J’ai créé un fork de cette fiche pour permettre un accès à tous, en français et sans fautes de tous les raccourcis par défaut sur Sublime Text 3. Les raccourcis présents sont les raccourcis par défaut. Si vous ajoutez des snippets, ou des plugins, je ne peut garantir la pérénité de ces derniers. Mémoriser tous les raccourcis en un seul bloc est inutile. C’est pourquoi j’ai regroupé les raccourcis en plusieurs catégories :
| # --- OSX ----- | |
| # When following error: | |
| # ld: unknown option: -platform_version | |
| # clang-10: error: linker command failed with exit code 1 (use -v to see invocation) | |
| Here the way to fix it | |
| info=$( ld -v 2>&1 > /dev/null ) | |
| platform=$([[ $info =~ ld64-([0-9]*) ]] && echo ${BASH_REMATCH[1]}) | |
| add at the end of the compiltaton command: -mlinker-version=$platform |
| # sort reads by read names | |
| samtools sort -n inputfile > output | |
| # convert sam to bam | |
| samtools view -bS file.sam > file.bam | |
| # convert bam to sam | |
| samtools view -h -o out.sam in.bam |
| #here order of the different step in the falcon pipeline (snakemake) | |
| name-mapping/ | |
| placement-split/ | |
| placement-chunks/ | |
| placement-run/ | |
| placement-gathered/ | |
| placement-output/ | |
| minced_bed/ | |
| minced_fasta/ | |
| index-pair/ |
| # To save the current env | |
| conda env export > environment.yaml | |
| #conda configuration | |
| conda config --show channels # to view your configuration's current state, | |
| conda config --show-sources # to view config file locations. | |
| # To test locally a new/modified package: | |
| conda create -n bioconda bioconda-utils | |
| conda activate bioconda |
| #filter out fasta sequence by pattern in header | |
| awk '/^>/ {P=index($0,"STRING")==0} {if(P) print} ' in.fasta > out.fasta | |
| #keeping fasta sequence based on pattern in header | |
| awk '/^>/ {ok=index($0,"Escherichia coli");} {if(ok) print;}' in.fasta | |
| # removing empty records (e.g. seq1 here) | |
| #>seq1 | |
| # | |
| #>seq2 |