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steineggerlab · Jul 16, 2021 · 9267fa8 · 9267fa8
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 # Probeit: probes generator for pathogen detection and genotyping
 Probeit is a software to generate probes which are for pathogen detection and genotyping. Probeit is open source GPL-licensed software implemented in python for Linux and MacOS.
 
+
+
 ### Publication
 
+
+### Get started
+###### Linux
+```
+# install probeit
+conda install -c https://161832-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages probeit
+# use posnetset workflow
+python probeit.py posnegset -p sample/positive.fasta -n sample/negative.fasta -o posnegset_output
+# to use snp workflow with amino acid SNPs
+python probeit.py snp  -r sample/ref.fasta -s sample/str.fasta  -p "10,11,19,20,21,22" -m "aa:orf1ab:L4715F,aa:S:Q52R,aa:S:E484K,aa:S:Q677H,aa:S:F888L,aa:E:L21F,aa:M:I82T"  -o 
+# to use snp workflow with nucleotide SNPs
+snp_aa_output -a sample/ref.gff
+python probeit.py snp  -r sample/ref.fasta -s sample/str.fasta  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C"  -o snp_nt_output
+```
+###### MacOS
+```
+# install probeit
+conda install -c https://161837-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages probeit
+# use posnetset workflow
+python probeit.py posnegset -p sample/positive.fasta -n sample/negative.fasta -o posnegset_output
+# to use snp workflow with amino acid SNPs
+python probeit.py snp  -r sample/ref.fasta -s sample/str.fasta  -p "10,11,19,20,21,22" -m "aa:orf1ab:L4715F,aa:S:Q52R,aa:S:E484K,aa:S:Q677H,aa:S:F888L,aa:E:L21F,aa:M:I82T"  -o 
+# to use snp workflow with nucleotide SNPs
+snp_aa_output -a sample/ref.gff
+python probeit.py snp  -r sample/ref.fasta -s sample/str.fasta  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C"  -o snp_nt_output
+```
+
+
 ### Installation
-##### To get source code of Probeit
+#### Installation using conda
+###### Linux
+```
+conda install -c https://161832-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages probeit
+```
+###### MacOS
+```
+conda install -c https://161837-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages probeit
+```
+#### Installation from source
+###### To get source code of Probeit
 ```
 # move to the directory where you want to install probeit.
 git clone https://github.com/steineggerlab/probeit.git
 cd probeit
 ```
-##### To create probeit environment
+###### To create probeit environment
 ```
 conda create -n probeit -c conda-forge -c anaconda -c bioconda pandas entrez-direct fire primer3-py bedtools  mmseqs2 seqkit genmap primer3 biopython
 ```
-##### To initiate setcover
+###### To initiate setcover
 ```
 cd setcover
 make
@@ -25,86 +65,33 @@ cd ..
 conda activate probeit  
 ```
 
-### Getting started
+
+### How to use
 We provide 2 types of workflows: posnegset for detection and snp for genotyping.
 #### **Probes generating for detection**
 For generating probes for detection Probeit posnegset is available. The posnegset  workflow finds sequences that are included in the positive genome but not included in the negative genome.
 ##### Easy User's Guide
 You can use some data in **probeit/sample** to test Probeit posnegset
 ```
-python probeit.py posnegset -p sample/positive.fasta -n sample/negative.fasta -o posnegset_output [additional opts]
+python probeit.py posnegset -p positive_genome -n negative_genome -o output_dir [additional opts]
 ```
 ##### Required Options
-###### **-p/--positive** FASTA file 
-Option for the genome which **MUST** be covered by the probes.
-###### **-n/--negative** FASTA file
-Option for the genome which **MUST NOT** to be covered by the probes. 
-###### **-o/--output** Dir
-Option for the output directory. Because Probeit posnegset workflow makes a new directory with given name, you don't have to create a directory. 
+###### **-p/--positive** FASTA file : Option for the genome which **MUST** be covered by the probes.
+###### **-n/--negative** FASTA file: Option for the genome which **MUST NOT** to be covered by the probes. 
+###### **-o/--output** Dir: Option for the output directory. Because Probeit posnegset workflow makes a new directory with given name, you don't have to create a directory. 
 
-##### Additional Options
-###### **window-size** INT[200]
-Option for the size of window for 2nd Probes
-###### **--not-cluster-positive** NONE
-When you **DO NOT** need to cluster positive genome, you can use this option.      
-###### **--probe-len1** INT [40]
-Option for length of 1st Probes. 
-###### **--probe-len2** INT [20]
-Option for length of 2nd Probes.      
-###### **--probe-error1** INT [0] 
-Option for the number of error allowed in 1st Probes.            
-###### **--probe-error2** INT [1] 
-Option for the number of error allowed in 2nd Probes.                         
-###### **--minimizing-covered1** INT [1]
-Option for the number of times each seq from positive genome should be covered by 1st Probes    
-###### **--minimizing-covered2** INT [1]
-Option for the number of times each 1st Probe should be covered by 2nd Probes                               
-###### **--minimizing-repeats1** INT [1] 
-Option for the number of random iterations when minimizing 1st Probes.     
-###### **--minimizing-repeats2** INT [10] 
-Option for the number of random iterations when minimizing 2nd Probes.                           
-###### **--minimizing-earlystop-criteria1** FLOAT [0.9]
-Option for proportion of seqs from positive genome covered by 1st Probes for earlystop upon minimizing of 1st Probes.                              
-###### **--minimizing-earlystop-criteria2** FLOAT [0.99]
-Option for proportion of 1st Probes covered by 2nd Probes for earlystop upon minimizing of 2nd Probes.  
 #### **Probes generating for genotyping** 
 For genotyping Probeit snp is available. The snp workflow extracts sequences containing a snp from a strain genome.
 ##### Easy User's Guide
 You can use some data in **probeit/sample** to test Probeit snp
 ```
-python probeit.py snp  -r sample/ref.fasta -s sample/str.fasta  -p "10,11,19,20,21,22" -m "aa:orf1ab:L4715F,aa:S:Q52R,aa:S:E484K,aa:S:Q677H,aa:S:F888L,aa:E:L21F,aa:M:I82T"  -o snp_aa_output -a sample/ref.gff [additional opts]
-```
-```
-python probeit.py snp  -r sample/ref.fasta -s sample/str.fasta  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C"  -o snp_nt_output [additional opts]
+python probeit.py snp  -r reference_genome -s strain_genome  -p podition_list -m snp_list  -o output_dir -a reference_annotation [additional opts]
 ```
 
 ##### Required Options
-###### **-r/--reference** FASTA file
-Option for the wildtype(reference) genome. 
-###### **-s/--strain** FASTA file
-Option for the strain genome.  format** as a parameter.
-###### **-p/--positions** COMMA SEPARATED INT ARRAY
-Option for The position list. Positons in the position list indicate the positions of SNPs in the 1st Probes.  
-###### **-m/--mutations** COMMA SEPARATED SNP ARRAY
-Option for SNP list of the strain. Both amino acid differences and nucleotide differences are allowed. 
-###### **-o/--output** DIR
-Option for the output directory.Because Probeit snp workflow makes a new directory with given name, you don't have to create a directory. 
-###### **-a/--annotation** GFF file
-Option for wild-type genome annotation. Only required when using amino acid differences in the -m option.
-##### Additional Options
-###### **--max-window** [NONE]
-When you need maximum window mode, then use this option. Default window mode is minimum window.
-###### **window-size** INT[200]
-Option for the size of window for 2nd Probes
-###### **--probe-len1** INT [40]
-Option for length of 1st Probes. 
-###### **--probe-len2** INT [20]
-Option for length of 2nd Probes. 
-###### **--probe-error2** INT [1] 
-Option for the number of error allowed in 2nd Probes.   
-###### **--minimizing-covered2** INT [1]
-Option for the number of times each 1st Probe should be covered by 2nd Probes                                           
-###### **--minimizing-repeats2** INT [10] 
-Option for the number of random iterations when minimizing 2nd Probes.                           
-###### **--minimizing-earlystop-criteria2** FLOAT [0.99]
-Option for proportion of 1st Probes covered by 2nd Probes for earlystop upon minimizing of 2nd Probes. 
+###### **-r/--reference** FASTA file: Option for the wildtype(reference) genome. 
+###### **-s/--strain** FASTA fileOption for the strain genome.  format** as a parameter.
+###### **-p/--positions** COMMA SEPARATED INT ARRAY: Option for The : position list. Positons in the position list indicate the positions of SNPs in the 1st Probes.  
+###### **-m/--mutations** COMMA SEPARATED SNP ARRAY: Option for SNP list of the strain. Both amino acid differences and nucleotide differences are allowed. 
+###### **-o/--output** DIR: Option for the output directory.Because Probeit snp workflow makes a new directory with given name, you don't have to create a directory. 
+###### **-a/--annotation** GFF file : Option for wild-type genome annotation. Only required when using amino acid differences in the -m option.