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Added new parameters
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for E-value, % of identity and bit score
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@iquasere
iquasere committed May 26, 2021
1 parent 8b44ff7 commit 3760e84
Showing 1 changed file with 32 additions and 19 deletions.
51 changes: 32 additions & 19 deletions upimapi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@

from uniprot_support import UniprotSupport

__version__ = '1.2.0'
__version__ = '1.2.1'

upmap = UniprotSupport()

Expand Down Expand Up @@ -53,11 +53,11 @@ def get_arguments(self):
help="If IDs in database are in 'full' format: tr|XXX|XXX")
parser.add_argument("--fasta", help="Output will be generated in FASTA format",
action="store_true", default=False)
parser.add_argument("--step", default='1000',
help="How many IDs to submit per request to the API (default is 1000)")
parser.add_argument("--step", type=int, default=1000,
help="How many IDs to submit per request to the API (default: 1000)")
parser.add_argument("--max-tries", default=3, type=int,
help="How many times to try obtaining information from UniProt before giving up")
parser.add_argument('-v', '--version', action='version', version='UPIMAPI ' + __version__)
parser.add_argument('-v', '--version', action='version', version=f'UPIMAPI {__version__}')

diamond_args = parser.add_argument_group('DIAMOND arguments')
diamond_args.add_argument("--use-diamond", action="store_true", default=False,
Expand All @@ -66,16 +66,22 @@ def get_arguments(self):
diamond_args.add_argument("-db", "--database", default=None,
help="""Reference database for annotation with DIAMOND. NOTICE: if database's IDs are
in 'full' format (tr|XXX|XXX), specify with ""--full-id" parameter.""")
diamond_args.add_argument("-t", "--threads", default=multiprocessing.cpu_count() - 2,
help="Number of threads to use in annotation steps")
diamond_args.add_argument("-mts", "--max-target-seqs", default='50',
help="Number of annotations to output per sequence inputed")
diamond_args.add_argument("-t", "--threads", type=int, default=multiprocessing.cpu_count() - 2,
help="Number of threads to use in annotation steps (default: total available - 2")
diamond_args.add_argument("--evalue", type=float, default=1e-3,
help="Maximum e-value to report annotations for (default: 0.001).")
diamond_args.add_argument("--pident", type=float, default=None,
help="Minimum pident to report annotations for.")
diamond_args.add_argument("--bitscore", type=float, default=None,
help="Minimum bit score to report annotations for (overrides e-value).")
diamond_args.add_argument("-mts", "--max-target-seqs", default=1,
help="Number of annotations to output per sequence inputed (default: 1)")
diamond_args.add_argument("-b", "--block-size",
help="Billions of sequence letters to be processed at a time (UPIMAPI determines best "
"value for this parameter if not set")
help="Billions of sequence letters to be processed at a time "
"(default: auto determine best value)")
diamond_args.add_argument("-c", "--index-chunks",
help="Number of chunks for processing the seed index (UPIMAPI determines best value "
"for this parameter if not set")
help="Number of chunks for processing the seed index "
"(default: auto determine best value)")

args = parser.parse_args()
args._output = args.output.rstrip('/')
Expand Down Expand Up @@ -332,10 +338,16 @@ def b_n_c(self, argsb, argsc):
return b, 3
return b, 4

def run_diamond(self, query, aligned, unaligned, database, threads='12', max_target_seqs='50', b=1, c=4):
self.run_command("diamond blastp --query {} --out {} --un {} --db {} --outfmt 6 --unal 1 --threads {} "
"--max-target-seqs {} -b {} -c {}".format(query, aligned, unaligned, database, threads,
max_target_seqs, b, c))
def run_diamond(self, query, aligned, unaligned, database, threads=12, max_target_seqs=50, b=1, c=4, e_value=0.01,
bit_score=None, pident=None):
command = (
f"diamond blastp --query {query} --out {aligned} --un {unaligned} --db {database} --outfmt 6 --unal 1 "
f"--threads {threads} --max-target-seqs {max_target_seqs} -b {b} -c {c} --evalue {e_value}")
if bit_score:
command += f' --min-score {bit_score}'
if pident:
command += f' --id {pident}'
self.run_command(command)

def upimapi(self):
args = self.get_arguments()
Expand All @@ -349,7 +361,8 @@ def upimapi(self):
(b, c) = self.b_n_c(argsb=args.block_size, argsc=args.index_chunks)
self.run_diamond(
args.input, '{}/aligned.blast'.format(args.output), '{}/unaligned.blast'.format(args.output),
args.database, threads=args.threads, max_target_seqs=args.max_target_seqs, b=b, c=c)
args.database, threads=args.threads, max_target_seqs=args.max_target_seqs, b=b, c=c,
e_value=args.evalue, bit_score=args.bitscore, pident=args.pident)
args.input = '{}/aligned.blast'.format(args.output)
args.blast = True

Expand All @@ -372,7 +385,7 @@ def upimapi(self):

self.recursive_uniprot_information(
ids, '{}/uniprotinfo.tsv'.format(args.output),
columns=columns, databases=databases, step=int(args.step), max_iter=args.max_tries)
columns=columns, databases=databases, step=args.step, max_iter=args.max_tries)

if args.use_diamond:
blast = self.parse_blast('{}/aligned.blast'.format(args
Expand All @@ -382,7 +395,7 @@ def upimapi(self):
pd.merge(blast, pd.read_csv('{}/uniprotinfo.tsv'.format(args.output), sep='\t'), left_on='sseqid',
right_on='Entry').to_excel('{}/UPIMAPI_results.xlsx'.format(args.output), index=False)
else:
self.recursive_uniprot_fasta(ids, '{}/uniprotinfo.fasta'.format(args.output), step=int(args.step))
self.recursive_uniprot_fasta(ids, '{}/uniprotinfo.fasta'.format(args.output), step=args.step)


if __name__ == '__main__':
Expand Down

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