From 7caba48a4e77d2c7a5e8f379d0dbcbf216b6a496 Mon Sep 17 00:00:00 2001
From: LauraU123 <laura.urbanska@stud.unibas.ch>
Date: Mon, 21 Nov 2022 15:24:48 +0100
Subject: [PATCH] fixed typos
---
.../match_reprtranscript_expressionlevel.py | 4 +-
scripts/new_exe_file.ipynb | 62 ++++++++++---------
2 files changed, 34 insertions(+), 32 deletions(-)
diff --git a/scripts/match_reprtranscript_expressionlevel.py b/scripts/match_reprtranscript_expressionlevel.py
index 2dfca50..8654850 100644
--- a/scripts/match_reprtranscript_expressionlevel.py
+++ b/scripts/match_reprtranscript_expressionlevel.py
@@ -2,7 +2,7 @@
import pandas as pd
import json
import re
-import rerpresentative_v4 as repr
+import representative as repr
import os
@@ -197,4 +197,4 @@ print("this is the function :\n\n {}".format(match_final))
if __name__ == "__main__":
match_reprTranscript_expressionLevel()
-
\ No newline at end of file
+
diff --git a/scripts/new_exe_file.ipynb b/scripts/new_exe_file.ipynb
index c79b091..5ff4ae1 100644
--- a/scripts/new_exe_file.ipynb
+++ b/scripts/new_exe_file.ipynb
@@ -2,50 +2,31 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 11,
"metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "usage: ipykernel_launcher.py [-h] --annotation ANNOTATION --expression_level\n",
- " EXPRESSION_LEVEL --output_csv OUTPUT_CSV\n",
- " --output_gtf OUTPUT_GTF --transcript_number\n",
- " TRANSCRIPT_NUMBER\n",
- "ipykernel_launcher.py: error: the following arguments are required: --annotation, --expression_level, --output_csv, --output_gtf, --transcript_number\n"
- ]
- },
- {
- "ename": "SystemExit",
- "evalue": "2",
+ "ename": "ModuleNotFoundError",
+ "evalue": "No module named 'rerpresentative_v4'",
"output_type": "error",
"traceback": [
- "An exception has occurred, use %tb to see the full traceback.\n",
- "\u001b[0;31mSystemExit\u001b[0m\u001b[0;31m:\u001b[0m 2\n"
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb Cell 1\u001b[0m in \u001b[0;36m<cell line: 7>\u001b[0;34m()\u001b[0m\n\u001b[1;32m <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=4'>5</a>\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mpoisson_sampling\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mps\u001b[39;00m\n\u001b[1;32m <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=5'>6</a>\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mwritegtf\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mgt\u001b[39;00m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=6'>7</a>\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mmatch_reprtranscript_expressionlevel\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mma\u001b[39;00m\n\u001b[1;32m <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=9'>10</a>\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mexe\u001b[39m(input_file, csv, gtf, transcript_nr):\n\u001b[1;32m <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=10'>11</a>\u001b[0m file_name,source_pathway_name_2,deposit_pathway_name_2 \u001b[39m=\u001b[39m te\u001b[39m.\u001b[39mextract_transcript(input_file, deposit_pathway_name \u001b[39m=\u001b[39m \u001b[39mTrue\u001b[39;00m, Input_free \u001b[39m=\u001b[39m Input_free)\n",
+ "File \u001b[0;32m~/code/transcript-sampler/scripts/match_reprtranscript_expressionlevel.py:5\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mjson\u001b[39;00m\n\u001b[1;32m 4\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mre\u001b[39;00m\n\u001b[0;32m----> 5\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mrerpresentative_v4\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mrepr\u001b[39;00m\n\u001b[1;32m 6\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mos\u001b[39;00m\n\u001b[1;32m 9\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mdict_reprTrans_to_df\u001b[39m(dict_reprTrans: \u001b[39mdict\u001b[39m):\n",
+ "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'rerpresentative_v4'"
]
}
],
"source": [
- "import os\n",
- "\n",
"import argparse\n",
"import transcript_extractor as te\n",
"import exon_length_filter as elf\n",
"import representative as rtcl\n",
- "import representative as rp\n",
+ "import poisson_sampling as ps\n",
+ "import writegtf as gt\n",
+ "import match_reprtranscript_expressionlevel as ma\n",
"\n",
- "if __name__ == '__main__':\n",
- " parser = argparse.ArgumentParser(\n",
- " description=\"transcript sampler\",\n",
- " formatter_class=argparse.ArgumentDefaultsHelpFormatter\n",
- " )\n",
- " parser.add_argument(\"--annotation\", required=True, help=\"gtf file with genome annotation\")\n",
- " #parser.add_argument(\"--expression_level\", required=True, help=\"csv file with expression level\")\n",
- " parser.add_argument(\"--output_csv\", required=True, help=\"output csv file\")\n",
- " parser.add_argument(\"--output_gtf\", required=True, help=\"output gtf file\")\n",
- " parser.add_argument(\"--transcript_number\", required=True, help=\"total number of transcripts to sample\")\n",
- " args = parser.parse_args()\n",
"\n",
"def exe(input_file, csv, gtf, transcript_nr):\n",
" file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, deposit_pathway_name = True, Input_free = Input_free)\n",
@@ -58,6 +39,27 @@
" print(\"Transcripts filtered\\n\")\n",
" elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = True)\n",
"\n",
+ " tsv_input = ma.output_tsv()\n",
+ " print(\"Poisson sampling of transcripts\")\n",
+ " ps.transcript_sampling(transcript_nr, tsv_input, csv)\n",
+ " print(\"output csv file ready\")\n",
+ " \n",
+ " print(\"writing output gtf file\")\n",
+ " gt.gtf_file_writer(input_file, csv, gtf)\n",
+ "\n",
+ "\n",
+ "\n",
+ "if __name__ == '__main__':\n",
+ " parser = argparse.ArgumentParser(\n",
+ " description=\"transcript sampler\",\n",
+ " formatter_class=argparse.ArgumentDefaultsHelpFormatter\n",
+ " )\n",
+ " parser.add_argument(\"--annotation\", required=True, help=\"gtf file with genome annotation\")\n",
+ " parser.add_argument(\"--output_csv\", required=True, help=\"output csv file\")\n",
+ " parser.add_argument(\"--output_gtf\", required=True, help=\"output gtf file\")\n",
+ " parser.add_argument(\"--transcript_number\", required=True, help=\"total number of transcripts to sample\")\n",
+ " args = parser.parse_args()\n",
+ " exe(args.annotation, args.output_csv, args.output_gtf, args.transcript_nr)\n",
"\n",
" #return(file_name,source_pathway_name,deposit_pathway_name)\n",
"\n"
--
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