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Added bin_map command #84

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Added bin_map command #84

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d4ba2bf
Updates to error messages
chlige Jan 30, 2023
4da7f86
Added bin_map command to generate bin annotations using contig to bin…
chlige Jan 30, 2023
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8 changes: 6 additions & 2 deletions CAT_pack/CAT
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ import sys

import about
import add_names
import bin_map
import bins
import contigs
import download
Expand All @@ -14,7 +15,7 @@ import summarise

def usage():
message = (
'usage: CAT (prepare | contigs | bin | bins | add_names | '
'usage: CAT (prepare | contigs | bin | bins | bin_map | add_names | '
'summarise | download) [-v / --version] [-h / --help]\n'
'CAT: error: one of the arguments prepare contigs bin bins '
'add_names summarise is required')
Expand All @@ -35,7 +36,7 @@ def version():

def help():
message = (
'usage: CAT (prepare | contigs | bin | bins | add_names | '
'usage: CAT (prepare | contigs | bin | bins | bin_map | add_names | '
'summarise) [-v / --version] [-h / --help]\n\n'
'Run Contig Annotation Tool (CAT) or '
'Bin Annotation Tool (BAT).\n\n'
Expand All @@ -44,6 +45,7 @@ def help():
' contigs\t\tRun CAT.\n'
' bin\t\t\tRun BAT on a single bin.\n'
' bins\t\t\tRun BAT on a set of bins.\n'
' bin_map\t\t\tRun BAT on a contig to bin map using files from a previous "contigs".\n'
' add_names\t\tAdd taxonomic names to CAT or BAT output files.\n'
' summarise\t\tSummarise a named CAT or BAT classification file.\n'
' download\t\tDownload and preprocess data from nr or GTDB'
Expand All @@ -70,6 +72,8 @@ def main():
single_bin.run()
elif sys.argv[1] == 'bins':
bins.run()
elif sys.argv[1] == 'bin_map':
bin_map.run()
elif sys.argv[1] == 'add_names':
add_names.run()
elif sys.argv[1] == 'summarise':
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2 changes: 1 addition & 1 deletion CAT_pack/add_names.py
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Expand Up @@ -35,7 +35,7 @@ def parse_arguments():
extra_args = [arg for (i, arg) in enumerate(extra_args) if
(i, arg) != (0, 'add_names')]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
sys.exit('error: too many arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))

# Add extra arguments.
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