Update README according to new subcommand

README.md

@@ -2,13 +2,45 @@
 
 Tools to design and analyse CRISPRi experiments
 
+## API
 
-# Command-line
+```python
+from crisprbact import on_target_predict
 
-## predict guide RNAs activity
+guide_rnas = on_target_predict("ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG")
+
+for guide_rna in guide_rnas:
+    print(guide_rna)
+
+```
+
+outputs :
+
+```
+{'target': 'TCATCACGGGCCTTCGCCACGCGCG', 'guide': 'TCATCACGGGCCTTCGCCAC', 'start': 82, 'stop': 102, 'pam': 80, 'ori': '-', 'pred': -0.4719254873780802}
+{'target': 'CATCACGGGCCTTCGCCACGCGCGC', 'guide': 'CATCACGGGCCTTCGCCACG', 'start': 81, 'stop': 101, 'pam': 79, 'ori': '-', 'pred': 1.0491308060379676}
+{'target': 'CGCGCGCGGCAAACAATCACAAACA', 'guide': 'CGCGCGCGGCAAACAATCAC', 'start': 63, 'stop': 83, 'pam': 61, 'ori': '-', 'pred': -0.9021152826078697}
+{'target': 'CCTGATCGGTATTGAACAGCATCTG', 'guide': 'CCTGATCGGTATTGAACAGC', 'start': 29, 'stop': 49, 'pam': 27, 'ori': '-', 'pred': 0.23853258873311955}
+```
+
+## Command-line
+
+### predict guide RNAs activity
 
 ```
-Usage: crisprbact predict [OPTIONS] [OUTPUT_FILE]
+Usage: crisprbact predict [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --help  Show this message and exit.
+
+Commands:
+  from-seq  Outputs candidate guide RNAs for the S.
+  from-str  Outputs candidate guide RNAs for the S.
+```
+
+#### From a string sequence:
+```
+Usage: crisprbact predict from-str [OPTIONS] [OUTPUT_FILE]
 
   Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-
   target activity from a target gene.
@@ -21,26 +53,55 @@ Options:
 ```
 
 
+```
+crisprbact predict from-str -t ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG guide-rnas.tsv
+```
 
-for example:
+You can pipe the results :
 
 ```
-crisprbact predict -t ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG guide-rnas.tsv
+crisprbact predict from-str -t ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG | tail -n +2 | wc -l
 ```
 
-You can pipe the results :
+#### From a sequence file
+
 ```
-crisprbact predict -t ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG | tail -n +2 | wc -l
+Usage: crisprbact predict from-seq [OPTIONS] [OUTPUT_FILE]
+
+  Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-
+  target activity from a target gene.
+
+  [OUTPUT_FILE] file where the precitions are saved. Default = "stdout"
+
+Options:
+  -t, --target FILENAME  Sequence file  [required]
+  -f, --seq-format TEXT  Sequence file format
+  --help                 Show this message and exit.
+
 ```
 
-### Output file 
+- Fasta file (could be multifasta)
+
+```
+poetry run crisprbact predict from-seq -t /tmp/seq.fasta guide-rnas.tsv
+```
 
+- GenBank file
 
 ```
-target	PAM position	prediction
-TCATCACGGGCCTTCGCCACGCGCG	80	-0.4719254873780802
-CATCACGGGCCTTCGCCACGCGCGC	79	1.0491308060379676
-CGCGCGCGGCAAACAATCACAAACA	61	-0.9021152826078697
-CCTGATCGGTATTGAACAGCATCTG	27	0.23853258873311955
+poetry run crisprbact predict from-seq -t /tmp/seq.gb -f gb guide-rnas.tsv
 ```
 
+### Output file
+
+```
+target	PAM position	prediction	input_id
+ATTTGTTGGCAACCCAGCCAGCCTT	855	-0.7310112260341689	CP027060.1
+CACGTCCGGCAATATTTCCGCGAAC	830	0.14773859036983505	CP027060.1
+TCCGAGCGGCAACGTCTCTGATAAC	799	-0.4922487382950619	CP027060.1
+GCTTAAAGGGCAAAATGTCACGCCT	769	-1.814666749464254	CP027060.1
+CTTAAAGGGCAAAATGTCACGCCTT	768	-0.4285147731290152	CP027060.1
+CGTTTGAGGAGATCCACAAAATTAT	732	-1.2437430146548256	CP027060.1
+CATGAATGGTATAAACCGGCGTGCC	680	-0.8043242669169294	CP027060.1
+
+```