Remove gtf header (#13)

* fix: do not write header for gtf file * fix: write bed files without header * update dockerfile * update dev env --------- Co-authored-by: CJ Herrmann <[email protected]>
zavolanlab · Oct 18, 2023 · b8d858b · b8d858b
1 parent 188e429
commit b8d858b
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -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"

diff --git a/environment-dev.yml b/environment-dev.yml
@@ -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

diff --git a/scRNAsim_toolz/sequence_extractor/pre_bedtools.py b/scRNAsim_toolz/sequence_extractor/pre_bedtools.py
@@ -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