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@ammarcsj
ammarcsj committed Oct 16, 2024
1 parent 5fe8d33 commit 27dae16
Showing 1 changed file with 183 additions and 14 deletions.
197 changes: 183 additions & 14 deletions tests/quicktests/run_pipeline_w_different_input_formats.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,39 @@
"cells": [
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"../../test_data/system_tests/quicktests does not yet exist\n",
"quicktests.zip successfully downloaded to ../../test_data/system_tests/quicktests.zip\n",
"quicktests.zip successfully unzipped\n"
]
},
{
"data": {
"text/plain": [
"'../../test_data/system_tests/quicktests'"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import alphabase\n",
"import alphabase.test_data_downloader\n",
"\n",
"alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=\"../../test_data/system_tests\").download()"
"alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=\"test_data/system_tests\").download()"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -31,9 +51,25 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-10-16 15:35:28,476 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:28,557 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n",
"2024-10-16 15:35:28,678 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:29,872 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:29,873 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
"2024-10-16 15:35:29,889 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:30,778 - directlfq.lfq_manager - INFO - Could not add additional columns to protein table, printing without additional columns.\n",
"2024-10-16 15:35:30,779 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:30,826 - directlfq.lfq_manager - INFO - Analysis finished!\n"
]
}
],
"source": [
"import directlfq.lfq_manager as lfq_manager\n",
"diann_quicktest_file_parquet = f\"{quicktest_folder_diann}/shortened_input.parquet\"\n",
Expand All @@ -43,9 +79,61 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-10-16 15:35:30,839 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:31,025 - directlfq.utils - INFO - using input type diann_precursors\n",
"2024-10-16 15:35:31,077 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:31,078 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n",
"2024-10-16 15:35:31,082 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:31,082 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
"2024-10-16 15:35:31,098 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:31,623 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:31,634 - directlfq.lfq_manager - INFO - Analysis finished!\n",
"2024-10-16 15:35:31,635 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:31,703 - directlfq.utils - INFO - using input type diann_peptide_based_on_precursor_ms1_and_ms2\n",
"2024-10-16 15:35:31,822 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:31,827 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:31,827 - directlfq.protein_intensity_estimation - INFO - 840 lfq-groups total\n",
"2024-10-16 15:35:32,152 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
"2024-10-16 15:35:32,173 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:32,237 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n",
"2024-10-16 15:35:32,298 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n",
"2024-10-16 15:35:32,443 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n",
"2024-10-16 15:35:32,492 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n",
"2024-10-16 15:35:32,554 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n",
"2024-10-16 15:35:32,609 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n",
"2024-10-16 15:35:32,710 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n",
"2024-10-16 15:35:32,771 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n",
"2024-10-16 15:35:32,976 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:33,004 - directlfq.lfq_manager - INFO - Analysis finished!\n",
"2024-10-16 15:35:33,006 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:33,077 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n",
"2024-10-16 15:35:33,179 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:33,184 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:33,185 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
"2024-10-16 15:35:33,280 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
"2024-10-16 15:35:33,289 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:33,610 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:33,630 - directlfq.lfq_manager - INFO - Analysis finished!\n",
"2024-10-16 15:35:33,632 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:33,702 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n",
"2024-10-16 15:35:33,780 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:33,786 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:33,787 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
"2024-10-16 15:35:33,885 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
"2024-10-16 15:35:33,895 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:34,274 - directlfq.lfq_manager - INFO - Could not add additional columns to protein table, printing without additional columns.\n",
"2024-10-16 15:35:34,275 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:34,334 - directlfq.lfq_manager - INFO - Analysis finished!\n"
]
}
],
"source": [
"# run diann\n",
"import directlfq.lfq_manager as lfq_manager\n",
Expand All @@ -64,9 +152,25 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-10-16 15:35:34,343 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:34,488 - directlfq.utils - INFO - using input type maxquant_peptides_leading_razor_protein\n",
"2024-10-16 15:35:34,533 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:34,535 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n",
"2024-10-16 15:35:34,541 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:34,542 - directlfq.protein_intensity_estimation - INFO - 49 lfq-groups total\n",
"2024-10-16 15:35:34,558 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:35,042 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:35,054 - directlfq.lfq_manager - INFO - Analysis finished!\n"
]
}
],
"source": [
"#run mq peptides\n",
"\n",
Expand All @@ -82,9 +186,35 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-10-16 15:35:35,061 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:35,240 - directlfq.utils - INFO - using input type maxquant_evidence_leading_razor_protein\n",
"2024-10-16 15:35:35,324 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:35,326 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n",
"2024-10-16 15:35:35,332 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:35,332 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
"2024-10-16 15:35:35,424 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
"2024-10-16 15:35:35,433 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:35,723 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:35,738 - directlfq.lfq_manager - INFO - Analysis finished!\n",
"2024-10-16 15:35:35,739 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:35,875 - directlfq.utils - INFO - using input type maxquant_evidence_leading_razor_protein\n",
"2024-10-16 15:35:35,960 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:35,961 - root - INFO - Normalizing only selected proteins\n",
"2024-10-16 15:35:35,968 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:35,969 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
"2024-10-16 15:35:35,986 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:36,558 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:36,573 - directlfq.lfq_manager - INFO - Analysis finished!\n"
]
}
],
"source": [
"#run mq evidence\n",
"\n",
Expand All @@ -100,9 +230,34 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-10-16 15:35:36,580 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:36,757 - directlfq.utils - INFO - using input type spectronaut_fragion_isotopes\n",
"2024-10-16 15:35:37,122 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:37,123 - root - INFO - Normalizing only selected proteins\n",
"2024-10-16 15:35:37,134 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:37,135 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
"2024-10-16 15:35:37,155 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:38,484 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:38,510 - directlfq.lfq_manager - INFO - Analysis finished!\n",
"2024-10-16 15:35:38,511 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
"2024-10-16 15:35:38,648 - directlfq.utils - INFO - using input type spectronaut_fragion_isotopes\n",
"2024-10-16 15:35:39,003 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
"2024-10-16 15:35:39,011 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
"2024-10-16 15:35:39,012 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
"2024-10-16 15:35:39,103 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
"2024-10-16 15:35:39,111 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
"2024-10-16 15:35:39,539 - directlfq.lfq_manager - INFO - Writing results files.\n",
"2024-10-16 15:35:39,566 - directlfq.lfq_manager - INFO - Analysis finished!\n"
]
}
],
"source": [
"# run spectronaut\n",
"import directlfq.lfq_manager as lfq_manager\n",
Expand All @@ -113,6 +268,20 @@
" lfq_manager.run_lfq(spectronaut_quicktest_file, selected_proteins_file=spectronaut_protein_subset, num_cores=1, compile_normalized_ion_table=True)\n",
" lfq_manager.run_lfq(spectronaut_quicktest_file)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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