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Merge pull request #1 from sannalda/development
Adding annotation checker and NCBI submission formatter
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| AUTHORS Siddarth Annaldasula, Katja Reichel | ||
| INSTITUTION Institut fuer Biologie-Botanik, Freie Universitaet Berlin, Altensteinstrasse 6, Berlin, Berlin 14195,Germany | ||
| SAMPLE AM09_01 | ||
| SOURCE Arnica montana L. silica-dried leaf sample | ||
| SPECIES Arnica montana | ||
| TAXONOMY cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae alliance; Madieae; Arnicinae; Arnica | ||
| TAXREF 436207 | ||
| SOURCE_MOD | ||
| /altitude="0 m" | ||
| /collected_by="Esther Sossai, Elke Zippel" | ||
| /collection_date="17-Jun-2023" | ||
| /country="Germany:Mecklenburg-Vorpommern:Barth" | ||
| /identified_by="Elke Zippel" | ||
| /lat_lon="54.393536 N 12.701389 E" | ||
| /tissue_type="leaf" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| name: annotation | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| - r | ||
| - default | ||
| - anaconda | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=conda_forge | ||
| - _openmp_mutex=4.5=2_gnu | ||
| - attrs=23.1.0=pyh71513ae_1 | ||
| - biopython=1.81=py311h2582759_0 | ||
| - brotli-python=1.1.0=py311hb755f60_0 | ||
| - bzip2=1.0.8=h7f98852_4 | ||
| - ca-certificates=2023.7.22=hbcca054_0 | ||
| - certifi=2023.7.22=pyhd8ed1ab_0 | ||
| - charset-normalizer=3.2.0=pyhd8ed1ab_0 | ||
| - colorama=0.4.6=pyhd8ed1ab_0 | ||
| - exceptiongroup=1.1.3=pyhd8ed1ab_0 | ||
| - h11=0.14.0=pyhd8ed1ab_0 | ||
| - idna=3.4=pyhd8ed1ab_0 | ||
| - ld_impl_linux-64=2.40=h41732ed_0 | ||
| - libblas=3.9.0=18_linux64_openblas | ||
| - libcblas=3.9.0=18_linux64_openblas | ||
| - libexpat=2.5.0=hcb278e6_1 | ||
| - libffi=3.4.2=h7f98852_5 | ||
| - libgcc-ng=13.2.0=h807b86a_2 | ||
| - libgfortran-ng=13.2.0=h69a702a_2 | ||
| - libgfortran5=13.2.0=ha4646dd_2 | ||
| - libgomp=13.2.0=h807b86a_2 | ||
| - liblapack=3.9.0=18_linux64_openblas | ||
| - libnsl=2.0.0=h7f98852_0 | ||
| - libopenblas=0.3.24=pthreads_h413a1c8_0 | ||
| - libsqlite=3.43.0=h2797004_0 | ||
| - libstdcxx-ng=13.2.0=h7e041cc_2 | ||
| - libuuid=2.38.1=h0b41bf4_0 | ||
| - libzlib=1.2.13=hd590300_5 | ||
| - ncurses=6.4=hcb278e6_0 | ||
| - numpy=1.26.0=py311h64a7726_0 | ||
| - openssl=3.1.3=hd590300_0 | ||
| - outcome=1.2.0=pyhd8ed1ab_0 | ||
| - packaging=23.1=pyhd8ed1ab_0 | ||
| - pip=23.2.1=pyhd8ed1ab_0 | ||
| - pysocks=1.7.1=pyha2e5f31_6 | ||
| - python=3.11.5=hab00c5b_0_cpython | ||
| - python-dotenv=1.0.0=pyhd8ed1ab_1 | ||
| - python_abi=3.11=4_cp311 | ||
| - readline=8.2=h8228510_1 | ||
| - requests=2.31.0=pyhd8ed1ab_0 | ||
| - selenium=4.12.0=pyhd8ed1ab_0 | ||
| - selenium-manager=4.12.0=he8a937b_0 | ||
| - setuptools=68.2.2=pyhd8ed1ab_0 | ||
| - sniffio=1.3.0=pyhd8ed1ab_0 | ||
| - sortedcontainers=2.4.0=pyhd8ed1ab_0 | ||
| - tk=8.6.12=h27826a3_0 | ||
| - tqdm=4.66.1=pyhd8ed1ab_0 | ||
| - trio=0.22.2=py311h38be061_0 | ||
| - trio-websocket=0.10.4=pyhd8ed1ab_0 | ||
| - typing_extensions=4.8.0=pyha770c72_0 | ||
| - tzdata=2023c=h71feb2d_0 | ||
| - urllib3=2.0.5=pyhd8ed1ab_0 | ||
| - webdriver-manager=4.0.0=pyhd8ed1ab_0 | ||
| - wheel=0.41.2=pyhd8ed1ab_0 | ||
| - wsproto=1.2.0=pyhd8ed1ab_0 | ||
| - xz=5.2.6=h166bdaf_0 | ||
| prefix: /home/sjannalda/mambaforge-pypy3/envs/annotation |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,20 @@ | ||
| def annotationSubmissionNCBIInphutFunc(wildcards): | ||
| output = [config["metadata_file"]] | ||
| if (not config["Standardization"]): | ||
| return output + ["{sample}/annotation/{sample}.original.cleaned.gb","{sample}/annotation/{sample}.original.fasta"] | ||
| else: | ||
| return output + ["{sample}/annotation/{sample}.standardardized.cleaned.gb","{sample}/annotation/{sample}.standardardized.fasta"] | ||
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| rule annotationSubmissionNCBI: | ||
| input: | ||
| gb=annotationSubmissionNCBIInphutFunc | ||
| output: | ||
| "{sample}/annotation/{sample}.submission.gb" | ||
| resources: | ||
| mem_mb=1000, | ||
| time="0-0:20:00" | ||
| conda: | ||
| "../envs/Annotation.yaml" | ||
| script: | ||
| "../scripts/AnnotationSubmission.py" |
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