Commit 4987e496 authored by eortega's avatar eortega
Browse files

deleted README.txt

parent bfc05ce5
## Contents of scripts folder
The scripts are numbered in the order they are run.
If in doubt use the scripts which are executable.
A more detailed description of the files is below the list (use ctrl + f)
* README.txt
* requirements_py-env.txt
* debug
* lib
* __pycahce__
## Coding practices
I tried to use as much as possible the Python Enhancement Proposal 8 (PEP-8).
A difference I use regularl is using double `##` at the begining of a line containing comments.
During the developement stages I comment some code lines that would be uncommented as a block. Having two '#' signs un real comments allows not to mistake them for command lines.
## This block of code calculate the proportion
for i in input_list:
# print("proportion of the list")
print(i / sum(list))
Concerning bash coding I use often double spaces to separate commands, parameters, and arguments. When using some long names it makes things more readable
for i in $(find $path_fasta -name *_R1.fq.gz)
# echo $i
root_name=$(basename -s _R1.fq.gz $i)
var=$(dirname $i)
echo -e "\n"phage $root_name -\> ${outdir}${root_name}.sam
echo $i ${i/_R1/_R2}
echo $virus_index
echo "#### MAPPING"
bowtie2 --phred33 -5 12 -p 24 -t -x $virus_index -1 $i -2 ${i/_R1/_R2} -S ${outdir}${root_name}.sam
echo "#### SORTING"
samtools sort -O BAM -o ${outdir}${root_name}.sort.bam ${outdir}${root_name}.sam
samtools index -b ${outdir}${root_name}.sort.bam
Sometimes I'll put the arguments in different lines having an indentation:
## A command with multiple parameters seaprated per line
samtools sort \
-O BAM \
-o ${outdir}${root_name}.sort.bam \
## Short commands in one single line
samtools index -b ${outdir}${root_name}.sort.bam
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