"""Command line interface for pysradb
"""
import argparse
import os
import re
import sys
import warnings
from io import StringIO
from textwrap import dedent
import pandas as pd
from . import __version__
from .exceptions import IncorrectFieldException
from .exceptions import MissingQueryException
from .geoweb import GEOweb
from .search import EnaSearch
from .search import GeoSearch
from .search import SraSearch
from .sradb import SRAdb
from .sradb import download_sradb_file
from .sraweb import SRAweb
from .utils import confirm
warnings.simplefilter(action="ignore", category=FutureWarning)
[docs]class ArgParser(argparse.ArgumentParser):
[docs] def error(self, message):
sys.stderr.write("error: %s\n" % message)
self.print_help()
sys.exit(2)
def _print_save_df(df, saveto=None):
if saveto:
if saveto.lower().endswith(".csv"):
# if the save file format is csv
df.to_csv(saveto, index=False, header=True)
else:
df.to_csv(saveto, index=False, header=True, sep="\t")
else:
if len(df.index):
to_print = (
df.replace(r"[\s]{2,}|\t", " ", regex=True)
.to_string(
index=False,
justify="left",
header=False,
col_space=0,
)
.lstrip()
)
to_print_split = to_print.split("\n")
to_print_split = map(lambda x: re.sub(r"\s\s+", "\t", x), to_print_split)
to_print = ["\t".join(df.columns)]
for line in to_print_split:
to_print.append(line.lstrip())
to_print = list(
map(lambda line: line.encode("ascii", "replace").decode(), to_print)
)
for line in to_print:
sys.stdout.write(line + os.linesep)
sys.stdout.flush()
###################### metadata ##############################
################################################################
################# download ##########################
[docs]def download(
out_dir, srx, srp, geo, skip_confirmation, col="sra_url", use_ascp=False, threads=1
):
if out_dir is None:
out_dir = os.path.join(os.getcwd(), "pysradb_downloads")
sradb = SRAweb()
geoweb = GEOweb()
# This block is triggered only if no -p or -g arguments are provided.
# In this case, the input is taken from the pipe and assumed to be SRA, not GEO
if not srp and not geo:
text = ""
for index, line in enumerate(sys.stdin):
line = line.strip(" \t\n\r")
line = re.sub(r"\s*\t+\s*", "\t", line)
if not line:
continue
text += "{}\n".format(line)
df = pd.read_csv(StringIO(text), sep="\t")
sradb.download(
df=df,
out_dir=out_dir,
filter_by_srx=srx,
skip_confirmation=True,
use_ascp=use_ascp,
url_col=col,
threads=threads,
)
# This block is triggered for downloads using the -p argument
if srp:
for srp_x in srp:
metadata = sradb.sra_metadata(srp_x, detailed=True)
sradb.download(
df=metadata,
out_dir=out_dir,
filter_by_srx=srx,
skip_confirmation=skip_confirmation,
use_ascp=use_ascp,
threads=threads,
)
# This block is triggered for downloads using the -g argument
if geo:
for geo_x in geo:
links, root_url = geoweb.get_download_links(geo_x)
geoweb.download(links=links, root_url=root_url, gse=geo_x, out_dir=out_dir)
sradb.close()
#########################################################
######################### search #################################
[docs]def search(saveto, db, verbosity, return_max, fields):
if fields["run_description"]:
verbosity = 1
if fields["detailed"]:
verbosity = 3
try:
if db == "ena":
instance = EnaSearch(
verbosity,
return_max,
fields["query"],
fields["accession"],
fields["organism"],
fields["layout"],
fields["mbases"],
fields["publication_date"],
fields["platform"],
fields["selection"],
fields["source"],
fields["strategy"],
fields["title"],
)
instance.search()
elif db == "geo":
instance = GeoSearch(
verbosity,
return_max,
fields["query"],
fields["accession"],
fields["organism"],
fields["layout"],
fields["mbases"],
fields["publication_date"],
fields["platform"],
fields["selection"],
fields["source"],
fields["strategy"],
fields["title"],
fields["geo_query"],
fields["geo_dataset_type"],
fields["geo_entry_type"],
)
instance.search()
else:
instance = SraSearch(
verbosity,
return_max,
fields["query"],
fields["accession"],
fields["organism"],
fields["layout"],
fields["mbases"],
fields["publication_date"],
fields["platform"],
fields["selection"],
fields["source"],
fields["strategy"],
fields["title"],
)
instance.search()
except (MissingQueryException, IncorrectFieldException) as e:
print(e)
return
if fields["stats"]:
instance.show_result_statistics()
if fields["graphs"]:
graph_types = tuple(fields["graphs"].split())
instance.visualise_results(graph_types, False)
_print_save_df(instance.get_df(), saveto)
[docs]def get_geo_search_info():
print(GeoSearch.info())
####################################################################
######################### gse-to-gsm ###############################
[docs]def gse_to_gsm(gse_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gse_to_gsm(
gse_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
####################################################################
######################## gse-to-srp ################################
[docs]def gse_to_srp(gse_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gse_to_srp(
gse_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
######################################################################
######################### gsm-to-gse #################################
[docs]def gsm_to_gse(gsm_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gsm_to_gse(
gsm_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
########################################################################
############################ gsm-to-srp ################################
[docs]def gsm_to_srp(gsm_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gsm_to_srp(
gsm_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
########################################################################
############################ gsm-to-srr ################################
[docs]def gsm_to_srr(gsm_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gsm_to_srr(
gsm_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
########################################################################
############################ gsm-to-srs ################################
[docs]def gsm_to_srs(gsm_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gsm_to_srs(
gsm_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
########################################################################
############################# gsm-to-srx ###############################
[docs]def gsm_to_srx(gsm_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.gsm_to_srx(
gsm_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srp-to-gse ##################################
[docs]def srp_to_gse(srp_id, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srp_to_gse(
srp_id,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srp-to-srr ##################################
[docs]def srp_to_srr(srp_id, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srp_to_srr(
srp_id,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srp-to-srs ##################################
[docs]def srp_to_srs(srp_id, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srp_to_srs(
srp_id,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srp-to-srx ##################################
[docs]def srp_to_srx(srp_id, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srp_to_srx(
srp_id,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srr-to-gsm ##################################
[docs]def srr_to_gsm(srr_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srr_to_gsm(
srr_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
########################################################################
########################### srr-to-srp ##################################
[docs]def srr_to_srp(srr_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srr_to_srp(
srr_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srr-to-srs ##################################
[docs]def srr_to_srs(srr_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srr_to_srs(
srr_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srr-to-srx ##################################
[docs]def srr_to_srx(srr_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srr_to_srx(
srr_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srs-to-gsm ##################################
[docs]def srs_to_gsm(srs_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srs_to_gsm(
srs_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srs-to-srx ##################################
[docs]def srs_to_srx(srs_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srs_to_srx(
srs_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srx-to-srp ##################################
[docs]def srx_to_srp(srx_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srx_to_srp(
srx_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srx-to-srr ##################################
[docs]def srx_to_srr(srx_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srx_to_srr(
srx_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### srx-to-srs ##################################
[docs]def srx_to_srs(srx_ids, saveto, detailed, desc, expand):
sradb = SRAweb()
df = sradb.srx_to_srs(
srx_ids,
detailed=detailed,
sample_attribute=desc,
expand_sample_attributes=expand,
)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
[docs]def parse_args(args=None):
"""Argument parser"""
parser = ArgParser(
description=dedent(
"""\
pysradb: Query NGS metadata and data from NCBI Sequence Read Archive.
version: {}.
Citation: 10.12688/f1000research.18676.1""".format(
__version__
)
),
formatter_class=CustomFormatterArgP,
)
# pysradb subcommands
subparsers = parser.add_subparsers(title="subcommands", dest="command")
# pysradb --version
parser.add_argument(
"--version",
action="version",
version="%(prog)s {version}".format(version=__version__),
)
# pysradb --citation
parser.add_argument(
"--citation",
action="version",
version=dedent(
"""
Choudhary, Saket. "pysradb: A Python Package to Query next-Generation Sequencing Metadata and Data from NCBI Sequence Read Archive." F1000Research, vol. 8, F1000 (Faculty of 1000 Ltd), Apr. 2019, p. 532 (https://f1000research.com/articles/8-532/v1)
@article{Choudhary2019,
doi = {10.12688/f1000research.18676.1},
url = {https://doi.org/10.12688/f1000research.18676.1},
year = {2019},
month = apr,
publisher = {F1000 (Faculty of 1000 Ltd)},
volume = {8},
pages = {532},
author = {Saket Choudhary},
title = {pysradb: A {P}ython package to query next-generation sequencing metadata and data from {NCBI} {S}equence {R}ead {A}rchive},
journal = {F1000Research}
}
"""
),
help="how to cite",
)
# pysradb metadata
subparser = subparsers.add_parser(
"metadata", help="Fetch metadata for SRA project (SRPnnnn)"
)
subparser.add_argument("--saveto", help="Save metadata dataframe to file")
subparser.add_argument(
"--assay", action="store_true", help="Include assay type in output"
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed", action="store_true", help="Display detailed metadata table"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srp_id", nargs="+")
subparser.set_defaults(func=metadata)
# pysradb download
subparser = subparsers.add_parser("download", help="Download SRA project (SRPnnnn)")
subparser.add_argument("--out-dir", help="Output directory root")
subparser.add_argument("--srx", "-x", help="Download only these SRX(s)", nargs="+")
subparser.add_argument("--srp", "-p", help="SRP ID", nargs="+")
subparser.add_argument("--geo", "-g", help="GEO ID", nargs="+")
subparser.add_argument(
"--skip-confirmation", "-y", action="store_true", help="Skip confirmation"
)
subparser.add_argument(
"--use_ascp", "-a", action="store_true", help="Use aspera instead of wget"
)
subparser.add_argument("--col", help="Specify column to download")
subparser.add_argument(
"--threads", "-t", help="Number of threads", default=1, type=int
)
subparser.set_defaults(func=download)
# pysradb search
subparser = subparsers.add_parser("search", help="Search SRA/ENA for matching text")
subparser.add_argument(
"-o", "--saveto", help="Save search result dataframe to file"
)
subparser.add_argument(
"-s",
"--stats",
action="store_true",
help="Displays some useful statistics for the search results.",
)
subparser.add_argument(
"-g",
"--graphs",
nargs="?",
const="all",
help=(
"Generates graphs to illustrate the search result. "
"By default all graphs are generated. \n"
"Alternatively, select a subset from the options below in a space-separated string:\n"
"daterange, organism, source, selection, platform, basecount"
),
)
subparser.add_argument(
"-d",
"--db",
choices=["ena", "geo", "sra"],
default="sra",
help="Select the db API (sra, ena, or geo) to query, default = sra. "
"Note: pysradb search works slightly differently when db = geo. \n"
"Please refer to 'pysradb search --geo-info' for more details.",
)
subparser.add_argument(
"-v",
"--verbosity",
choices=[0, 1, 2, 3],
default=2,
help=(
"Level of search result details (0, 1, 2 or 3), default = 2\n"
"0: run accession only\n"
"1: run accession and experiment title\n"
"2: accession numbers, titles and sequencing information\n"
"3: records in 2 and other information such as download url, sample attributes, etc"
),
type=int,
)
subparser.add_argument(
"--run-description",
action="store_true",
help="Displays run accessions and descriptions only. Equivalent to --verbosity 1",
)
subparser.add_argument(
"--detailed",
action="store_true",
help="Displays detailed search results. Equivalent to --verbosity 3.",
)
subparser.add_argument(
"-m",
"--max",
default=20,
help="Maximum number of entries to return, default = 20",
type=int,
)
subparser.add_argument(
"-q",
"--query",
nargs="+",
help="Main query string. Note that if no query is supplied, at least one of the "
"following flags must be present:",
)
subparser.add_argument("-A", "--accession", help="Accession number")
subparser.add_argument(
"-O", "--organism", nargs="+", help="Scientific name of the sample organism"
)
subparser.add_argument(
"-L",
"--layout",
choices=["SINGLE", "PAIRED"],
help="Library layout. Accepts either SINGLE or PAIRED",
type=str.upper,
)
subparser.add_argument(
"-M",
"--mbases",
help="Size of the sample rounded to the nearest megabase",
type=int,
)
subparser.add_argument(
"-D",
"--publication-date",
help="Publication date of the run in the format dd-mm-yyyy. If a date range is desired, "
"enter the start date, followed by end date, separated by a colon ':'.\n "
"Example: 01-01-2010:31-12-2010",
)
subparser.add_argument("-P", "--platform", nargs="+", help="Sequencing platform")
subparser.add_argument("-E", "--selection", nargs="+", help="Library selection")
subparser.add_argument("-C", "--source", nargs="+", help="Library source")
subparser.add_argument(
"-S", "--strategy", nargs="+", help="Library preparation strategy"
)
subparser.add_argument("-T", "--title", nargs="+", help="Experiment title")
# The following arguments are for GEO DataSets only
subparser.add_argument(
"-I",
"--geo-info",
action="store_true",
help="Displays information on how to query GEO DataSets via 'pysradb search --db geo ...', "
"including accepted inputs for -G/--geo-query, -Y/--geo-dataset-type and -Z/--geo-entry-type. ",
)
subparser.add_argument(
"-G",
"--geo-query",
nargs="+",
help="Main query string for GEO DataSet. This flag is only used when db is set to be geo."
"Please refer to 'pysradb search --geo-info' for more details.",
)
subparser.add_argument(
"-Y",
"--geo-dataset-type",
nargs="+",
help="GEO DataSet Type. This flag is only used when --db is set to be geo."
"Please refer to 'pysradb search --geo-info' for more details.",
)
subparser.add_argument(
"-Z",
"--geo-entry-type",
nargs="+",
help="GEO Entry Type. This flag is only used when --db is set to be geo."
"Please refer to 'pysradb search --geo-info' for more details.",
)
subparser.set_defaults(func=search)
# pysradb gse-to-gsm
subparser = subparsers.add_parser("gse-to-gsm", help="Get GSM for a GSE")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [sample_accession (SRS),
run_accession (SRR),
sample_alias (GSM),
run_alias (GSM_r)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("gse_ids", nargs="+")
subparser.set_defaults(func=gse_to_gsm)
# pysradb gse-to-srp
subparser = subparsers.add_parser("gse-to-srp", help="Get SRP for a GSE")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [experiment_accession (SRX),
run_accession (SRR),
sample_accession (SRS),
experiment_alias (GSM_),
run_alias (GSM_r),
sample_alias (GSM)]
""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("gse_ids", nargs="+")
subparser.set_defaults(func=gse_to_gsm)
# pysradb gsm-to-gse
subparser = subparsers.add_parser("gsm-to-gse", help="Get GSE for a GSM")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [sample_accession (SRS),
run_accession (SRR),
sample_alias (GSM),
run_alias (GSM_r)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("gsm_ids", nargs="+")
subparser.set_defaults(func=gsm_to_gse)
# pysradb gsm-to-srp
subparser = subparsers.add_parser("gsm-to-srp", help="Get SRP for a GSM")
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [experiment_accession (SRX),
sample_accession (SRS),
run_accession (SRR),
experiment_alias (GSM),
sample_alias (GSM),
run_alias (GSM_r),
study_alias (GSE)]""",
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("gsm_ids", nargs="+")
subparser.set_defaults(func=gsm_to_srp)
# pysradb gsm-to-srr
subparser = subparsers.add_parser("gsm-to-srr", help="Get SRR for a GSM")
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [experiment_accession (SRX),
sample_accession (SRS),
study_accession (SRS),
run_alias (GSM_r),
sample_alias (GSM),
study_alias (GSE)]""",
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("gsm_ids", nargs="+")
subparser.set_defaults(func=gsm_to_srr)
# pysradb gsm-to-srs
subparser = subparsers.add_parser("gsm-to-srs", help="Get SRS for a GSM")
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [experiment_accession (SRX),
run_accession (SRR),
study_accession (SRP),
run_alias (GSM_r),
experiment_alias (GSM),
study_alias (GSE)]""",
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("gsm_ids", nargs="+")
subparser.set_defaults(func=gsm_to_srs)
# pysradb gsm-to-srx
subparser = subparsers.add_parser("gsm-to-srx", help="Get SRX for a GSM")
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [experiment_accession (SRX),
sample_accession (SRS),
run_accession (SRR),
experiment_alias (GSM),
sample_alias (GSM),
run_alias (GSM_r),
study_alias (GSE)]""",
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("gsm_ids", nargs="+")
subparser.set_defaults(func=gsm_to_srx)
# pysradb srp-to-gse
subparser = subparsers.add_parser("srp-to-gse", help="Get GSE for a SRP")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="Output additional columns: [sample_accession, run_accession]",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srp_id")
subparser.set_defaults(func=srp_to_gse)
# pysradb srp-to-srr
subparser = subparsers.add_parser("srp-to-srr", help="Get SRR for a SRP")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [experiment_accession (SRX),
sample_accession (SRS),
study_alias (GSE),
experiment_alias (GSM),
sample_alias (GSM_),
run_alias (GSM_r)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srp_id")
subparser.set_defaults(func=srp_to_srr)
# pysradb srp-to-srs
subparser = subparsers.add_parser("srp-to-srs", help="Get SRS for a SRP")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [run_accession (SRR),
study_accession (SRP),
experiment_alias (GSM),
sample_alias (GSM_),
run_alias (GSM_r),
study_alias (GSE)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srp_id")
subparser.set_defaults(func=srp_to_srs)
# pysradb srp-to-srx
subparser = subparsers.add_parser("srp-to-srx", help="Get SRX for a SRP")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [sample_accession (SRS),
run_accession (SRR),
experiment_alias (GSM),
sample_alias (GSM_),
run_alias (GSM_r)',
study_alias (GSE)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srp_id")
subparser.set_defaults(func=srp_to_srx)
# pysradb srr-to-gsm
subparser = subparsers.add_parser("srr-to-gsm", help="Get GSM for a SRR")
subparser.add_argument(
"--detailed",
action="store_true",
help="""'Output additional columns: [experiment_accession (SRX),
study_accession (SRP),
run_alias (GSM_r),
sample_alias (GSM_),
experiment_alias (GSM),
study_alias (GSE)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srr_ids", nargs="+")
subparser.set_defaults(func=srr_to_gsm)
# pysradb srr-to-srp
subparser = subparsers.add_parser("srr-to-srp", help="Get SRP for a SRR")
subparser.add_argument(
"--detailed",
action="store_true",
help="""'Output additional columns: [experiment_accession (SRX),
sample_accession (SRS),
run_alias (GSM_r),
experiment_alias (GSM),
sample_alias (GSM_),
study_alias (GSE)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srr_ids", nargs="+")
subparser.set_defaults(func=srr_to_srp)
# pysradb srr-to-srs
subparser = subparsers.add_parser("srr-to-srs", help="Get SRS for a SRR")
subparser.add_argument(
"--detailed",
action="store_true",
help="""'Output additional columns: [experiment_accession (SRX),
study_accession (SRP),
run_alias (GSM_r),
sample_alias (GSM_),
experiment_alias (GSM),
study_alias (GSE)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srr_ids", nargs="+")
subparser.set_defaults(func=srr_to_srs)
# pysradb srr-to-srx
subparser = subparsers.add_parser("srr-to-srx", help="Get SRX for a SRR")
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [sample_accession (SRS),
study_accession (SRP),
run_alias (GSM_r),
experiment_alias (GSM),
sample_alias (GSM_),
study_alias (GSE)]""",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srr_ids", nargs="+")
subparser.set_defaults(func=srr_to_srx)
# pysradb srs-to-gsm
subparser = subparsers.add_parser("srs-to-gsm", help="Get GSM for a SRS")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="Output additional columns: [run_accession, study_accession]",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srs_ids", nargs="+")
subparser.set_defaults(func=srs_to_gsm)
# pysradb srs-to-srx
subparser = subparsers.add_parser("srs-to-srx", help="Get SRX for a SRS")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="Output additional columns: [run_accession, study_accession]",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srs_ids", nargs="+")
subparser.set_defaults(func=srs_to_srx)
# pysradb srx-to-srp
subparser = subparsers.add_parser("srx-to-srp", help="Get SRP for a SRX")
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed",
action="store_true",
help="""Output additional columns: [run_accession (SRR),
sample_accession (SRS),
experiment_alias (GSM),
run_alias (GSM_r),
sample_alias (GSM),
study_alias (GSE)]""",
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srx_ids", nargs="+")
subparser.set_defaults(func=srx_to_srp)
# pysradb srx-to-srr
subparser = subparsers.add_parser("srx-to-srr", help="Get SRR for a SRX")
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--detailed",
action="store_true",
help="Output additional columns: [sample_accession, study_accession]",
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srx_ids", nargs="+")
subparser.set_defaults(func=srx_to_srr)
# pysradb srx-to-srs
subparser = subparsers.add_parser("srx-to-srs", help="Get SRS for a SRX")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument(
"--detailed",
action="store_true",
help="Output additional columns: [run_accession, study_accession]",
)
subparser.add_argument(
"--desc", action="store_true", help="Should sample_attribute be included"
)
subparser.add_argument(
"--expand", action="store_true", help="Should sample_attribute be expanded"
)
subparser.add_argument("srx_ids", nargs="+")
subparser.set_defaults(func=srx_to_srs)
args = parser.parse_args(args=None if sys.argv[1:] else ["--help"])
if args.command == "metadata":
metadata(
args.srp_id,
args.assay,
args.desc,
args.detailed,
args.expand,
args.saveto,
)
elif args.command == "download":
download(
args.out_dir,
args.srx,
args.srp,
args.geo,
args.skip_confirmation,
args.col,
args.use_ascp,
args.threads,
)
elif args.command == "search":
flags = vars(args)
if flags.pop("geo_info"):
get_geo_search_info()
else:
search(
flags.pop("saveto"),
flags.pop("db"),
flags.pop("verbosity"),
flags.pop("max"),
flags,
)
elif args.command == "gse-to-gsm":
gse_to_gsm(args.gse_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "gse-to-srp":
gse_to_srp(args.gse_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "gsm-to-gse":
gsm_to_gse(args.gsm_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "gsm-to-srp":
gsm_to_srp(args.gsm_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "gsm-to-srr":
gsm_to_srr(args.gsm_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "gsm-to-srs":
gsm_to_srs(args.gsm_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "gsm-to-srx":
gsm_to_srx(args.gsm_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srp-to-gse":
srp_to_gse(args.srp_id, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srp-to-srr":
srp_to_srr(args.srp_id, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srp-to-srs":
srp_to_srs(args.srp_id, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srp-to-srx":
srp_to_srx(args.srp_id, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srr-to-gsm":
srr_to_gsm(args.srr_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srr-to-srp":
srr_to_srp(args.srr_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srr-to-srs":
srr_to_srs(args.srr_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srr-to-srx":
srr_to_srx(args.srr_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srs-to-gsm":
srs_to_gsm(args.srs_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srs-to-srx":
srs_to_srx(args.srs_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srx-to-srp":
srx_to_srp(args.srx_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srx-to-srr":
srx_to_srr(args.srx_ids, args.saveto, args.detailed, args.desc, args.expand)
elif args.command == "srx-to-srs":
srx_to_srs(args.srx_ids, args.saveto, args.detailed, args.desc, args.expand)
if __name__ == "__main__":
parse_args(sys.argv[1:])