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Commit 7caba48a authored by Laura Urbanska's avatar Laura Urbanska
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fixed typos

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scripts/match_reprtranscript_expressionlevel.py
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View file @ 7caba48a
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
import pandas as pd import pandas as pd
import json import json
import re import re
import rerpresentative_v4 as repr import representative as repr
import os import os
...@@ -197,4 +197,4 @@ print("this is the function :\n\n {}".format(match_final)) ...@@ -197,4 +197,4 @@ print("this is the function :\n\n {}".format(match_final))
if __name__ == "__main__": if __name__ == "__main__":
match_reprTranscript_expressionLevel() match_reprTranscript_expressionLevel()
\ No newline at end of file
scripts/new_exe_file.ipynb
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− 30
View file @ 7caba48a
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
import os
import argparse import argparse
import transcript_extractor as te import transcript_extractor as te
import exon_length_filter as elf import exon_length_filter as elf
import representative as rtcl import representative as rtcl
import representative as rp import poisson_sampling as ps
import writegtf as gt
import match_reprtranscript_expressionlevel as ma
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="transcript sampler",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument("--annotation", required=True, help="gtf file with genome annotation")
#parser.add_argument("--expression_level", required=True, help="csv file with expression level")
parser.add_argument("--output_csv", required=True, help="output csv file")
parser.add_argument("--output_gtf", required=True, help="output gtf file")
parser.add_argument("--transcript_number", required=True, help="total number of transcripts to sample")
args = parser.parse_args()
def exe(input_file, csv, gtf, transcript_nr): def exe(input_file, csv, gtf, transcript_nr):
file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, deposit_pathway_name = True, Input_free = Input_free) file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, deposit_pathway_name = True, Input_free = Input_free)
inter_mediate_file_directory = input_file +"_intermediate_file.txt" inter_mediate_file_directory = input_file +"_intermediate_file.txt"
print("Transcripts are filtered based on transcript score. Please wait...") print("Transcripts are filtered based on transcript score. Please wait...")
pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory) pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory)
print("Transcripts filtered\n") print("Transcripts filtered\n")
elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = True) elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = True)
tsv_input = ma.output_tsv()
print("Poisson sampling of transcripts")
ps.transcript_sampling(transcript_nr, tsv_input, csv)
print("output csv file ready")
print("writing output gtf file")
gt.gtf_file_writer(input_file, csv, gtf)
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="transcript sampler",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument("--annotation", required=True, help="gtf file with genome annotation")
parser.add_argument("--output_csv", required=True, help="output csv file")
parser.add_argument("--output_gtf", required=True, help="output gtf file")
parser.add_argument("--transcript_number", required=True, help="total number of transcripts to sample")
args = parser.parse_args()
exe(args.annotation, args.output_csv, args.output_gtf, args.transcript_nr)
#return(file_name,source_pathway_name,deposit_pathway_name) #return(file_name,source_pathway_name,deposit_pathway_name)
``` ```
%% Output %% Output
usage: ipykernel_launcher.py [-h] --annotation ANNOTATION --expression_level ---------------------------------------------------------------------------
EXPRESSION_LEVEL --output_csv OUTPUT_CSV ModuleNotFoundError Traceback (most recent call last)
--output_gtf OUTPUT_GTF --transcript_number /home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb Cell 1 in <cell line: 7>()
TRANSCRIPT_NUMBER <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=4'>5</a> import poisson_sampling as ps
ipykernel_launcher.py: error: the following arguments are required: --annotation, --expression_level, --output_csv, --output_gtf, --transcript_number <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=5'>6</a> import writegtf as gt
----> <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=6'>7</a> import match_reprtranscript_expressionlevel as ma
An exception has occurred, use %tb to see the full traceback. <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=9'>10</a> def exe(input_file, csv, gtf, transcript_nr):
SystemExit: 2 <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=10'>11</a> file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, deposit_pathway_name = True, Input_free = Input_free)
File ~/code/transcript-sampler/scripts/match_reprtranscript_expressionlevel.py:5, in <module>
3 import json
4 import re
----> 5 import rerpresentative_v4 as repr
6 import os
9 def dict_reprTrans_to_df(dict_reprTrans: dict):
ModuleNotFoundError: No module named 'rerpresentative_v4'
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
``` ```
......
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