Coding stye and list of files added to scripts/README.md. README.txt is now README.md

phages/scripts/03_mapping.sh

@@ -23,22 +23,22 @@ virus_index=/home/enrique/work/Gandon/coevolution/phages/data/refs/indexes_Sv/Sv
 
 
 
-for i in $(find $path_fasta -name *_R1.fq.gz)
+for i in  $(find  $path_fasta  -name *_R1.fq.gz)
 do
     # echo $i
-    root_name=$(basename -s _R1.fq.gz $i)
+    root_name=$(basename -s  _R1.fq.gz $i)
     var=$(dirname $i)
     outdir=${var/data\/trimmed/results/mapping}/
 
-    echo -e "\n"phage $root_name -\> ${outdir}${root_name}.sam
-    echo $i ${i/_R1/_R2}
+    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 
+    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
+    samtools sort  -O BAM  -o ${outdir}${root_name}.sort.bam  ${outdir}${root_name}.sam
+    samtools index  -b ${outdir}${root_name}.sort.bam
 
 done

phages/scripts/README.md

+## 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)
+
+Files:
+
+* 00_create_py_env.sh
+* 01_quality_check.sh*
+* 02_trimm_and_clean.sh*
+* 03_mapping.sh*
+* 04_snpcalling.sh*
+* 05b_convert_protospacer_dico2fasta.py*
+* 06b_blast_protospaces.sh*
+* 07_2_run_vcf_parser_all_files.py
+* 07_2_test.py
+* 07_run_vcf_parser_all_files.py*
+
+* procedure.sh
+* README.txt
+* requirements_py-env.txt
+
+* vcf_parser3.py
+
+Folders:
+
+* debug
+* lib
+* __pycahce__
+
+
+
+## Coding practices
+
+I tried to use as much as possible the Python Enhancement Proposal 8 (PEP-8). https://www.python.org/dev/peps/pep-0008/
+
+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.
+
+Example:
+
+```python
+## 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
+
+Example:
+
+```bash
+for i in  $(find  $path_fasta  -name *_R1.fq.gz)
+do
+    # echo $i
+    root_name=$(basename -s  _R1.fq.gz $i)
+    var=$(dirname $i)
+    outdir=${var/data\/trimmed/results/mapping}/
+
+    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
+
+done
+```
+
+Sometimes I'll put the arguments in different lines having an indentation:
+
+```bash
+## A command with multiple parameters seaprated per line
+samtools sort  \
+    -O BAM  \
+    -o ${outdir}${root_name}.sort.bam  \
+    ${outdir}${root_name}.sam
+
+## Short commands in one single line
+samtools index  -b ${outdir}${root_name}.sort.bam
+```
+

phages/scripts/README.txt

@@ -3,7 +3,7 @@
 The scripts are numbered in the order they are run.
 If in doubt use the scripts which are executable.
 
-The description of the files is here below
+A more detailed description of the files is below the list (use ctrl + f)
 
 Files:
 
@@ -26,7 +26,64 @@ Files:
 
 Folders:
 
+* debug
+* lib
+* __pycahce__
 
-Files to ignore for a while ^_^
 
-### 
\ No newline at end of file
+
+## Coding practices
+
+I tried to use as much as possible the Python Enhancement Proposal 8 (PEP-8). https://www.python.org/dev/peps/pep-0008/
+
+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.
+
+Example:
+
+```python
+## 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
+
+Example:
+
+```bash
+for i in  $(find  $path_fasta  -name *_R1.fq.gz)
+do
+    # echo $i
+    root_name=$(basename -s  _R1.fq.gz $i)
+    var=$(dirname $i)
+    outdir=${var/data\/trimmed/results/mapping}/
+
+    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
+
+done
+```
+
+Sometimes I'll put the arguments in different lines having an indentation:
+
+```bash
+## A command with multiple parameters seaprated per line
+samtools sort  \
+    -O BAM  \
+    -o ${outdir}${root_name}.sort.bam  \
+    ${outdir}${root_name}.sam
+
+## Short commands in one single line
+samtools index  -b ${outdir}${root_name}.sort.bam
+```
+