add_option => add_argument

jcvi/algorithms/supermap.py

@@ -147,14 +147,14 @@ def supermap(blast_file, filter="intersection", dialect="blast", clip=0):
 
     filter_choices = ("ref", "query", "intersection", "union")
     dialect_choices = ("blast", "coords")
-    p.add_option(
+    p.add_argument(
         "--filter",
         choices=filter_choices,
         default="intersection",
         help="Available filters",
     )
-    p.add_option("--dialect", choices=dialect_choices, help="Input format")
-    p.add_option(
+    p.add_argument("--dialect", choices=dialect_choices, help="Input format")
+    p.add_argument(
         "--clip",
         default=0,
         type=int,

jcvi/annotation/ahrd.py

@@ -554,7 +554,7 @@ def fix(args):
     Fix ugly names from Uniprot.
     """
     p = OptionParser(fix.__doc__)
-    p.add_option(
+    p.add_argument(
         "--ignore_sym_pat",
         default=False,
         action="store_true",
@@ -650,19 +650,19 @@ def batch(args):
     ahrd_weights = {"blastp": [0.5, 0.3, 0.2], "blastx": [0.6, 0.4, 0.0]}
     blast_progs = tuple(ahrd_weights.keys())
 
-    p.add_option(
+    p.add_argument(
         "--path",
         default="~/code/AHRD/",
         help="Path where AHRD is installed",
     )
-    p.add_option(
+    p.add_argument(
         "--blastprog",
         default="blastp",
         choices=blast_progs,
         help="Specify the blast program being run. Based on this option,"
         + " the AHRD parameters (score_weights) will be modified",
     )
-    p.add_option(
+    p.add_argument(
         "--iprscan",
         default=None,
         help="Specify path to InterProScan results file if available."

jcvi/annotation/automaton.py

@@ -63,9 +63,13 @@ def augustus(args):
     annotation.reformat.augustus().
     """
     p = OptionParser(augustus.__doc__)
-    p.add_option("--species", default="maize", help="Use species model for prediction")
-    p.add_option("--hintsfile", help="Hint-guided AUGUSTUS")
-    p.add_option("--nogff3", default=False, action="store_true", help="Turn --gff3=off")
+    p.add_argument(
+        "--species", default="maize", help="Use species model for prediction"
+    )
+    p.add_argument("--hintsfile", help="Hint-guided AUGUSTUS")
+    p.add_argument(
+        "--nogff3", default=False, action="store_true", help="Turn --gff3=off"
+    )
     p.set_home("augustus")
     p.set_cpus()
     opts, args = p.parse_args(args)
@@ -112,7 +116,7 @@ def star(args):
     Run star on a folder with reads.
     """
     p = OptionParser(star.__doc__)
-    p.add_option(
+    p.add_argument(
         "--single", default=False, action="store_true", help="Single end mapping"
     )
     p.set_fastq_names()
@@ -163,7 +167,7 @@ def cufflinks(args):
     Run cufflinks on a folder containing tophat results.
     """
     p = OptionParser(cufflinks.__doc__)
-    p.add_option("--gtf", help="Reference annotation")
+    p.add_argument("--gtf", help="Reference annotation")
     p.set_cpus()
     opts, args = p.parse_args(args)
 
@@ -219,23 +223,23 @@ def tophat(args):
     from jcvi.formats.fastq import guessoffset
 
     p = OptionParser(tophat.__doc__)
-    p.add_option("--gtf", help="Reference annotation")
-    p.add_option(
+    p.add_argument("--gtf", help="Reference annotation")
+    p.add_argument(
         "--single", default=False, action="store_true", help="Single end mapping"
     )
-    p.add_option(
+    p.add_argument(
         "--intron",
         default=15000,
         type=int,
         help="Max intron size",
     )
-    p.add_option(
+    p.add_argument(
         "--dist",
         default=-50,
         type=int,
         help="Mate inner distance",
     )
-    p.add_option(
+    p.add_argument(
         "--stdev",
         default=50,
         type=int,

jcvi/annotation/depth.py

@@ -64,13 +64,13 @@ def bed(args):
     Write bed files where the bases have at least certain depth.
     """
     p = OptionParser(bed.__doc__)
-    p.add_option(
+    p.add_argument(
         "-o",
         dest="output",
         default="stdout",
         help="Output file name",
     )
-    p.add_option(
+    p.add_argument(
         "--cutoff",
         dest="cutoff",
         default=10,

jcvi/annotation/maker.py

@@ -351,7 +351,7 @@ def batcheval(args):
     from jcvi.formats.gff import make_index
 
     p = OptionParser(evaluate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--type",
         default="CDS",
         help="list of features to extract, use comma to separate (e.g."
@@ -450,17 +450,17 @@ def split(args):
     from jcvi.formats.bed import Bed
 
     p = OptionParser(split.__doc__)
-    p.add_option(
+    p.add_argument(
         "--key",
         default="Name",
         help="Key in the attributes to extract predictor.gff",
     )
-    p.add_option(
+    p.add_argument(
         "--parents",
         default="match",
         help="list of features to extract, use comma to separate (e.g.'gene,mRNA')",
     )
-    p.add_option(
+    p.add_argument(
         "--children",
         default="match_part",
         help="list of features to extract, use comma to separate (e.g."

jcvi/annotation/pasa.py

@@ -81,7 +81,7 @@ def assemble(args):
     """
     p = OptionParser(assemble.__doc__)
     p.set_pasa_opts()
-    p.add_option(
+    p.add_argument(
         "--prepare",
         default=False,
         action="store_true",
@@ -228,7 +228,7 @@ def compare(args):
     """
     p = OptionParser(compare.__doc__)
     p.set_pasa_opts(action="compare")
-    p.add_option(
+    p.add_argument(
         "--prepare",
         default=False,
         action="store_true",
@@ -320,7 +320,7 @@ def longest(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(longest.__doc__)
-    p.add_option(
+    p.add_argument(
         "--prefix",
         default="pasa",
         help="Replace asmbl_ with prefix",
@@ -393,31 +393,31 @@ def consolidate(args):
 
     supported_modes = ["name", "coords"]
     p = OptionParser(consolidate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--slop",
         default=False,
         action="store_true",
         help="allow minor variation in terminal 5'/3' UTR start/stop position",
     )
-    p.add_option(
+    p.add_argument(
         "--inferUTR",
         default=False,
         action="store_true",
         help="infer presence of UTRs from exon coordinates",
     )
-    p.add_option(
+    p.add_argument(
         "--mode",
         default="name",
         choices=supported_modes,
         help="method used to determine overlapping loci",
     )
-    p.add_option(
+    p.add_argument(
         "--summary",
         default=False,
         action="store_true",
         help="Generate summary table of consolidation process",
     )
-    p.add_option(
+    p.add_argument(
         "--clusters",
         default=False,
         action="store_true",

jcvi/annotation/qc.py

@@ -165,26 +165,26 @@ def trimUTR(args):
     from jcvi.formats.base import SetFile
 
     p = OptionParser(trimUTR.__doc__)
-    p.add_option(
+    p.add_argument(
         "--trim5",
         default=None,
         type=str,
         help="File containing gene list for 5' UTR trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--trim3",
         default=None,
         type=str,
         help="File containing gene list for 3' UTR trimming",
     )
-    p.add_option(
+    p.add_argument(
         "--trimrange",
         default=None,
         type=str,
         help="File containing gene list for UTR trim back"
         + "based on suggested (start, stop) coordinate range",
     )
-    p.add_option(
+    p.add_argument(
         "--refgff",
         default=None,
         type=str,

jcvi/annotation/reformat.py

@@ -209,9 +209,9 @@ def plot(args):
     from jcvi.graphics.chromosome import ChromosomeMap
 
     p = OptionParser(plot.__doc__)
-    p.add_option("--firstn", type=int, help="Only plot the first N genes")
-    p.add_option("--ymax", type=int, help="Y-axis max value")
-    p.add_option("--log", action="store_true", help="Write plotting data")
+    p.add_argument("--firstn", type=int, help="Only plot the first N genes")
+    p.add_argument("--ymax", type=int, help="Y-axis max value")
+    p.add_argument("--log", action="store_true", help="Write plotting data")
     opts, args, iopts = p.set_image_options(args, figsize="6x4")
 
     if len(args) != 2:
@@ -305,7 +305,7 @@ def instantiate(args):
     """
     p = OptionParser(instantiate.__doc__)
     p.set_annot_reformat_opts()
-    p.add_option(
+    p.add_argument(
         "--extended_stride",
         default=False,
         action="store_true",
@@ -594,13 +594,13 @@ def annotate(args):
     valid_resolve_choices = ["alignment", "overlap"]
 
     p = OptionParser(annotate.__doc__)
-    p.add_option(
+    p.add_argument(
         "--resolve",
         default="alignment",
         choices=valid_resolve_choices,
         help="Resolve ID assignment based on a certain metric",
     )
-    p.add_option(
+    p.add_argument(
         "--atg_name",
         default=False,
         action="store_true",
@@ -611,14 +611,14 @@ def annotate(args):
         "Optional parameters (alignment):\n"
         + "Use if resolving ambiguities based on sequence `alignment`",
     )
-    g1.add_option(
+    g1.add_argument(
         "--pid",
         dest="pid",
         default=35.0,
         type=float,
         help="Percent identity cutoff",
     )
-    g1.add_option(
+    g1.add_argument(
         "--score",
         dest="score",
         default=250.0,
@@ -631,21 +631,21 @@ def annotate(args):
         + "Use if resolving ambiguities based on `overlap` length\n"
         + "Parameters equivalent to `intersectBed`",
     )
-    g2.add_option(
+    g2.add_argument(
         "-f",
         dest="f",
         default=0.5,
         type=float,
         help="Minimum overlap fraction (0.0 - 1.0)",
     )
-    g2.add_option(
+    g2.add_argument(
         "-r",
         dest="r",
         default=False,
         action="store_true",
         help="Require fraction overlap to be reciprocal",
     )
-    g2.add_option(
+    g2.add_argument(
         "-s",
         dest="s",
         default=True,
@@ -944,34 +944,34 @@ def rename(args):
     import string
 
     p = OptionParser(rename.__doc__)
-    p.add_option(
+    p.add_argument(
         "-a",
         dest="gene_increment",
         default=10,
         type=int,
         help="Increment for continuous genes",
     )
-    p.add_option(
+    p.add_argument(
         "-b",
         dest="gap_increment",
         default=1000,
         type=int,
         help="Increment for gaps",
     )
-    p.add_option(
+    p.add_argument(
         "--pad0",
         default=6,
         type=int,
         help="Pad gene identifiers with 0",
     )
-    p.add_option(
+    p.add_argument(
         "--spad0",
         default=4,
         type=int,
         help="Pad gene identifiers on small scaffolds",
     )
-    p.add_option("--prefix", default="Bo", help="Genome prefix")
-    p.add_option(
+    p.add_argument("--prefix", default="Bo", help="Genome prefix")
+    p.add_argument(
         "--jgi",
         default=False,
         action="store_true",
@@ -1072,7 +1072,7 @@ def reindex(args):
     from tempfile import mkstemp
 
     p = OptionParser(reindex.__doc__)
-    p.add_option(
+    p.add_argument(
         "--scores", type=str, help="read from existing EMBOSS `needle` scores file"
     )
     p.set_outfile()
@@ -1235,7 +1235,7 @@ def publocus(args):
     Medtr1g007060.2		MTR_1g007060B
     """
     p = OptionParser(publocus.__doc__)
-    p.add_option("--locus_tag", default="MTR_", help="GenBank locus tag")
+    p.add_argument("--locus_tag", default="MTR_", help="GenBank locus tag")
     opts, args = p.parse_args(args)
 
     if len(args) != 1: