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Remove gtf header #13

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merged 5 commits into from
Oct 18, 2023
Merged

Remove gtf header #13

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56ee68d
fix: do not write header for gtf file
ninsch3000 Oct 13, 2023
1752a7f
fix: write bed files without header
ninsch3000 Oct 18, 2023
1c2c815
Merge branch 'dev' into remove_gtf_header
balajtimate Oct 18, 2023
40bf800
update dockerfile
balajtimate Oct 18, 2023
83408fe
update dev env
balajtimate Oct 18, 2023
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3 changes: 2 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@ LABEL maintainer="Máté Balajti <[email protected]>"
# COPY THE YAML & INSTALL SOFTWARE WITH CONDA
WORKDIR /usr/src/app
COPY ./ ./
RUN conda env create --file environment.yml
RUN conda env create --file environment.yml \
&& conda clean --all

# VARIABLES
ARG WORKDIR="/home/USER"
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8 changes: 8 additions & 0 deletions environment-dev.yml
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Expand Up @@ -3,6 +3,14 @@ channels:
- conda-forge
- bioconda
dependencies:
- pip>=20.2.3
- biopython>=1.78
- polars==0.16.17
- gtfparse
- numpy>=1.23.3
- pandas>=1.4.4
- python>=3.6, <=3.10
- pyarrow
- black
- coverage
- flake8
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2 changes: 1 addition & 1 deletion scRNAsim_toolz/sequence_extractor/pre_bedtools.py
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Expand Up @@ -43,5 +43,5 @@ def pre_bedtools_mode(args):
args.output_bed_file = "default_output.bed"

pd.concat([gtf_df_pos, gtf_df_neg]).to_csv(
args.output_bed_file, sep="\t", index=False
args.output_bed_file, sep="\t", index=False, header=False
) # gtf_df_pos and gtf_df_neg must be dataframes
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