"""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, MissingQueryException
from .geodb import download_geo_matrix, parse_geo_matrix_to_tsv
from .geoweb import GEOweb
from .search import EnaSearch, GeoSearch, SraSearch
from .sradb import SRAdb, download_sradb_file
from .sraweb import SRAweb
from .utils import confirm
pd.set_option("display.max_rows", None)
pd.set_option("display.max_columns", None)
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)
[docs]
def pretty_print_df(df, include_header=True):
"""Pretty print"""
def format_value(v):
"""Convert value to string, handling None and pd.NA"""
if v is None or pd.isna(v):
return "-"
return str(v)
if include_header:
print("\t".join(map(str, list(df.columns))))
for index, row in df.iterrows():
print("\t".join(map(format_value, row.tolist())))
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 df is None:
print
elif len(df.index):
pretty_print_df(df)
###################### metadata ##############################
################################################################
################# download ##########################
[docs]
def download(
out_dir,
srx,
srp,
geo,
skip_confirmation,
col="public_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
# TODO: at some point, we need to fix this
if not srp and not geo:
df = pd.read_csv(sys.stdin, 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 srp_to_pmid(srp_ids, saveto):
sradb = SRAweb()
df = sradb.srp_to_pmid(srp_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def sra_to_pmid(sra_ids, saveto):
"""Backward compatibility wrapper for sra_to_pmid"""
sradb = SRAweb()
df = sradb.sra_to_pmid(sra_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def gse_to_pmid(gse_ids, saveto):
sradb = SRAweb()
df = sradb.gse_to_pmid(gse_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def pmid_to_gse(pmid_ids, saveto):
sradb = SRAweb()
df = sradb.pmid_to_gse(pmid_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def pmid_to_srp(pmid_ids, saveto):
sradb = SRAweb()
df = sradb.pmid_to_srp(pmid_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def pmc_to_identifiers(pmc_ids, saveto):
sradb = SRAweb()
df = sradb.pmc_to_identifiers(pmc_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def pmid_to_identifiers(pmid_ids, saveto):
sradb = SRAweb()
df = sradb.pmid_to_identifiers(pmid_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def doi_to_gse(doi_ids, saveto):
sradb = SRAweb()
df = sradb.doi_to_gse(doi_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def doi_to_srp(doi_ids, saveto):
sradb = SRAweb()
df = sradb.doi_to_srp(doi_ids)
_print_save_df(df, saveto)
sradb.close()
[docs]
def doi_to_identifiers(doi_ids, saveto):
sradb = SRAweb()
df = sradb.doi_to_identifiers(doi_ids)
_print_save_df(df, saveto)
sradb.close()
#########################################################################
########################### geo-matrix ##################################
[docs]
def geo_matrix(accession, to_tsv, output_dir):
# Download the GEO Matrix file
matrix_file = download_geo_matrix(accession, output_dir=output_dir)
print(f"Downloaded GEO Matrix file to: {matrix_file}")
# If --to-tsv is specified, parse the file to TSV
if to_tsv:
output_tsv = os.path.join(output_dir, f"{accession}_matrix.tsv")
df = parse_geo_matrix_to_tsv(matrix_file, output_tsv)
print(f"Parsed GEO Matrix file to TSV: {output_tsv}")
#########################################################################
[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", default="public_url"
)
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 (SRP),
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)
# pysradb geo-matrix
subparser = subparsers.add_parser(
"geo-matrix", help="Download and parse GEO Matrix files"
)
subparser.add_argument(
"--accession", required=True, help="GEO accession (e.g., GSE234190)"
)
subparser.add_argument(
"--to-tsv", action="store_true", help="Convert the matrix file to TSV format"
)
subparser.add_argument(
"--output-dir",
default=".",
help="Output directory (default: current directory)",
)
subparser.set_defaults(func=geo_matrix)
# pysradb srp-to-pmid
subparser = subparsers.add_parser(
"srp-to-pmid", help="Get PMIDs for SRP accessions"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("srp_ids", nargs="+", help="SRP accession(s)")
subparser.set_defaults(func=srp_to_pmid)
# pysradb gse-to-pmid
subparser = subparsers.add_parser(
"gse-to-pmid", help="Get PMIDs for GSE accessions"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("gse_ids", nargs="+", help="GSE accession(s)")
subparser.set_defaults(func=gse_to_pmid)
# pysradb pmid-to-gse
subparser = subparsers.add_parser(
"pmid-to-gse", help="Get GSE accessions from PMIDs"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("pmid_ids", nargs="+", help="PMID(s)")
subparser.set_defaults(func=pmid_to_gse)
# pysradb pmid-to-srp
subparser = subparsers.add_parser(
"pmid-to-srp", help="Get SRP accessions from PMIDs"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("pmid_ids", nargs="+", help="PMID(s)")
subparser.set_defaults(func=pmid_to_srp)
# pysradb pmc-to-identifiers
subparser = subparsers.add_parser(
"pmc-to-identifiers", help="Extract database identifiers from PMC articles"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("pmc_ids", nargs="+", help="PMC ID(s)")
subparser.set_defaults(func=pmc_to_identifiers)
# pysradb pmid-to-identifiers
subparser = subparsers.add_parser(
"pmid-to-identifiers", help="Extract database identifiers from PubMed articles"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("pmid_ids", nargs="+", help="PMID(s)")
subparser.set_defaults(func=pmid_to_identifiers)
# pysradb doi-to-gse
subparser = subparsers.add_parser("doi-to-gse", help="Get GSE accessions from DOIs")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("doi_ids", nargs="+", help="DOI(s)")
subparser.set_defaults(func=doi_to_gse)
# pysradb doi-to-srp
subparser = subparsers.add_parser("doi-to-srp", help="Get SRP accessions from DOIs")
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("doi_ids", nargs="+", help="DOI(s)")
subparser.set_defaults(func=doi_to_srp)
# pysradb doi-to-identifiers
subparser = subparsers.add_parser(
"doi-to-identifiers", help="Extract database identifiers from articles via DOI"
)
subparser.add_argument("--saveto", help="Save output to file")
subparser.add_argument("doi_ids", nargs="+", help="DOI(s)")
subparser.set_defaults(func=doi_to_identifiers)
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)
elif args.command == "geo-matrix":
geo_matrix(args.accession, args.to_tsv, args.output_dir)
elif args.command == "srp-to-pmid":
srp_to_pmid(args.srp_ids, args.saveto)
elif args.command == "gse-to-pmid":
gse_to_pmid(args.gse_ids, args.saveto)
elif args.command == "pmid-to-gse":
pmid_to_gse(args.pmid_ids, args.saveto)
elif args.command == "pmid-to-srp":
pmid_to_srp(args.pmid_ids, args.saveto)
elif args.command == "pmc-to-identifiers":
pmc_to_identifiers(args.pmc_ids, args.saveto)
elif args.command == "pmid-to-identifiers":
pmid_to_identifiers(args.pmid_ids, args.saveto)
elif args.command == "doi-to-gse":
doi_to_gse(args.doi_ids, args.saveto)
elif args.command == "doi-to-srp":
doi_to_srp(args.doi_ids, args.saveto)
elif args.command == "doi-to-identifiers":
doi_to_identifiers(args.doi_ids, args.saveto)
if __name__ == "__main__":
parse_args(sys.argv[1:])
