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Merge pull request #9 from compomics/fix-no-write-output
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Fix write_output=False bug
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@rodvrees
rodvrees authored Feb 27, 2025
2 parents c5a1a81 + 5400864 commit 95ca902
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Showing 2 changed files with 81 additions and 77 deletions.
2 changes: 1 addition & 1 deletion im2deep/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
"""IM2Deep: Deep learning framework for peptide collisional cross section prediction."""

__version__ = "1.0.1"
__version__ = "1.0.2"
156 changes: 80 additions & 76 deletions im2deep/im2deep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,83 +71,87 @@ def predict_ccs(
use_charge_state,
)

if write_output:
LOGGER.info("Writing output file...")
output_file = open(output_file, "w")
if ion_mobility:
if not multi:
if not ion_mobility:
output_file.write("modified_seq,charge,predicted CCS\n")
for peptidoform, charge, CCS in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_ccs"],
):
output_file.write(f"{peptidoform},{charge},{CCS}\n")
output_file.close()
else:
LOGGER.info("Converting CCS to IM values...")
psm_list_pred_df["predicted_im"] = ccs2im(
psm_list_pred_df["predicted_ccs"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
LOGGER.info("Writing output file...")
output_file = open(output_file, "w")
output_file.write("modified_seq,charge,predicted IM\n")
for peptidoform, charge, IM in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_im"],
):
output_file.write(f"{peptidoform},{charge},{IM}\n")
output_file.close()
psm_list_pred_df["predicted_im"] = ccs2im(
psm_list_pred_df["predicted_ccs"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
if write_output:
LOGGER.info("Writing output file for ion mobility prediction...")
with open(output_file, "w") as f:
f.write("modified_seq,charge,predicted IM\n")
for peptidoform, charge, IM in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_im"],
):
f.write(f"{peptidoform},{charge},{IM}\n")
LOGGER.info("IM2Deep finished!")
return psm_list_pred_df["predicted_im"]
else:
if not ion_mobility:
output_file.write(
"modified_seq,charge,predicted CCS single,predicted CCS multi 1,predicted CCS multi 2\n"
)
for peptidoform, charge, CCS_single, CCS_multi_1, CCS_multi_2 in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_ccs"],
pred_df["predicted_ccs_multi_1"],
pred_df["predicted_ccs_multi_2"],
):
output_file.write(
f"{peptidoform},{charge},{CCS_single},{CCS_multi_1},{CCS_multi_2}\n"
psm_list_pred_df["predicted_im"] = ccs2im(
psm_list_pred_df["predicted_ccs"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
psm_list_pred_df["predicted_im_multi_1"] = ccs2im(
pred_df["predicted_ccs_multi_1"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
psm_list_pred_df["predicted_im_multi_2"] = ccs2im(
pred_df["predicted_ccs_multi_2"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
if write_output:
LOGGER.info("Writing output file for multi-ion mobility prediction...")
with open(output_file, "w") as f:
f.write(
"modified_seq,charge,predicted IM single,predicted IM multi 1,predicted IM multi 2\n"
)
else:
LOGGER.info("Converting CCS to IM values...")
psm_list_pred_df["predicted_im_multi_1"] = ccs2im(
pred_df["predicted_ccs_multi_1"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
psm_list_pred_df["predicted_im_multi_2"] = ccs2im(
pred_df["predicted_ccs_multi_2"],
psm_list_pred_df["peptidoform"].apply(lambda x: x.theoretical_mz),
psm_list_pred_df["charge"],
)
LOGGER.info("Writing output file...")
output_file = open(output_file, "w")
output_file.write(
"modified_seq,charge,predicted IM single,predicted IM multi 1,predicted IM multi 2\n"
)
for peptidoform, charge, IM_single, IM_multi_1, IM_multi_2 in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_im"],
psm_list_pred_df["predicted_im_multi_1"],
psm_list_pred_df["predicted_im_multi_2"],
):
output_file.write(
f"{peptidoform},{charge},{IM_single},{IM_multi_1},{IM_multi_2}\n"
)
output_file.close()

LOGGER.info("IM2Deep finished!")

if not ion_mobility:
return psm_list_pred_df["predicted_ccs"]
for peptidoform, charge, IM_single, IM_multi_1, IM_multi_2 in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_im"],
psm_list_pred_df["predicted_im_multi_1"],
psm_list_pred_df["predicted_im_multi_2"],
):
f.write(f"{peptidoform},{charge},{IM_single},{IM_multi_1},{IM_multi_2}\n")
LOGGER.info("IM2Deep finished!")
return psm_list_pred_df["predicted_im"]
else:
return psm_list_pred_df["predicted_im"]
if not multi:
if write_output:
LOGGER.info("Writing output file for CCS prediction...")
with open(output_file, "w") as f:
f.write("modified_seq,charge,predicted CCS\n")
for peptidoform, charge, CCS in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_ccs"],
):
f.write(f"{peptidoform},{charge},{CCS}\n")
LOGGER.info("IM2Deep finished!")
return psm_list_pred_df["predicted_ccs"]
else:
if write_output:
LOGGER.info("Writing output file for multi-CCS prediction...")
with open(output_file, "w") as f:
f.write(
"modified_seq,charge,predicted CCS single,predicted CCS multi 1,predicted CCS multi 2\n"
)
for peptidoform, charge, CCS_single, CCS_multi_1, CCS_multi_2 in zip(
psm_list_pred_df["peptidoform"],
psm_list_pred_df["charge"],
psm_list_pred_df["predicted_ccs"],
pred_df["predicted_ccs_multi_1"],
pred_df["predicted_ccs_multi_2"],
):
f.write(
f"{peptidoform},{charge},{CCS_single},{CCS_multi_1},{CCS_multi_2}\n"
)
LOGGER.info("IM2Deep finished!")
return psm_list_pred_df["predicted_ccs"]

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