Source code for pyXLMS.exporter._to_xlinkdb
#!/usr/bin/env python3
# 2025 (c) Micha Johannes Birklbauer
# https://github.com/michabirklbauer/
# micha.birklbauer@gmail.com
from __future__ import annotations
import pandas as pd
from ..data._crosslink import Crosslink
from ..data._util import check_input
from ..transform._util import check_available_keys
from ._util import __get_filename
from typing import Optional
from typing import List
def __xls_to_xlinkdb(
xls: List[Crosslink],
filename: Optional[str],
) -> pd.DataFrame:
r"""Exports crosslinks to XLinkDB format.
Parameters
----------
xls : list of Crosslink
A list of crosslinks.
filename : str, or None
If not None, the data will be written to a file with the specified filename.
Returns
-------
pd.DataFrame
A pandas DataFrame in XLinkDB format.
Notes
-----
This function should not be called directly, it is called from ``to_xlinkdb()``.
"""
peptide_a = list()
protein_a = list()
labeled_position_a = list()
peptide_b = list()
protein_b = list()
labeled_position_b = list()
probability = list()
for xl in xls:
peptide_a.append(xl["alpha_peptide"])
protein_a.append(xl["alpha_proteins"][0])
labeled_position_a.append(xl["alpha_peptide_crosslink_position"] - 1)
peptide_b.append(xl["beta_peptide"])
protein_b.append(xl["beta_proteins"][0])
labeled_position_b.append(xl["beta_peptide_crosslink_position"] - 1)
probability.append(1)
xlinkdb_df = pd.DataFrame(
{
"Peptide A": peptide_a,
"Protein A": protein_a,
"Labeled Position A": labeled_position_a,
"Peptide B": peptide_b,
"Protein B": protein_b,
"Labeled Position B": labeled_position_b,
"Probability": probability,
}
)
if filename is not None:
xlinkdb_df.to_csv(
__get_filename(filename, "tsv"), sep="\t", header=False, index=False
)
return xlinkdb_df
[docs]
def to_xlinkdb(
crosslinks: List[Crosslink],
filename: Optional[str],
) -> pd.DataFrame:
r"""Exports a list of crosslinks to XLinkDB format.
Exports a list of crosslinks to XLinkDB format. The tool XLinkDB is accessible
via the link
`xlinkdb.gs.washington.edu/xlinkdb <https://xlinkdb.gs.washington.edu/xlinkdb/index.php>`_.
Requires that ``alpha_proteins`` and ``beta_proteins`` fields are set for all crosslinks.
Parameters
----------
crosslinks : list of Crosslink
A list of crosslinks.
filename : str, or None
If not None, the exported data will be written to a file with the specified filename.
The filename should not contain a file extension and consist only of alpha-numeric
characters (a-Z, 0-9).
Returns
-------
pd.DataFrame
A pandas DataFrame containing crosslinks in XLinkDB format.
Raises
------
TypeError
If a wrong data type is provided.
TypeError
If 'crosslinks' parameter contains elements of mixed data type.
ValueError
If the filename contains any non-alpha-numeric characters.
ValueError
If the provided 'crosslinks' parameter contains no elements.
RuntimeError
If not all of the required information is present in the input data.
Notes
-----
XLinkDB input format requires a column with probabilities that the crosslinks are correct. Since that is not available
from most crosslink search engines, this is simply set to a constant ``1``.
Examples
--------
>>> from pyXLMS.exporter import to_xlinkdb
>>> from pyXLMS.parser import read
>>> pr = read(
... "data/xi/1perc_xl_boost_Links_xiFDR2.2.1.csv",
... engine="xiSearch/xiFDR",
... crosslinker="DSS",
... )
>>> crosslinks = pr["crosslinks"]
>>> to_xlinkdb(crosslinks, filename="crosslinksForXLinkDB")
Peptide A Protein A Labeled Position A Peptide B Protein B Labeled Position B Probability
0 VVDELVKVMGR Cas9 6 VVDELVKVMGR Cas9 6 1
1 MLASAGELQKGNELALPSK Cas9 9 VVDELVKVMGR Cas9 6 1
2 MDGTEELLVKLNR Cas9 9 MDGTEELLVKLNR Cas9 9 1
3 MTNFDKNLPNEK Cas9 5 SKLVSDFR Cas9 1 1
4 DFQFYKVR Cas9 5 MIAKSEQEIGK Cas9 3 1
.. ... ... ... ... ... ... ...
222 LPKYSLFELENGR Cas9 2 SDKNR Cas9 2 1
223 DKQSGK Cas9 1 DKQSGK Cas9 1 1
224 AGFIKR Cas9 4 SDNVPSEEVVKK Cas9 10 1
225 EKIEK Cas9 1 KVTVK Cas9 0 1
226 LSKSR Cas9 2 LSKSR Cas9 2 1
[227 rows x 7 columns]
>>> from pyXLMS.exporter import to_xlinkdb
>>> from pyXLMS.parser import read
>>> pr = read(
... "data/xi/1perc_xl_boost_Links_xiFDR2.2.1.csv",
... engine="xiSearch/xiFDR",
... crosslinker="DSS",
... )
>>> crosslinks = pr["crosslinks"]
>>> df = to_xlinkdb(crosslinks, filename=None)
"""
_ok = check_input(crosslinks, "crosslinks", list, Crosslink)
_ok = check_input(filename, "filename", str) if filename is not None else True
if filename is not None and not filename.isalnum():
raise ValueError(
"Parameter filename must only contain alpha-numeric characters and no file extension!"
)
if len(crosslinks) == 0:
raise ValueError("Provided crosslinks contain no elements!")
_ok = check_available_keys(["alpha_proteins", "beta_proteins"], crosslinks)
return __xls_to_xlinkdb(crosslinks, filename)
