README : add output section

README.md

@@ -39,3 +39,21 @@ optional arguments:
                         list of start codons allowed separate with space ex : -s ATG CTG GTG
   -v, --version         show program's version number and exit
 ```
+
+You can try running  :
+`python3 src/ORFs_scanning.py -i data/toy.fa -o results_test.csv -s ATG CTG GTG`
+
+## Output
+
+The main output is a csv file containing the following informations :
+
+
+- **posStart** : position of the start codon found (in nucleotide)
+- **codonStart** : start codon 
+- **posStop** : position of the stop codon found (in nucleotide)
+- **codonStop** : stop codon
+- **lengthInAA** : length of the ORF in amino acid
+- **seqKozak** : sequence surrounding the start codon used for the calculation of the score Kozak
+- **scoreKozak** : score Kozak
+- **seqORF** : sequence of the ORF in nucleotide
+- **seqAA** : translation of the ORF

src/ORFs_scanning.py

@@ -8,9 +8,7 @@ import csv
 
 
 def check_files(path):
-    if os.path.isfile(path) :
-        print("the file exists OK\n")
-    else:
+    if not os.path.isfile(path) :
         print("the input file does not exist")
         exit(2)
 

test

+posStart,codonStart,posStop,codonStop,lengthInAA,seqKozak,scoreKozak,seqORF,seqAA
+36,CTG,177,TAG,47.0,2.13,CCTACCTGAGG,CTGAGGCCGCCATCCACGCCGGTTGAGTCGCGTTCTGCCGCCTCCCGCCTGTGGTGCCTCCTGAACTGCGTCCGCCGTCTAGGTAAGTTTAAAGCTCAGGTCGAGACCGGGCCTTTGTCCGGCGCTCCCTTGGAGCCTACC,LRPPSTPVESRSAASRLWCLLNCVRRLGKFKAQVETGPLSGAPLEPT
+70,CTG,97,TGA,9.0,2.22,GCGTTCTGCCG,CTGCCGCCTCCCGCCTGTGGTGCCTCC,LPPPACGAS
+84,CTG,177,TAG,31.0,2.03,CCCGCCTGTGG,CTGTGGTGCCTCCTGAACTGCGTCCGCCGTCTAGGTAAGTTTAAAGCTCAGGTCGAGACCGGGCCTTTGTCCGGCGCTCCCTTGGAGCCTACC,LWCLLNCVRRLGKFKAQVETGPLSGAPLEPT
+96,CTG,177,TAG,27.0,2.12,GCCTCCTGAAC,CTGAACTGCGTCCGCCGTCTAGGTAAGTTTAAAGCTCAGGTCGAGACCGGGCCTTTGTCCGGCGCTCCCTTGGAGCCTACC,LNCVRRLGKFKAQVETGPLSGAPLEPT
+101,CTG,119,TAA,6.0,1.98,CTGAACTGCGT,CTGCGTCCGCCGTCTAGG,LRPPSR
+205,CTG,394,TAG,63.0,2.11,TTTGCCTGACC,CTGACCCTGCTTGCTCAACTCTACGTCTTTGTTTCGTTTTCTGTTCTGCGCCGTTACAGATCGAAAGTTCCACCCCTTTCCCTTTCATTCACGACTGACTGCCGGCTTGGCCCACGGCCAAGTACCGGCGACTCCGTTGGCTCGGAGCCAGCGACAGCCCATCCTATAGCACTCTCCAGGAGAGAAATT,LTLLAQLYVFVSFSVLRRYRSKVPPLSLSFTTDCRLGPRPSTGDSVGSEPATAHPIALSRREI
+211,CTG,394,TAG,61.0,2.96,TGACCCTGCTT,CTGCTTGCTCAACTCTACGTCTTTGTTTCGTTTTCTGTTCTGCGCCGTTACAGATCGAAAGTTCCACCCCTTTCCCTTTCATTCACGACTGACTGCCGGCTTGGCCCACGGCCAAGTACCGGCGACTCCGTTGGCTCGGAGCCAGCGACAGCCCATCCTATAGCACTCTCCAGGAGAGAAATT,LLAQLYVFVSFSVLRRYRSKVPPLSLSFTTDCRLGPRPSTGDSVGSEPATAHPIALSRREI
+245,CTG,371,TAG,42.0,1.02,GTTTTCTGTTC,CTGTTCTGCGCCGTTACAGATCGAAAGTTCCACCCCTTTCCCTTTCATTCACGACTGACTGCCGGCTTGGCCCACGGCCAAGTACCGGCGACTCCGTTGGCTCGGAGCCAGCGACAGCCCATCCTA,LFCAVTDRKFHPFPFHSRLTAGLAHGQVPATPLARSQRQPIL
+250,CTG,394,TAG,48.0,1.83,CTGTTCTGCGC,CTGCGCCGTTACAGATCGAAAGTTCCACCCCTTTCCCTTTCATTCACGACTGACTGCCGGCTTGGCCCACGGCCAAGTACCGGCGACTCCGTTGGCTCGGAGCCAGCGACAGCCCATCCTATAGCACTCTCCAGGAGAGAAATT,LRRYRSKVPPLSLSFTTDCRLGPRPSTGDSVGSEPATAHPIALSRREI
+299,CTG,371,TAG,24.0,1.73,CACGACTGACT,CTGACTGCCGGCTTGGCCCACGGCCAAGTACCGGCGACTCCGTTGGCTCGGAGCCAGCGACAGCCCATCCTA,LTAGLAHGQVPATPLARSQRQPIL
+303,CTG,450,NoStopCodon,48.666666666666664,1.55,ACTGACTGCCG,CTGCCGGCTTGGCCCACGGCCAAGTACCGGCGACTCCGTTGGCTCGGAGCCAGCGACAGCCCATCCTATAGCACTCTCCAGGAGAGAAATTTAGTACACAGTTGGGGGCTCGTCCGGGATACGAGCGCCCCTTTATTCCCTAGGCA,LPAWPTAKYRRLRWLGASDSPSYSTLQERNLVHSWGLVRDTSAPLFPR