Updated readme for get_PAM.py and update_ref_genome.py

phages/scripts/README.md

@@ -194,6 +194,68 @@ The commands used to launch the scripts up here as well as the supplementary com
 It contains a pre-treatment of data to create sub-groups using symbolic links.
 
 
+
+### update_ref_genome.py
+
+Allows to create a consensus fasta file from the reference fasta
+and a VCF file from which the variants will be integrated.
+It filters the variants with a minimum frequency of 0.45.
+
+It is equivalent to bcftools consensus:
+`bcftools consensus --sample unknown -f NC_007019.1.fasta TO-WT_S83.vcf.gz -o test.fasta`
+
+
+### get_PAM.py -- Getting new PAMs
+
+From the genome of Streptococcus virus 2972 we'll be looking for new PAMs (Protospacer Associated Motif).
+
+The original scripts were made to teach Antoine Nicot how to program.
+
+The researced patterns are: **AGAA** and **GGAA**; as well as the reverse complementary sequences **TTCT** and **TTCC**.
+
+The PAMS are little sequences of 4 nucleotides located on the 3' side of a protospacer sequence. The lenght of a protospacer taken into account is 32 + 4 (protospacer + PAM).
+
+
+#### Example of sequences & Nomenclature
+
+Here are the templates of sequences.
+
+The PAM sequences are found in 3 prime of the protospacers.
+Each needs a unique name of ID for the fasta header.
+
+```
+>PAM_Coord_ref_genome Motif=AGAA;Strand=+;Protospacer_length=N
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGAA
+>PAM_Coord_ref_genome Motif=GGAA;Strand=+;Protospacer_length=N
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGAA
+>PAM_Coord_ref_genome Motif=AGAA;Strand=-;Protospacer_length=N
+TTCTxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>PAM_Coord_ref_genome Motif=GGAA;Strand=-;Protospacer_length=N
+TTCCxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+```
+
+The nomenclature of the fasta header goes as follows:
+
+```
+>PAM_152_Sv2972 M=AGAA;Strand=+;Protospacer_length=32
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGAA
+>PAM_10863_Sv2972 M=TTCT;Strand=-;Protospacer_length=32
+TTCTxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+```
+
+Mandatory fields for ID field in header FASTA. No spaces
+
+* **PAM** = Type of sequence **P**rotospacer **A**ssociated **M**otif
+* **152** = The coordinate of the first nucleotide of the motif.
+* **Sv2972** = Reference genome used to find these sequences
+
+Comment field for FASTA format. No strict rules. I used Definition=Value without spaces. Each separated by a semi-colon
+
+* **Motif=AGAA** = Motif The motif used to find that sequence
+* **Strand=+** = The strand where the sequence is. If the motif is on the strand -, the sequence present will be the reverse complementary.
+* **Protospacer_length** = The lenght of sequence concidered to be a protospacer without the lenght of the PAM.
+
+
 ### README.md
 
 This file :-P
@@ -235,3 +297,5 @@ toy examples and commands to be called from the other scripts
 
 Dispensable.
 Created by python automatically when importing a `*.py`
+
+