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add ignore zero anchor parameter for skip no matches in batch search #598

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merged 1 commit into from
Sep 27, 2023
Merged

add ignore zero anchor parameter for skip no matches in batch search #598

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17 changes: 16 additions & 1 deletion jcvi/compara/catalog.py
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Original file line number Diff line number Diff line change
Expand Up @@ -666,6 +666,12 @@ def ortholog(args):
dotplot_group.add_option(
"--no_dotplot", default=False, action="store_true", help="Do not make dotplot"
)
p.add_option(
"--ignore_zero_anchor",
default=False,
action="store_true",
help="Ignore this pair of ortholog identification instead of throwing an error when performing many pairs of cataloging."
)

opts, args = p.parse_args(args)

Expand All @@ -674,6 +680,7 @@ def ortholog(args):

a, b = args
dbtype = opts.dbtype
ignore_zero_anchor = opts.ignore_zero_anchor
suffix = ".cds" if dbtype == "nucl" else ".pep"
abed, afasta = a + ".bed", a + suffix
bbed, bfasta = b + ".bed", b + suffix
Expand Down Expand Up @@ -727,7 +734,15 @@ def ortholog(args):
dargs += ["--no_strip_names"]
if opts.liftover_dist:
dargs += ["--liftover_dist={}".format(opts.liftover_dist)]
scan(dargs)
try:
scan(dargs)
except ValueError as e:
if ignore_zero_anchor:
logging.debug(f"{e}")
logging.debug("Ignoring this error and continuing...")
return
else:
raise ValueError(e)
if quota:
quota_main([lifted_anchors, "--quota={0}".format(quota), "--screen"])
if need_update(anchors, pdf, warn=True) and not opts.no_dotplot:
Expand Down