Repository 'ncbi_blast_plus'
hg clone https://testtoolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus

Changeset 42:3f4e7df708f2 (2019-02-22)
Previous changeset 41:0f4669378764 (2018-11-14) Next changeset 43:16e4b61b56e5 (2019-05-09)
Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty
modified:
tools/ncbi_blast_plus/blastxml_to_tabular.py
tools/ncbi_blast_plus/check_no_duplicates.py
tools/ncbi_blast_plus/repository_dependencies.xml
tools/ncbi_blast_plus/tool_dependencies.xml
b
diff -r 0f4669378764 -r 3f4e7df708f2 tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Wed Nov 14 06:23:31 2018 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Fri Feb 22 09:58:23 2019 -0500
[
b'@@ -81,12 +81,14 @@\n else:\n     from galaxy import eggs  # noqa - ignore flake8 F401\n     import pkg_resources\n+\n     pkg_resources.require("elementtree")\n     from elementtree import ElementTree\n \n if len(sys.argv) == 4 and sys.argv[3] in ["std", "x22", "ext"]:\n     # False positive if user really has a BLAST XML file called \'std\' or \'ext\'...\n-    sys.exit("""ERROR: The script API has changed, sorry.\n+    sys.exit(\n+        """ERROR: The script API has changed, sorry.\n \n Instead of the old style:\n \n@@ -99,7 +101,8 @@\n For more information, use:\n \n $ python blastxml_to_tabular.py -h\n-""")\n+"""\n+    )\n \n usage = """usage: %prog [options] blastxml[,...]\n \n@@ -113,16 +116,29 @@\n extended column names are supported.\n """\n parser = OptionParser(usage=usage)\n-parser.add_option(\'-o\', \'--output\', dest=\'output\', default=None,\n-                  help=\'output filename (defaults to stdout)\',\n-                  metavar="FILE")\n-parser.add_option("-c", "--columns", dest="columns", default=\'std\',\n-                  help="[std|ext|col1,col2,...] standard 12 columns, extended 25 columns, or list of column names")\n+parser.add_option(\n+    "-o",\n+    "--output",\n+    dest="output",\n+    default=None,\n+    help="output filename (defaults to stdout)",\n+    metavar="FILE",\n+)\n+parser.add_option(\n+    "-c",\n+    "--columns",\n+    dest="columns",\n+    default="std",\n+    help="[std|ext|col1,col2,...] standard 12 columns, "\n+    "extended 25 columns, or list of column names",\n+)\n (options, args) = parser.parse_args()\n \n-colnames = (\'qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,\'\n-            \'sstart,send,evalue,bitscore,sallseqid,score,nident,positive,\'\n-            \'gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles\').split(\',\')\n+colnames = (\n+    "qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,"\n+    "sstart,send,evalue,bitscore,sallseqid,score,nident,positive,"\n+    "gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles"\n+).split(",")\n \n if len(args) < 1:\n     sys.exit("ERROR: No BLASTXML input files given; run with --help to see options.")\n@@ -148,7 +164,9 @@\n     assert set(colnames).issuperset(cols), cols\n     if not cols:\n         sys.exit("No columns selected!")\n-    extended = max(colnames.index(c) for c in cols) >= 12  # Do we need any higher columns?\n+    extended = (\n+        max(colnames.index(c) for c in cols) >= 12\n+    )  # Do we need any higher columns?\n del out_fmt\n \n for in_file in args:\n@@ -213,7 +231,8 @@\n                 # <Hit_accession>P56514</Hit_accession>\n                 # or,\n                 # <Hit_id>Subject_1</Hit_id>\n-                # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>\n+                # <Hit_def>gi|57163783|ref|NP_001009242.1|\n+                # rhodopsin [Felis catus]</Hit_def>\n                 # <Hit_accession>Subject_1</Hit_accession>\n                 #\n                 # apparently depending on the parse_deflines switch\n@@ -225,11 +244,15 @@\n                 # <Hit_accession>2</Hit_accession>\n                 sseqid = hit.findtext("Hit_id").split(None, 1)[0]\n                 hit_def = sseqid + " " + hit.findtext("Hit_def")\n-                if re_default_subject_id.match(sseqid) and sseqid == hit.findtext("Hit_accession"):\n+                if re_default_subject_id.match(sseqid) and sseqid == hit.findtext(\n+                    "Hit_accession"\n+                ):\n                     # Place holder ID, take the first word of the subject definition\n                     hit_def = hit.findtext("Hit_def")\n                     sseqid = hit_def.split(None, 1)[0]\n-                if sseqid.startswith("gnl|BL_ORD_ID|") and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"):\n+                if sseqid.startswith(\n+                    "gnl|BL_ORD_ID|"\n+                ) and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"):\n                     # Alternative place holder ID, again take the first word of hit_def\n                     hit_def = '..b'dtext("Hsp_hit-from"),  # sstart,\n+                        hsp.findtext("Hsp_hit-to"),  # send,\n+                        evalue,  # hsp.findtext("Hsp_evalue") in scientific notation\n+                        bitscore,  # hsp.findtext("Hsp_bit-score") rounded\n+                    ]\n \n                     if extended:\n                         try:\n-                            sallseqid = ";".join(name.split(None, 1)[0] for name in hit_def.split(" >"))\n-                            salltitles = "<>".join(name.split(None, 1)[1] for name in hit_def.split(" >"))\n+                            sallseqid = ";".join(\n+                                name.split(None, 1)[0] for name in hit_def.split(" >")\n+                            )\n+                            salltitles = "<>".join(\n+                                name.split(None, 1)[1] for name in hit_def.split(" >")\n+                            )\n                         except IndexError as e:\n-                            sys.exit("Problem splitting multuple hits?\\n%r\\n--> %s" % (hit_def, e))\n+                            sys.exit(\n+                                "Problem splitting multuple hits?\\n%r\\n--> %s"\n+                                % (hit_def, e)\n+                            )\n                         # print(hit_def, "-->", sallseqid)\n                         positive = hsp.findtext("Hsp_positive")\n                         ppos = "%0.2f" % (100 * float(positive) / float(length))\n                         qframe = hsp.findtext("Hsp_query-frame")\n                         sframe = hsp.findtext("Hsp_hit-frame")\n                         if blast_program == "blastp":\n-                            # Probably a bug in BLASTP that they use 0 or 1 depending on format\n+                            # Probably a bug in BLASTP that they use 0 or 1\n+                            # depending on format\n                             if qframe == "0":\n                                 qframe = "1"\n                             if sframe == "0":\n                                 sframe = "1"\n                         slen = int(hit.findtext("Hit_len"))\n-                        values.extend([sallseqid,\n-                                       hsp.findtext("Hsp_score"),  # score,\n-                                       nident,\n-                                       positive,\n-                                       hsp.findtext("Hsp_gaps"),  # gaps,\n-                                       ppos,\n-                                       qframe,\n-                                       sframe,\n-                                       # NOTE - for blastp, XML shows original seq, tabular uses XXX masking\n-                                       q_seq,\n-                                       h_seq,\n-                                       str(qlen),\n-                                       str(slen),\n-                                       salltitles,\n-                                       ])\n+                        values.extend(\n+                            [\n+                                sallseqid,\n+                                hsp.findtext("Hsp_score"),  # score,\n+                                nident,\n+                                positive,\n+                                hsp.findtext("Hsp_gaps"),  # gaps,\n+                                ppos,\n+                                qframe,\n+                                sframe,\n+                                # NOTE - for blastp, XML shows original seq,\n+                                # tabular uses XXX masking\n+                                q_seq,\n+                                h_seq,\n+                                str(qlen),\n+                                str(slen),\n+                                salltitles,\n+                            ]\n+                        )\n                     if cols:\n                         # Only a subset of the columns are needed\n                         values = [values[colnames.index(c)] for c in cols]\n'
b
diff -r 0f4669378764 -r 3f4e7df708f2 tools/ncbi_blast_plus/check_no_duplicates.py
--- a/tools/ncbi_blast_plus/check_no_duplicates.py Wed Nov 14 06:23:31 2018 -0500
+++ b/tools/ncbi_blast_plus/check_no_duplicates.py Fri Feb 22 09:58:23 2019 -0500
[
@@ -31,7 +31,7 @@
     if not magic:
         # Empty file, special case
         continue
-    elif magic == b'\x1f\x8b':
+    elif magic == b"\x1f\x8b":
         # Gzipped
         handle = gzip.open(filename, "rt")
     elif magic[0:1] == b">":
b
diff -r 0f4669378764 -r 3f4e7df708f2 tools/ncbi_blast_plus/repository_dependencies.xml
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Wed Nov 14 06:23:31 2018 -0500
+++ b/tools/ncbi_blast_plus/repository_dependencies.xml Fri Feb 22 09:58:23 2019 -0500
b
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
-    <repository changeset_revision="3eada762af11" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="1250aab8b97a" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file
b
diff -r 0f4669378764 -r 3f4e7df708f2 tools/ncbi_blast_plus/tool_dependencies.xml
--- a/tools/ncbi_blast_plus/tool_dependencies.xml Wed Nov 14 06:23:31 2018 -0500
+++ b/tools/ncbi_blast_plus/tool_dependencies.xml Fri Feb 22 09:58:23 2019 -0500
b
@@ -1,6 +1,6 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="blast" version="2.5.0">
-        <repository changeset_revision="de5976f2c96d" name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="de5976f2c96d" name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file