_gene2go: USE Gene2GoReader FROM goatools.anno.genetogo_reader')
+    print(
+        "DEPRECATED read_ncbi_gene2go: USE Gene2GoReader FROM goatools.anno.genetogo_reader"
+    )
     # pylint: disable=protected-access
     frm = sys._getframe().f_back.f_code
-    print('DEPRECATED read_ncbi_gene2go CALLED FROM: {PY} BY {FNC}'.format(
-        PY=frm.co_filename, FNC=frm.co_name))
-    fin = kws['gene2go'] if 'gene2go' in kws else os.path.join(os.getcwd(), "gene2go")
+    print(
+        "DEPRECATED read_ncbi_gene2go CALLED FROM: {PY} BY {FNC}".format(
+            PY=frm.co_filename, FNC=frm.co_name
+        )
+    )
+    fin = kws["gene2go"] if "gene2go" in kws else os.path.join(os.getcwd(), "gene2go")
     dnld_ncbi_gene_file(fin, force_dnld, loading_bar=loading_bar)
     return read_ncbi_gene2go(fin, taxids, **kws)
 
+
 # pylint: disable=unused-argument
 def dnld_ncbi_gene_file(fin, force_dnld=False, log=sys.stdout, loading_bar=True):
     """Download a file from NCBI Gene's ftp server."""
     if not os.path.exists(fin) or force_dnld:
         import gzip
+
         fin_dir, fin_base = os.path.split(fin)
         fin_gz = "{F}.gz".format(F=fin_base)
         fin_gz = os.path.join(fin_dir, fin_gz)
@@ -84,68 +95,98 @@ def dnld_ncbi_gene_file(fin, force_dnld=False, log=sys.stdout, loading_bar=True)
         ## wget.download(fin_ftp, bar=loading_bar)
         ## rsp = wget(fin_ftp)
         ftp_get(fin_ftp, fin_gz)
-        with gzip.open(fin_gz, 'rb') as zstrm:
+        with gzip.open(fin_gz, "rb") as zstrm:
             if log is not None:
                 log.write("\n  READ GZIP:  {F}\n".format(F=fin_gz))
-            with open(fin, 'wb') as ostrm:
+            with open(fin, "wb") as ostrm:
                 ostrm.write(zstrm.read())
                 if log is not None:
                     log.write("  WROTE UNZIPPED: {F}\n".format(F=fin))
 
+
 def dnld_annofile(fin_anno, anno_type):
     """Download annotation file, if needed"""
     if os.path.exists(fin_anno):
         return
     anno_type = get_anno_desc(fin_anno, anno_type)
-    if anno_type == 'gene2go':
+    if anno_type == "gene2go":
         dnld_ncbi_gene_file(fin_anno)
-    if anno_type in {'gaf', 'gpad'}:
+    if anno_type in {"gaf", "gpad"}:
         dnld_annotation(fin_anno)
 
-def read_ncbi_gene2go(fin_gene2go, taxids=None, namespace='BP', **kws):
+
+def read_ncbi_gene2go(fin_gene2go, taxids=None, namespace="BP", **kws):
     """Read NCBI's gene2go. Return gene2go data for user-specified taxids."""
-    print('DEPRECATED read_ncbi_gene2go: USE Gene2GoReader FROM goatools.anno.genetogo_reader')
+    print(
+        "DEPRECATED read_ncbi_gene2go: USE Gene2GoReader FROM goatools.anno.genetogo_reader"
+    )
     # pylint: disable=protected-access
     frm = sys._getframe().f_back.f_code
-    print('DEPRECATED read_ncbi_gene2go CALLED FROM: {PY} BY {FNC}'.format(
-        PY=frm.co_filename, FNC=frm.co_name))
+    print(
+        "DEPRECATED read_ncbi_gene2go CALLED FROM: {PY} BY {FNC}".format(
+            PY=frm.co_filename, FNC=frm.co_name
+        )
+    )
     obj = Gene2GoReader(fin_gene2go, taxids=taxids)
     # By default, return id2gos. User can cause go2geneids to be returned by:
     #   >>> read_ncbi_gene2go(..., go2geneids=True
-    if 'taxid2asscs' not in kws:
+    if "taxid2asscs" not in kws:
         if len(obj.taxid2asscs) == 1:
             taxid = next(iter(obj.taxid2asscs))
-            kws_ncbi = {k:v for k, v in kws.items() if k in AnnoOptions.keys_exp}
-            kws_ncbi['taxid'] = taxid
+            kws_ncbi = {k: v for k, v in kws.items() if k in AnnoOptions.keys_exp}
+            kws_ncbi["taxid"] = taxid
             return obj.get_id2gos(namespace, **kws_ncbi)
     # Optional detailed associations split by taxid and having both ID2GOs & GO2IDs
     # e.g., taxid2asscs = defaultdict(lambda: defaultdict(lambda: defaultdict(set))
     t2asscs_ret = obj.get_taxid2asscs(taxids, **kws)
-    t2asscs_usr = kws.get('taxid2asscs', defaultdict(lambda: defaultdict(lambda: defaultdict(set))))
-    if 'taxid2asscs' in kws:
+    t2asscs_usr = kws.get(
+        "taxid2asscs", defaultdict(lambda: defaultdict(lambda: defaultdict(set)))
+    )
+    if "taxid2asscs" in kws:
         obj.fill_taxid2asscs(t2asscs_usr, t2asscs_ret)
     return obj.get_id2gos_all(t2asscs_ret)
 
+
 def get_gaf_hdr(fin_gaf):
     """Read Gene Association File (GAF). Return GAF version and data info."""
     return GafReader(fin_gaf, hdr_only=True).hdr
 
+
 # pylint: disable=line-too-long
-def read_gaf(fin_gaf, prt=sys.stdout, hdr_only=False, namespace='BP', allow_missing_symbol=False, **kws):
+def read_gaf(
+    fin_gaf,
+    prt=sys.stdout,
+    hdr_only=False,
+    namespace="BP",
+    allow_missing_symbol=False,
+    **kws
+):
     """Read Gene Association File (GAF). Return data."""
     return GafReader(
-        fin_gaf, hdr_only=hdr_only, prt=prt, allow_missing_symbol=allow_missing_symbol, godag=kws.get('godag')).get_id2gos(
-            namespace, **kws)
+        fin_gaf,
+        hdr_only=hdr_only,
+        prt=prt,
+        allow_missing_symbol=allow_missing_symbol,
+        godag=kws.get("godag"),
+    ).get_id2gos(namespace, **kws)
+
 
 def get_b2aset(a2bset):
     """Given gene2gos, return go2genes. Given go2genes, return gene2gos."""
-    print('DEPRECATED get_b2aset MOVED: USE get_b2aset IN goatools.utils')
+    print("DEPRECATED get_b2aset MOVED: USE get_b2aset IN goatools.utils")
     # pylint: disable=protected-access
     frm = sys._getframe().f_back.f_code
-    print('DEPRECATED get_b2aset CALLED FROM: {PY} BY {FNC}'.format(PY=frm.co_filename, FNC=frm.co_name))
+    print(
+        "DEPRECATED get_b2aset CALLED FROM: {PY} BY {FNC}".format(
+            PY=frm.co_filename, FNC=frm.co_name
+        )
+    )
     return utils_get_b2aset(a2bset)
 
-def get_assc_pruned(assc_geneid2gos, min_genecnt=None, max_genecnt=None, prt=sys.stdout):
+
+def get_assc_pruned(
+    assc_geneid2gos, min_genecnt=None, max_genecnt=None, prt=sys.stdout
+):
     """Remove GO IDs associated with large numbers of genes. Used in stochastic simulations."""
     # DEFN WAS: get_assc_pruned(assc_geneid2gos, max_genecnt=None, prt=sys.stdout):
     #      ADDED min_genecnt argument and functionality
@@ -156,29 +197,35 @@ def get_assc_pruned(assc_geneid2gos, min_genecnt=None, max_genecnt=None, prt=sys
     go2genes_prun = {}
     for goid, genes in go2genes_orig.items():
         num_genes = len(genes)
-        if (min_genecnt is None or num_genes >= min_genecnt) and \
-           (max_genecnt is None or num_genes <= max_genecnt):
+        if (min_genecnt is None or num_genes >= min_genecnt) and (
+            max_genecnt is None or num_genes <= max_genecnt
+        ):
             go2genes_prun[goid] = genes
     num_was = len(go2genes_orig)
     num_now = len(go2genes_prun)
     gos_rm = set(go2genes_orig.keys()).difference(set(go2genes_prun.keys()))
-    assert num_was-num_now == len(gos_rm)
+    assert num_was - num_now == len(gos_rm)
     if prt is not None:
         if min_genecnt is None:
             min_genecnt = 1
         if max_genecnt is None:
             max_genecnt = "Max"
-        prt.write("{N:4} GO IDs pruned. Kept {NOW} GOs assc w/({m} to {M} genes)\n".format(
-            m=min_genecnt, M=max_genecnt, N=num_was-num_now, NOW=num_now))
+        prt.write(
+            "{N:4} GO IDs pruned. Kept {NOW} GOs assc w/({m} to {M} genes)\n".format(
+                m=min_genecnt, M=max_genecnt, N=num_was - num_now, NOW=num_now
+            )
+        )
     return utils_get_b2aset(go2genes_prun), gos_rm
 
+
 def read_annotations(**kws):
     """Read annotations from either a GAF file or NCBI's gene2go file."""
     # Read and save annotation lines
     objanno = get_objanno_g_kws(**kws)
     # Return associations
     return objanno.get_id2gos(**kws) if objanno is not None else {}
 
+
 def get_tcntobj(go2obj, **kws):
     """Return a TermCounts object if the user provides an annotation file, otherwise None."""
     # kws: gpad gaf gene2go id2gos