init

IOalignment.py

+import re
+
+class IOAlignment:
+    """Classe pour le parsing de fichier fasta et de configuration"""
+    def __init__(self, Fi):
+        self.__fi = Fi
+
+    def ParseFasta(self):
+        """Parse un fichier fasta et retourne un dictionnaire contenant les fasta par labels
+
+        
+
+        Returns:
+	    -------
+	    res : dict
+            dictionnaire des séquences issus du fichier fasta avec comme clés les labels
+        """
+        f = open(self.__fi, "r")
+        currentSeq = ""
+        res = dict()
+
+        for l in f:
+            l = l.rstrip()
+
+            if l[0] == ">":
+                # si la ligne commence par '>', stocker le label
+                currentSeq = l[1:]
+                res[currentSeq] = ""
+            else:
+                # sinon ajouter la séquence ADN au label correspondant
+                if currentSeq == "":
+                    raise TypeError
+                if not re.match("[ACTG]*", "ATGC"):
+                    raise TypeError
+                res[currentSeq] += l
+
+        return res

README.md

-# MABS-2
+# Projet-MABS-2
 
 
 
@@ -15,14 +15,14 @@ Already a pro? Just edit this README.md and make it your own. Want to make it ea
 
 ```
 cd existing_repo
-git remote add origin https://gitlab.univ-lille.fr/thomas.wacquet.etu/mabs-2.git
+git remote add origin https://gitlab.univ-lille.fr/thomas.wacquet.etu/projet-mabs-2.git
 git branch -M main
 git push -uf origin main
 ```
 
 ## Integrate with your tools
 
-- [ ] [Set up project integrations](https://gitlab.univ-lille.fr/thomas.wacquet.etu/mabs-2/-/settings/integrations)
+- [ ] [Set up project integrations](https://gitlab.univ-lille.fr/thomas.wacquet.etu/projet-mabs-2/-/settings/integrations)
 
 ## Collaborate with your team
 

data/Grippe_A.fna

+>lcl|NC_007357.1_cds_YP_308664.1_1 [gene=PB2] [locus_tag=FLUAVH5N1_s1gp1] [db_xref=GeneID:3654615] [protein=polymerase] [protein_id=YP_308664.1] [location=28..2307] [gbkey=CDS]
+ATGGAAAGAATAAAAGAACTAAGAGATCTAATGTCGCAGTCCCGCACTCGCGAGATACTAACAAAAACCACTGTGGATCA
+TATGGCCATAATCAAGAAATACACATCAGGAAGACAAGAGAAGAACCCTGCTCTCAGAATGAAATGGATGATGGCAATGA
+AATATCCAATCACAGCAGACAAGAGAATAATGGAGATGATTCCTGAAAGGAATGAGCAAGGACAAACGCTTTGGAGCAAG
+ACAAATGATGCTGGGTCGGACAGAGTGATGGTGTCTCCCCTAGCTGTAACTTGGTGGAACAGGAATGGGCCGACAACAAG
+TACAGTCCATTATCCAAAGGTTTACAAAACATACTTTGAGAAGGTTGAAAGGTTAAAACATGGAACCTTCGGTCCCGTTC
+ATTTCCGAAACCAAGTTAAAATACGTCGCCGGGTGGATATAAACCCGGGCCATGCAGATCTCAGTGCTAAAGAAGCACAA
+GATGTTATCATGGAGGTCGTTTTCCCAAATGAAGTGGGAGCTAGAATATTGACATCAGAGTCGCAATTGACAATAACAAA
+AGAGAAGAAAGAAGAGCTCCAGGATTGTAAAATTGCTCCTTTAATGGTGGCATACATGTTGGAAAGAGAACTGGTCCGCA
+AAACCAGATTTCTACCGGTAGCAGGCGGAACAAGCAGTGTGTACATTGAGGTATTGCATTTGACTCAAGGGACCTGTTGG
+GAACAGATGTACACTCCCGGCGGAGAAGTAAGAAATGATGATGTTGACCAGAGTTTGATCATCGCTGCCAGAAACATTGT
+TAGGAGAGCAACAGTATCAGCGGACCCACTGGCATCACTCTTGGAGATGTGTCACAGCACACAAATTGGGGGAATAAGGA
+TGGTGGACATCCTTAGGCAAAACCCAACTGAGGAGCAAGCTGTGGATATATGCAAAGCAGCAATGGGTTTGAGGATCAGT
+TCATCCTTTAGCTTTGGAGGCTTCACTTTCAAAAGAACAAATGGATCATCCGTCAAGAAGGAAGAGGAAGTGCTTACAGG
+CAACCTCCAAACATTGAAAATAAAAGTACATGAGGGGTATGAAGAATTCACAATGGTTGGGCGGAGAGCAACAGCTATCC
+TGAGGAAAGCAACTAGAAGGCTGATTCAGTTGATAGTAAGTGGAAGAGATGAACAATCAATCGCTGAAGCGATCATTGTA
+GCAATGGTGTTCTCACAGGAGGATTGCATGATAAAGGCAGTCCGAGGCGATCTGAATTTCGTGAACAGAGCAAACCAAAG
+ATTGAACCCCATGCATCAACTCCTGAGGCACTTCCAAAAAGATGCAAAAGTGCTGTTTCAGAACTGGGGAATTGAACCTA
+TTGACAATGTCATGGGGATGATCGGAATATTACCTGACATGACTCCAAGCGCAGAGATGTCACTGAGAGGAGTGAGAGTT
+AGTAAGATGGGAGTAGATGAATATTCCAGCACGGAGAGAGTGGTGGTGAGTATTGACCGTTTCTTGAGGGTCCGAGATCA
+GCAGGGGAACGTACTCTTATCTCCTGAAGAGGTTAGTGAAACACAGGGAACAGAGAAGTTGACAATAACATATTCATCCT
+CAATGATGTGGGAAATCAACGGTCCTGAGTCAGTGCTTGTTAACACTTATCAATGGATCATCAGGAATTGGGAGACTGTA
+AAGATTCAATGGTCTCAAGATCCCACAATGCTGTACAATAAGATGGAGTTTGAATCGTTCCAATCCTTGGTGCCAAAGGC
+TGCCAGAAGCCAATATAGTGGATTTGTGAGAACACTATTCCAACAGATGCGTGATGTTTTGGGGACATTTGATACTGTCC
+AAATAATCAAGCTGCTACCATTTGCAGCAGCCCCACCGGAGCCGAGCAGAATGCAGTTTTCTTCTCTAACTGTGAATGTG
+AGAGGCTCAGGAATGAGAATACTCGTGAGGGGTAACTCCCCCGTGTTCAACTACAACAAGGCAACCAAAAGGCTTACAGT
+CCTCGGAAAGGACGCAGGTGCATTAACAGAAGATCCAGACGAGGGAACAGCCGGGGTGGAATCTGCAGTATTGAGGGGAT
+TCCTAATTCTAGGCAGAGAGGACAAAAGATATGGACCCGCATTGAGCATCAATGAACTGAGCAATCTTGCAAAAGGGGAG
+AAGGCTAATGTATTGATAATGCAAGGAGACGTGGTGTTGGTAATGAAACGGAAACGGGACTTTAGCATACTTACTGACAG
+CCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAG
+>lcl|NC_007358.1_cds_YP_308665.1_2 [gene=PB1] [locus_tag=FLUAVH5N1_s2gp1] [db_xref=GeneID:3654616] [protein=polymerase] [protein_id=YP_308665.1] [location=25..2298] [gbkey=CDS]
+ATGGATGTCAATCCGACTTTACTTTTCTTAAAAGTGCCAGCGCAAAATGCTATAAGTACCACATTCCCTTATACTGGAGA
+TCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATATTCAGAAAAGGGGA
+AATGGACAACGAACACAGAGACTGGAGCACCCCAACTCAATCCGATTGATGGACCACTACCTGAGGATAATGAGCCGAGT
+GGGTATGCACAAACAGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCGTG
+TCTTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAGCTGACCCAAGGTCGCCAAACCTATGACTGGACATTGA
+AAAGAAACCAGCCGGCTGCAACCGCTTTGGCCAACACTATAGAGGTCTTCAGATCGAATGGTCTAACAGCCAATGAATCG
+GGAAGGCTAATAGATTTCCTCAAAGACGTGATGGAATCAATGGATAAGGGAGAAATGGAAATAATAACACATTTCCAGAG
+AAAGAGAAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAAAAACAAAGGCTGAACA
+AAAGGAGCTACCTAATAAGAGCACTGACACTGAACACAATGACAAAAGACGCAGAAAGAGGCAAATTGAAGAGGCGGGCA
+ATTGCAACACCCGGGATGCAAATCAGAGGATTCGTGTACTTTGTCGAAACACTAGCGAGGAGTATCTGTGAGAAACTTGA
+GCAATCTGGACTCCCCGTCGGAGGGAATGAAAAGAAGGCTAAATTGGCAAATGTCGTGAGGAAGATGATGACTAACTCAC
+AAGATACAGAGCTCTCTTTTACAATTACTGGAGACAACACCAAATGGAATGAGAATCAGAACCCTCGGATGTTTCTAGCA
+ATGATAACATACATCACAAGGAACCAACCTGAATGGTTTAGAAATGTCTTAAGCATTGCTCCTATAATGTTCTCAAACAA
+GATGGCAAGATTAGGGAAAGGATACATGTTCGAAAGTAAGAGCATGAAGCTACGGACACAAATACCAGCAGAAATGCTTG
+CAAGCATTGACTTGAAATACTTCAACGAATCAACGAGAAAGAAAATCGAGAAAATAAGACCTCTACTAATAGATGGCACA
+GCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAATATGCTGAGTACAGTCTTAGGAGTTTCAATCCTGAATCTTGG
+GCAGAAGAGGTACACCAAAACCACATACTGGTGGGACGGACTCCAATCCTCTGATGATTTCGCTCTCATAGTGAATGCAC
+CAAATCATGAGGGAATAGAAGCAGGGGTGGATAGGTTCTATAGGACTTGCAAACTAGTTGGAATCAATATGACCAAGAAG
+AAGTCTTACATAAATCGGACAGGAACATGTGAATTCACAAGCTTCTTCTACCGCTATGGGTTCGTAGCCAACTTCAGTAT
+GGAGCTGCCCAGCTTTGGAGTGTCTGGGATTAATGAATCGGCTGACATGAGCATTGGTGTTACAGTGATAAAGAACAATA
+TGATGGACAACGACCTTGGACCAGCAACAGCTCAGATGGCTCTTCAGCTATTCATTAAGGACTACAGATACCCATACCGA
+TGCCACAGGGGGGATACACAAATCCAAACGAGGAGATCATTCGAGCTGAAGAAGCTGTGGGAGCAGACCCGCTCAAAGGC
+AGGACTGTTGGTTTCAGATGGAGGACCAAACCCATACAATATCCGGAATCTCCACATTCCGGAGGCTGGCTTGAAGTGGG
+AATTGATGGATGAAGACTACCAGGGCAGACTGTGTAATCCTCTGAACCCGTTTGTTAGTCATAAGGAAATTGAGTCTGTC
+AACAATGCTGTGGTAATGCCAGCTCATGGCCCAGCCAAGAGCATGGAATATGATGCAGTTGCGACTACACATTCATGGAT
+TCCCAAGAGGAATCGTTCCATTCTCAACACCAGCCAAAGGGGGATTCTTGAGGATGAACAGATGTATCAGAAGTGCTGCA
+ATCTATTCGAGAAATTCTTCCCTAGCAGTTCATATCGGAGGCCAGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCT
+AGGGCCCGAATTGATGCACGAATTGACTTCGAGTCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTG
+TTCCACCATTGAAGAGCTCGGACGGCAAAAATAG
+>lcl|NC_007358.1_cds_YP_473348.1_3 [gene=PB1-F2] [locus_tag=FLUAVH5N1_s2gp2] [db_xref=GeneID:3896424] [protein=PB1-F2 protein] [protein_id=YP_473348.1] [location=119..391] [gbkey=CDS]
+ATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATATTCAGAAAAGGGGAAATGGACAACGAAC
+ACAGAGACTGGAGCACCCCAACTCAATCCGATTGATGGACCACTACCTGAGGATAATGAGCCGAGTGGGTATGCACAAAC
+AGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCGTGTCTTGAAACGATGG
+AAGTTGTTCAGCAAACAAGAGTGGATAAGCTGA
+>lcl|NC_007359.1_cds_YP_308666.1_4 [gene=PA] [locus_tag=FLUAVH5N1_s3gp1] [db_xref=GeneID:3654617] [protein=polymerase] [protein_id=YP_308666.1] [location=25..2175] [gbkey=CDS]
+ATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATTGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGA
+TCCGAAAATCGAAACGAACAAATTTGCCGCAATATGCACGCACTTAGAAGTCTGTTTCATGTATTCAGATTTCCACTTTA
+TTGATGAACGGGGCGAATCAACAATTATAGAATCTGGCGATCCCAATGCATTATTGAAACACCGGTTTGAAATAATCGAA
+GGGAGGGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGGAGTTGAGAAGCCTAAATTTCTCCC
+AGATTTGTATGACTACAAGGAGAACCGATTTATTGAAATTGGAGTGACACGGAGGGAAGTTCACACATACTATCTAGAAA
+AAGCCAACAAGATAAAATCTGAGAAGACACACATTCACATATTCTCATTCACTGGAGAGGAAATGGCCACCAAAGCGGAC
+TACACCCTTGATGAAGAAAGCAGGGCCCGAATCAAAACCAGGCTGTTCACTATAAGGCAGGAAATGGCCAGTAGGGGTTT
+ATGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGAGACAGTTGAAGAAAGATTTGAAATCACAGGGACTATGTGCAGGC
+TTGCCGACCAAAGTCTCCCACCTAATTTCTCCAGCCTTGAAAAATTTAGAGCCTATGTGGATGGATTCGAACCGAACGGC
+TGCATTGAGGGCAAGCTTTCTCAAATGTCGAAAGAAGTAAACGCCAGAATTGAGCCATTTCTGAAGACAACACCACGCCC
+TCTTAGATTACCTGATGGGCCTCCCTGCTCTCAGCGGTCGAAGTTTTTGCTGATGGATGCCCTTAAATTAAGCATCGAAG
+ACCCGAGTCATGAGGGGGAGGGGATACCGCTATATGATGCAATCAAATGCATGAAAACATTTTTCGGCTGGAAAGAGCCC
+AACATTGTAAAACCACATGAAAAAGGCATAAACCCCAATTACCTCCTGGCTTGGAAGCAGGTGCTGGCAGAGCTCCAAGA
+TATTGAAAACGAGGAGAAAATTCCAAAGACAAAGAACATGAGGAAAACAAGCCAATTGAAGTGGGCACTTGGTGAGAATA
+TGGCACCAGAGAAAGTAGACTTTGAGGATTGCAAAGATGTTAGCGATCTAAGGCAGTATGACAGTGATGAACCAAAGCCT
+AGATCACTAGCAAGCTGGATCCAGAGTGAATTCAACAAGGCATGCGAATTGACAGATTCAAGTTGGATTGAACTTGATGA
+AATAGGGGAAGACGTTGCTCCAATTGAGCACATTGCAAGTATGAGAAGGAACTATTTCACAGCGGAAGTATCCCATTGCA
+GGGCTACTGAATACATAATGAAGGGAGTGTACATAAACACAGCTTTGTTGAATGCATCCTGTGCAGCCATGGATGACTTC
+CAACTGATCCCAATGATAAGCAAATGCAGAACCAAAGAAGGAAGACGGAAAACTAACCTGTATGGATTCCTTATAAAAGG
+AAGATCCCATTTGAGAAATGACACCGATGTGGTAAACTTTGTGAGTATGGAATTCTCTCTTACTGATCCGAGGCTGGAGC
+CACACAGATGGGAAAAGTACTGCGTTCTTCGGATAGGAGACATGCTCTTACGGACTGAAATAGGCCAAGTGTCAAGGCCC
+ATGTTTCTTTATGTGAGAACCAATGGAACCTCCAAGATCAAGATGAAATGGGGCATGGAAATGAGGCGATGCCCTTTTCA
+ATCCCTTCAACAGATTGAGAGCATGATTGAGGCCGAGTCTTCTGTCAAAGAAAAAGACATGACTAAAGAATTCTTTGAAA
+ACAAATCAGAAACATGGCCAATTGGAGAATCACCCAAGGGAGTGGAGGAAGGCTCCATCGGGAAGGTGTGCAGAACCTTA
+CTGGCTAAATCTGTTTTCAACAGTCTATATGCATCTCCACAACTCGAGGGGTTTTCAGCTGAATCAAGAAAATTGCTTCT
+CATTGTTCAGGCACTTAGGGACAACCTGGAACCTGGAACCTTCGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCC
+TGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTAAGATAG
+>lcl|NC_007359.1_cds_YP_006495800.1_5 [gene=PA-X] [locus_tag=FLUAVH5N1_s3gp2] [db_xref=GeneID:13229455] [protein=PA-X protein] [exception=ribosomal slippage] [protein_id=YP_006495800.1] [location=join(25..594,596..784)] [gbkey=CDS]
+ATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATTGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGA
+TCCGAAAATCGAAACGAACAAATTTGCCGCAATATGCACGCACTTAGAAGTCTGTTTCATGTATTCAGATTTCCACTTTA
+TTGATGAACGGGGCGAATCAACAATTATAGAATCTGGCGATCCCAATGCATTATTGAAACACCGGTTTGAAATAATCGAA
+GGGAGGGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGGAGTTGAGAAGCCTAAATTTCTCCC
+AGATTTGTATGACTACAAGGAGAACCGATTTATTGAAATTGGAGTGACACGGAGGGAAGTTCACACATACTATCTAGAAA
+AAGCCAACAAGATAAAATCTGAGAAGACACACATTCACATATTCTCATTCACTGGAGAGGAAATGGCCACCAAAGCGGAC
+TACACCCTTGATGAAGAAAGCAGGGCCCGAATCAAAACCAGGCTGTTCACTATAAGGCAGGAAATGGCCAGTAGGGGTTT
+ATGGGATTCCTTCGTCAGTCCGAGAGAGGCGAAGAGACAGTTGAAGAAAGATTTGAAATCACAGGGACTATGTGCAGGCT
+TGCCGACCAAAGTCTCCCACCTAATTTCTCCAGCCTTGAAAAATTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCT
+GCATTGAGGGCAAGCTTTCTCAAATGTCGAAAGAAGTAA
+>lcl|NC_007362.1_cds_YP_308669.1_6 [gene=HA] [locus_tag=FLUAVH5N1_s4gp1] [db_xref=GeneID:3654620] [protein=hemagglutinin] [protein_id=YP_308669.1] [location=22..1728] [gbkey=CDS]
+ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
+CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
+ATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
+CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
+CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
+CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCATGGGAGGTCCTCCTTTTTC
+AGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGA
+TCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACTTACA
+TTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGA
+AGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA
+ATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGT
+GTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAA
+TATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAGAGAGAGAGAAGAAGAAAAAAGAGAGG
+ACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCA
+ATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG
+ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGATAGAGAATTTAAA
+CAAGCAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTC
+TAGACTTTCATGACTCAAATGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGT
+AATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCA
+GTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT
+CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGA
+TCGTTACAATGCAGAATTTGCATTTAA
+>lcl|NC_007360.1_cds_YP_308667.1_7 [gene=NP] [locus_tag=FLUAVH5N1_s5gp1] [db_xref=GeneID:3654618] [protein=nucleocapsid protein] [protein_id=YP_308667.1] [location=46..1542] [gbkey=CDS]
+ATGGCGTCTCAGGGCACCAAACGATCTTATGAACAGATGGAAACTGGTGGAGAACGCCAGAATGCTACTGAGATCAGAGC
+ATCTGTTGGAAGAATGGTTGGTGGAATTGGGAGGTTTTATATACAGATGTGCACTGAACTCAAACTCAGCGACTATGAAG
+GAAGGCTGATTCAGAACAGCATAACAATAGAGAGAATGGTTCTCTCTGCATTTGATGAAAGGAGGAACAAATACCTGGAA
+GAACATCCCAGTGCGGGGAAGGACCCAAAGAAAACTGGAGGTCCAATCTACCGAAGAAGAGACGGAAAATGGGTGAGAGA
+GCTGATTCTGTATGACAAAGAGGAGATCAGGAGAATTTGGCGTCAAGCGAACAATGGAGAAGATGCAACTGCTGGTCTCA
+CTCACATGATGATCTGGCATTCCAATCTAAATGATGCCACATACCAGAGAACAAGAGCTCTCGTGCGTACTGGGATGGAC
+CCTAGAATGTGCTCTCTGATGCAAGGATCAACTCTCCCGAGGAGATCTGGAGCTGCTGGTGCGGCAGTAAAGGGAGTCGG
+AACGATGGTGATGGAACTAATTCGGATGATAAAGCGAGGGATTAACGATCGGAATTTCTGGAGAGGTGAAAATGGGCGAA
+GAACAAGAATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAATTCCAAACAGCAGCACAAAGAGCAATGATGGAT
+CAGGTACGGGAAAGCAGAAATCCTGGGAATGCTGAGATTGAAGATCTCATATTTCTGGCACGGTCTGCACTCATCCTGAG
+AGGATCAGTGGCCCACAAGTCCTGCTTGCCTGCTTGTGTGTACGGGCTTGCCGTGGCCAGTGGATATGACTTTGAGAGAG
+AAGGGTACTCTCTGGTCGGGATTGATCCTTTCCGTCTGCTGCAAAACAGCCAGGTCTTTAGTCTAATTAGACCAAATGAG
+AATCCAGCACATAAAAGTCAATTGGTGTGGATGGCATGCCATTCTGCAGCATTTGAAGATCTGAGAGTCTCAAGCTTCAT
+CAGAGGGACAAGAGTGGCCCCAAGGGGACAACTATCTACTAGAGGAGTTCAAATTGCTTCAAATGAGAACATGGAAACAA
+TGGACTCCAGCACTCTTGAACTGAGAAGCAGATATTGGGCTATAAGGACCAGGAGTGGAGGAAACACCAACCAGCAGAGA
+GCATCTGCAGGACAAATCAGTGTGCAGCCTACTTTCTCGGTACAGAGAAATCTTCCCTTCGAAAGAGCGACCATTATGGC
+GGCATTCACAGGGAATACAGAGGGCAGAACATCTGACATGAGGACTGAAATCATAAGGATGATGGAAAGCTCCAGACCAG
+AAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGAC
+ATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAATATGACAATTGA
+>lcl|NC_007361.1_cds_YP_308668.1_8 [gene=NA] [locus_tag=FLUAVH5N1_s6gp1] [db_xref=GeneID:3654619] [protein=neuraminidase] [protein_id=YP_308668.1] [location=21..1430] [gbkey=CDS]
+ATGAATCCAAATCAGAAGATAATAACCATTGGATCAATCTGTATGGTAGTTGGGATAATTAGCTTGATGTTACAAATTGG
+GAACATAATCTCAATATGGGTCAGTCATTCAATTCAGACAGGGAATCAACACCAAGCTGAACCATGCAATCAAAGCATTA
+TTACTTATGAAAACAACACCTGGGTAAATCAAACATATGTCAACATCAGCAATACCAATTTTCTTACTGAAAAAGCTGTG
+GCTTCAGTAACATTAGCGGGCAATTCATCTCTTTGCCCCATTAGCGGATGGGCTGTACACAGTAAGGACAACGGTATAAG
+AATCGGTTCCAAGGGGGATGTGTTTGTTATAAGAGAGCCGTTCATCTCATGCTCCCACTTGGAATGCAGAACTTTCTTTT
+TGACTCAGGGAGCCTTGCTGAATGACAAGCACTCCAATGGGACCGTCAAAGACAGAAGCCCTCACAGAACATTGATGAGT
+TGTCCTGTGGGTGAGGCTCCCTCCCCATATAACTCAAGGTTTGAGTCTGTTGCTTGGTCGGCAAGTGCTTGCCATGATGG
+CACCAGTTGGTTGACAATTGGAATTTCTGGCCCAGACAATGGGGCTGTGGCTGTATTGAAATACAACGGCATAATAACAG
+ACACTATCAAGAGTTGGAGGAACAACATACTGAGAACTCAAGAGTCTGAATGTGCATGTGTAAATGGCTCTTGCTTTACT
+GTAATGACTGACGGACCAAGTAATGGGCAGGCCTCATATAAGATCTTCAAAATGGAAAAAGGGAAAGTAGTTAAATCAGT
+CGAATTGAATGCCCCTAATTATCACTATGAGGAGTGCTCCTGTTATCCTGATGCTGGCGAAATCACATGTGTGTGCAGGG
+ATAATTGGCATGGCTCAAATCGGCCATGGGTATCTTTCAATCAAAATTTGGAGTATCAAATAGGATATATATGCAGTGGA
+GTTTTCGGAGACAATCCACGCCCCAATGATGGAACAGGCAGTTGTGGTCCGGTGTCCCCTAACGGGGCATATGGAGTAAA
+AGGGTTTTCATTTAAATACGGCAATGGTGTTTGGATCGGGAGAACCAAAAGCACTAATTCCAGGAGCGGCTTTGAAATGA
+TTTGGGATCCAAATGGGTGGACTGGAACGGACAGTAGCTTCTCGGTGAAACAAGATATCGTAGCAATAACTGATTGGTCA
+GGATATAGCGGGAGTTTTGTCCAGCATCCAGAACTGACAGGATTAGATTGCATAAGACCTTGTTTCTGGGTTGAGCTAAT
+CAGAGGGCGGCCCAAAGAGAGCACAATTTGGACTAGTGGGAGCAGCATATCTTTTTGTGGTGTAAATAGTGACACTGTGG
+GTTGGTCTTGGCCAGACGATGCCGAGTTGCCATTCACCATTGACAAGTAG
+>lcl|NC_007363.1_cds_YP_308670.1_9 [gene=M2] [locus_tag=FLUAVH5N1_s7gp1] [db_xref=GeneID:3654621] [protein=matrix protein 2] [protein_id=YP_308670.1] [location=join(26..51,740..1007)] [gbkey=CDS]
+ATGAGTCTTCTAACCGAGGTCGAAACGCCTACCAAAAACGAATGGGAGTGCAAATGCAGCGATTCAAGTGATCCTCTTGT
+TGTTGCCGCAAGTATCATTGGGATACTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTC
+GCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAG
+CAGAGTGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAA
+>lcl|NC_007363.1_cds_YP_308671.1_10 [gene=M1] [locus_tag=FLUAVH5N1_s7gp2] [db_xref=GeneID:8656647] [protein=matrix protein 1] [protein_id=YP_308671.1] [location=26..784] [gbkey=CDS]
+ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAG
+ACTTGAGGATGTCTTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCAC
+CTCTGACTAAAGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTC
+CAGAATGCCTTAAATGGAAATGGAGATCCAAACAATATGGATAGGGCAGTTAAGCTATACAAGAAGCTGAAAAGAGAAAT
+AACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGTATGGGTCTCATATACAACA
+GGATGGGAACGGTGACCACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCAGATTCACAGCATCGG
+TCTCACAGACAGATGGCAACTACCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAA
+GGCTATGGAGCAGATGGCTGGATCGAGTGAGCAGGCAGCGGAAGCCATGGAGGTTGCTAGTCAGGCTAGGCAGATGGTGC
+AGGCAATGAGGACAATTGGGACTCATCCTAGCTCCAGTGCCGGTCTGAAAGATAATCTTCTTGAAAATTTGCAGGCCTAC
+CAAAAACGAATGGGAGTGCAAATGCAGCGATTCAAGTGA
+>lcl|NC_007364.1_cds_YP_308672.1_11 [gene=NEP] [locus_tag=FLUAVH5N1_s8gp1] [db_xref=GeneID:3654622] [protein=nonstructural protein 2] [protein_id=YP_308672.1] [location=join(15..44,517..852)] [gbkey=CDS]
+ATGGATTCCAACACGATAACCTCGTTTCAGGACATTTTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATCGGTGGA
+CTTGAATGGAATGATAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAATCCATGATGAGAATGGGGG
+ACCTTCACTCCCTCCAAAACAGAAACGCTACATGGCGAAACGAGTTGAGTCAGAAGTTTGAAGAGATCAGATGGCTCATT
+GCTGAATGTAGAAATATACTGACAAAGACTGAAAATAGCTTTGAACAGATAACATTTTTGCAAGCATTGCAACTCTTACT
+TGAAGTTGAGAGTGAGATAAGGACCTTCTCTTTTCAGCTTATTTAA
+>lcl|NC_007364.1_cds_YP_308673.1_12 [gene=NS1] [locus_tag=FLUAVH5N1_s8gp2] [db_xref=GeneID:8656648] [protein=nonstructural protein 1] [protein_id=YP_308673.1] [location=15..707] [gbkey=CDS]
+ATGGATTCCAACACGATAACCTCGTTTCAGGTAGATTGTTATCTATGGCACATAAGAAAGCTACTCAGTATGAGAGACAT
+GTGTGATGCCCCCTTTGATGACAGGCTCCGAAGAGACCAAAAGGCATTAAAGGGAAGAGGCAGCACACTTGGACTCGATT
+TAAGAGTGGCTACAATGGAGGGGAAAAAGATCGTTGAGGACATCCTGAAGAGTGAGACAAATGAAAACCTCAAAATAGCC
+ATTGCTTCCAGTCCTGCTCCTCGGTATATCACCGATATGAGCATAGAGGAGATGAGCCGAGAATGGTACATGCTGATGCC
+TAGGCAGAAAATAACTGGAGGCCTTATGGTGAAAATGGACCAAGCCATAATGGATAAAAGAATTATCCTTAAAGCAAATT
+TCTCAGTTCTATTTGATCAACTAGAGACATTAGTCTCTCTGAGGGCATTCACAGAAAGTGGTGCTATTGTGGCTGAAATA
+TTTCCCATTCCCTCCGTACCAGGACATTTTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATCGGTGGACTTGAATG
+GAATGATAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAATCCATGATGAGAATGGGGGACCTTCAC
+TCCCTCCAAAACAGAAACGCTACATGGCGAAACGAGTTGAGTCAGAAGTTTGA

data/grippe.fasta

+>NC_007357.1 Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) polymerase (PB2) gene, complete cds
+AGCAAAAGCAGGTCAATTATATTCAATATGGAAAGAATAAAAGAACTAAGAGATCTAATGTCGCAGTCCCGCACTCGCGA
+GATACTAACAAAAACCACTGTGGATCATATGGCCATAATCAAGAAATACACATCAGGAAGACAAGAGAAGAACCCTGCTC
+TCAGAATGAAATGGATGATGGCAATGAAATATCCAATCACAGCAGACAAGAGAATAATGGAGATGATTCCTGAAAGGAAT
+GAGCAAGGACAAACGCTTTGGAGCAAGACAAATGATGCTGGGTCGGACAGAGTGATGGTGTCTCCCCTAGCTGTAACTTG
+GTGGAACAGGAATGGGCCGACAACAAGTACAGTCCATTATCCAAAGGTTTACAAAACATACTTTGAGAAGGTTGAAAGGT
+TAAAACATGGAACCTTCGGTCCCGTTCATTTCCGAAACCAAGTTAAAATACGTCGCCGGGTGGATATAAACCCGGGCCAT
+GCAGATCTCAGTGCTAAAGAAGCACAAGATGTTATCATGGAGGTCGTTTTCCCAAATGAAGTGGGAGCTAGAATATTGAC
+ATCAGAGTCGCAATTGACAATAACAAAAGAGAAGAAAGAAGAGCTCCAGGATTGTAAAATTGCTCCTTTAATGGTGGCAT
+ACATGTTGGAAAGAGAACTGGTCCGCAAAACCAGATTTCTACCGGTAGCAGGCGGAACAAGCAGTGTGTACATTGAGGTA
+TTGCATTTGACTCAAGGGACCTGTTGGGAACAGATGTACACTCCCGGCGGAGAAGTAAGAAATGATGATGTTGACCAGAG
+TTTGATCATCGCTGCCAGAAACATTGTTAGGAGAGCAACAGTATCAGCGGACCCACTGGCATCACTCTTGGAGATGTGTC
+ACAGCACACAAATTGGGGGAATAAGGATGGTGGACATCCTTAGGCAAAACCCAACTGAGGAGCAAGCTGTGGATATATGC
+AAAGCAGCAATGGGTTTGAGGATCAGTTCATCCTTTAGCTTTGGAGGCTTCACTTTCAAAAGAACAAATGGATCATCCGT
+CAAGAAGGAAGAGGAAGTGCTTACAGGCAACCTCCAAACATTGAAAATAAAAGTACATGAGGGGTATGAAGAATTCACAA
+TGGTTGGGCGGAGAGCAACAGCTATCCTGAGGAAAGCAACTAGAAGGCTGATTCAGTTGATAGTAAGTGGAAGAGATGAA
+CAATCAATCGCTGAAGCGATCATTGTAGCAATGGTGTTCTCACAGGAGGATTGCATGATAAAGGCAGTCCGAGGCGATCT
+GAATTTCGTGAACAGAGCAAACCAAAGATTGAACCCCATGCATCAACTCCTGAGGCACTTCCAAAAAGATGCAAAAGTGC
+TGTTTCAGAACTGGGGAATTGAACCTATTGACAATGTCATGGGGATGATCGGAATATTACCTGACATGACTCCAAGCGCA
+GAGATGTCACTGAGAGGAGTGAGAGTTAGTAAGATGGGAGTAGATGAATATTCCAGCACGGAGAGAGTGGTGGTGAGTAT
+TGACCGTTTCTTGAGGGTCCGAGATCAGCAGGGGAACGTACTCTTATCTCCTGAAGAGGTTAGTGAAACACAGGGAACAG
+AGAAGTTGACAATAACATATTCATCCTCAATGATGTGGGAAATCAACGGTCCTGAGTCAGTGCTTGTTAACACTTATCAA
+TGGATCATCAGGAATTGGGAGACTGTAAAGATTCAATGGTCTCAAGATCCCACAATGCTGTACAATAAGATGGAGTTTGA
+ATCGTTCCAATCCTTGGTGCCAAAGGCTGCCAGAAGCCAATATAGTGGATTTGTGAGAACACTATTCCAACAGATGCGTG
+ATGTTTTGGGGACATTTGATACTGTCCAAATAATCAAGCTGCTACCATTTGCAGCAGCCCCACCGGAGCCGAGCAGAATG
+CAGTTTTCTTCTCTAACTGTGAATGTGAGAGGCTCAGGAATGAGAATACTCGTGAGGGGTAACTCCCCCGTGTTCAACTA
+CAACAAGGCAACCAAAAGGCTTACAGTCCTCGGAAAGGACGCAGGTGCATTAACAGAAGATCCAGACGAGGGAACAGCCG
+GGGTGGAATCTGCAGTATTGAGGGGATTCCTAATTCTAGGCAGAGAGGACAAAAGATATGGACCCGCATTGAGCATCAAT
+GAACTGAGCAATCTTGCAAAAGGGGAGAAGGCTAATGTATTGATAATGCAAGGAGACGTGGTGTTGGTAATGAAACGGAA
+ACGGGACTTTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGTTGAATAGTTT
+AAAAACGACCTTGTTTCTACT
+>NC_007358.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) polymerase (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds
+AGCAAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTAAAAGTGCCAGCGCAAAATGCTATAAG
+TACCACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAA
+CACATCAATATTCAGAAAAGGGGAAATGGACAACGAACACAGAGACTGGAGCACCCCAACTCAATCCGATTGATGGACCA
+CTACCTGAGGATAATGAGCCGAGTGGGTATGCACAAACAGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCCCA
+CCCAGGGATCTTTGAAAACTCGTGTCTTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAGCTGACCCAAGGTC
+GCCAAACCTATGACTGGACATTGAAAAGAAACCAGCCGGCTGCAACCGCTTTGGCCAACACTATAGAGGTCTTCAGATCG
+AATGGTCTAACAGCCAATGAATCGGGAAGGCTAATAGATTTCCTCAAAGACGTGATGGAATCAATGGATAAGGGAGAAAT
+GGAAATAATAACACATTTCCAGAGAAAGAGAAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAG
+GGAAGAAAAAACAAAGGCTGAACAAAAGGAGCTACCTAATAAGAGCACTGACACTGAACACAATGACAAAAGACGCAGAA
+AGAGGCAAATTGAAGAGGCGGGCAATTGCAACACCCGGGATGCAAATCAGAGGATTCGTGTACTTTGTCGAAACACTAGC
+GAGGAGTATCTGTGAGAAACTTGAGCAATCTGGACTCCCCGTCGGAGGGAATGAAAAGAAGGCTAAATTGGCAAATGTCG
+TGAGGAAGATGATGACTAACTCACAAGATACAGAGCTCTCTTTTACAATTACTGGAGACAACACCAAATGGAATGAGAAT
+CAGAACCCTCGGATGTTTCTAGCAATGATAACATACATCACAAGGAACCAACCTGAATGGTTTAGAAATGTCTTAAGCAT
+TGCTCCTATAATGTTCTCAAACAAGATGGCAAGATTAGGGAAAGGATACATGTTCGAAAGTAAGAGCATGAAGCTACGGA
+CACAAATACCAGCAGAAATGCTTGCAAGCATTGACTTGAAATACTTCAACGAATCAACGAGAAAGAAAATCGAGAAAATA
+AGACCTCTACTAATAGATGGCACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAATATGCTGAGTACAGTCTT
+AGGAGTTTCAATCCTGAATCTTGGGCAGAAGAGGTACACCAAAACCACATACTGGTGGGACGGACTCCAATCCTCTGATG
+ATTTCGCTCTCATAGTGAATGCACCAAATCATGAGGGAATAGAAGCAGGGGTGGATAGGTTCTATAGGACTTGCAAACTA
+GTTGGAATCAATATGACCAAGAAGAAGTCTTACATAAATCGGACAGGAACATGTGAATTCACAAGCTTCTTCTACCGCTA
+TGGGTTCGTAGCCAACTTCAGTATGGAGCTGCCCAGCTTTGGAGTGTCTGGGATTAATGAATCGGCTGACATGAGCATTG
+GTGTTACAGTGATAAAGAACAATATGATGGACAACGACCTTGGACCAGCAACAGCTCAGATGGCTCTTCAGCTATTCATT
+AAGGACTACAGATACCCATACCGATGCCACAGGGGGGATACACAAATCCAAACGAGGAGATCATTCGAGCTGAAGAAGCT
+GTGGGAGCAGACCCGCTCAAAGGCAGGACTGTTGGTTTCAGATGGAGGACCAAACCCATACAATATCCGGAATCTCCACA
+TTCCGGAGGCTGGCTTGAAGTGGGAATTGATGGATGAAGACTACCAGGGCAGACTGTGTAATCCTCTGAACCCGTTTGTT
+AGTCATAAGGAAATTGAGTCTGTCAACAATGCTGTGGTAATGCCAGCTCATGGCCCAGCCAAGAGCATGGAATATGATGC
+AGTTGCGACTACACATTCATGGATTCCCAAGAGGAATCGTTCCATTCTCAACACCAGCCAAAGGGGGATTCTTGAGGATG
+AACAGATGTATCAGAAGTGCTGCAATCTATTCGAGAAATTCTTCCCTAGCAGTTCATATCGGAGGCCAGTTGGAATTTCC
+AGCATGGTGGAGGCCATGGTGTCTAGGGCCCGAATTGATGCACGAATTGACTTCGAGTCTGGAAGGATTAAGAAAGAAGA
+GTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCGGACGGCAAAAATAGTGAATTTAGCTTGTCCTTCATG
+AAAAAATGCCTTGTTTCTACT
+>NC_007359.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) polymerase (PA) and PA-X protein (PA-X) genes, complete cds
+AGCAAAAGCAGGTACTGATCCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATTGTCGAGCTTGCGGAAAA
+GGCAATGAAAGAATATGGGGAAGATCCGAAAATCGAAACGAACAAATTTGCCGCAATATGCACGCACTTAGAAGTCTGTT
+TCATGTATTCAGATTTCCACTTTATTGATGAACGGGGCGAATCAACAATTATAGAATCTGGCGATCCCAATGCATTATTG
+AAACACCGGTTTGAAATAATCGAAGGGAGGGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGG
+AGTTGAGAAGCCTAAATTTCTCCCAGATTTGTATGACTACAAGGAGAACCGATTTATTGAAATTGGAGTGACACGGAGGG
+AAGTTCACACATACTATCTAGAAAAAGCCAACAAGATAAAATCTGAGAAGACACACATTCACATATTCTCATTCACTGGA
+GAGGAAATGGCCACCAAAGCGGACTACACCCTTGATGAAGAAAGCAGGGCCCGAATCAAAACCAGGCTGTTCACTATAAG
+GCAGGAAATGGCCAGTAGGGGTTTATGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGAGACAGTTGAAGAAAGATTTG
+AAATCACAGGGACTATGTGCAGGCTTGCCGACCAAAGTCTCCCACCTAATTTCTCCAGCCTTGAAAAATTTAGAGCCTAT
+GTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCGAAAGAAGTAAACGCCAGAATTGAGCC
+ATTTCTGAAGACAACACCACGCCCTCTTAGATTACCTGATGGGCCTCCCTGCTCTCAGCGGTCGAAGTTTTTGCTGATGG
+ATGCCCTTAAATTAAGCATCGAAGACCCGAGTCATGAGGGGGAGGGGATACCGCTATATGATGCAATCAAATGCATGAAA
+ACATTTTTCGGCTGGAAAGAGCCCAACATTGTAAAACCACATGAAAAAGGCATAAACCCCAATTACCTCCTGGCTTGGAA
+GCAGGTGCTGGCAGAGCTCCAAGATATTGAAAACGAGGAGAAAATTCCAAAGACAAAGAACATGAGGAAAACAAGCCAAT
+TGAAGTGGGCACTTGGTGAGAATATGGCACCAGAGAAAGTAGACTTTGAGGATTGCAAAGATGTTAGCGATCTAAGGCAG
+TATGACAGTGATGAACCAAAGCCTAGATCACTAGCAAGCTGGATCCAGAGTGAATTCAACAAGGCATGCGAATTGACAGA
+TTCAAGTTGGATTGAACTTGATGAAATAGGGGAAGACGTTGCTCCAATTGAGCACATTGCAAGTATGAGAAGGAACTATT
+TCACAGCGGAAGTATCCCATTGCAGGGCTACTGAATACATAATGAAGGGAGTGTACATAAACACAGCTTTGTTGAATGCA
+TCCTGTGCAGCCATGGATGACTTCCAACTGATCCCAATGATAAGCAAATGCAGAACCAAAGAAGGAAGACGGAAAACTAA
+CCTGTATGGATTCCTTATAAAAGGAAGATCCCATTTGAGAAATGACACCGATGTGGTAAACTTTGTGAGTATGGAATTCT
+CTCTTACTGATCCGAGGCTGGAGCCACACAGATGGGAAAAGTACTGCGTTCTTCGGATAGGAGACATGCTCTTACGGACT
+GAAATAGGCCAAGTGTCAAGGCCCATGTTTCTTTATGTGAGAACCAATGGAACCTCCAAGATCAAGATGAAATGGGGCAT
+GGAAATGAGGCGATGCCCTTTTCAATCCCTTCAACAGATTGAGAGCATGATTGAGGCCGAGTCTTCTGTCAAAGAAAAAG
+ACATGACTAAAGAATTCTTTGAAAACAAATCAGAAACATGGCCAATTGGAGAATCACCCAAGGGAGTGGAGGAAGGCTCC
+ATCGGGAAGGTGTGCAGAACCTTACTGGCTAAATCTGTTTTCAACAGTCTATATGCATCTCCACAACTCGAGGGGTTTTC
+AGCTGAATCAAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGAACCTGGAACCTTCGATCTTGGGGGGC
+TATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACA
+CATGCACTAAGATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTTTCTACT
+>NC_007362.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) hemagglutinin (HA) gene, complete cds
+GCAGGGGTATAATCTGTCAAAATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTG
+CATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAG
+ACATACTGGAAAAGACACACAATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTA
+GCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAG
+TCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATT
+TTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATAC
+CATGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTA
+CAATAATACCAACCAAGAAGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCT
+ATCAAAACCCAACCACTTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCC
+AAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAA
+TGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAAT
+ATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTC
+ACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAGAGAGA
+GAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTT
+GGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGA
+GTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGA
+AAGGAGGATAGAGAATTTAAACAAGCAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTC
+TCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGG
+GATAATGCAAAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAA
+CGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAA
+TGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCT
+TTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATTTAAATTTGTGAGTTCAGATTGTAGTTAAAAACACC
+>NC_007360.1 Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) nucleocapsid protein (NP) gene, complete cds
+AGCAAAAGCAGGGTAGATAATCACTCACTGAGTGACATCAACATCATGGCGTCTCAGGGCACCAAACGATCTTATGAACA
+GATGGAAACTGGTGGAGAACGCCAGAATGCTACTGAGATCAGAGCATCTGTTGGAAGAATGGTTGGTGGAATTGGGAGGT
+TTTATATACAGATGTGCACTGAACTCAAACTCAGCGACTATGAAGGAAGGCTGATTCAGAACAGCATAACAATAGAGAGA
+ATGGTTCTCTCTGCATTTGATGAAAGGAGGAACAAATACCTGGAAGAACATCCCAGTGCGGGGAAGGACCCAAAGAAAAC
+TGGAGGTCCAATCTACCGAAGAAGAGACGGAAAATGGGTGAGAGAGCTGATTCTGTATGACAAAGAGGAGATCAGGAGAA
+TTTGGCGTCAAGCGAACAATGGAGAAGATGCAACTGCTGGTCTCACTCACATGATGATCTGGCATTCCAATCTAAATGAT
+GCCACATACCAGAGAACAAGAGCTCTCGTGCGTACTGGGATGGACCCTAGAATGTGCTCTCTGATGCAAGGATCAACTCT
+CCCGAGGAGATCTGGAGCTGCTGGTGCGGCAGTAAAGGGAGTCGGAACGATGGTGATGGAACTAATTCGGATGATAAAGC
+GAGGGATTAACGATCGGAATTTCTGGAGAGGTGAAAATGGGCGAAGAACAAGAATTGCATATGAGAGAATGTGCAACATC
+CTCAAAGGGAAATTCCAAACAGCAGCACAAAGAGCAATGATGGATCAGGTACGGGAAAGCAGAAATCCTGGGAATGCTGA
+GATTGAAGATCTCATATTTCTGGCACGGTCTGCACTCATCCTGAGAGGATCAGTGGCCCACAAGTCCTGCTTGCCTGCTT
+GTGTGTACGGGCTTGCCGTGGCCAGTGGATATGACTTTGAGAGAGAAGGGTACTCTCTGGTCGGGATTGATCCTTTCCGT
+CTGCTGCAAAACAGCCAGGTCTTTAGTCTAATTAGACCAAATGAGAATCCAGCACATAAAAGTCAATTGGTGTGGATGGC
+ATGCCATTCTGCAGCATTTGAAGATCTGAGAGTCTCAAGCTTCATCAGAGGGACAAGAGTGGCCCCAAGGGGACAACTAT
+CTACTAGAGGAGTTCAAATTGCTTCAAATGAGAACATGGAAACAATGGACTCCAGCACTCTTGAACTGAGAAGCAGATAT
+TGGGCTATAAGGACCAGGAGTGGAGGAAACACCAACCAGCAGAGAGCATCTGCAGGACAAATCAGTGTGCAGCCTACTTT
+CTCGGTACAGAGAAATCTTCCCTTCGAAAGAGCGACCATTATGGCGGCATTCACAGGGAATACAGAGGGCAGAACATCTG
+ACATGAGGACTGAAATCATAAGGATGATGGAAAGCTCCAGACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAG
+CTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTCGGAGACAA
+TGCAGAGGAATATGACAATTGAAGAAAAATACCCTTGTTTCTACT
+>NC_007361.1 Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) neuraminidase (NA) gene, complete cds
+AGCAAAAGCAGGAGATTAAAATGAATCCAAATCAGAAGATAATAACCATTGGATCAATCTGTATGGTAGTTGGGATAATT
+AGCTTGATGTTACAAATTGGGAACATAATCTCAATATGGGTCAGTCATTCAATTCAGACAGGGAATCAACACCAAGCTGA
+ACCATGCAATCAAAGCATTATTACTTATGAAAACAACACCTGGGTAAATCAAACATATGTCAACATCAGCAATACCAATT
+TTCTTACTGAAAAAGCTGTGGCTTCAGTAACATTAGCGGGCAATTCATCTCTTTGCCCCATTAGCGGATGGGCTGTACAC
+AGTAAGGACAACGGTATAAGAATCGGTTCCAAGGGGGATGTGTTTGTTATAAGAGAGCCGTTCATCTCATGCTCCCACTT
+GGAATGCAGAACTTTCTTTTTGACTCAGGGAGCCTTGCTGAATGACAAGCACTCCAATGGGACCGTCAAAGACAGAAGCC
+CTCACAGAACATTGATGAGTTGTCCTGTGGGTGAGGCTCCCTCCCCATATAACTCAAGGTTTGAGTCTGTTGCTTGGTCG
+GCAAGTGCTTGCCATGATGGCACCAGTTGGTTGACAATTGGAATTTCTGGCCCAGACAATGGGGCTGTGGCTGTATTGAA
+ATACAACGGCATAATAACAGACACTATCAAGAGTTGGAGGAACAACATACTGAGAACTCAAGAGTCTGAATGTGCATGTG
+TAAATGGCTCTTGCTTTACTGTAATGACTGACGGACCAAGTAATGGGCAGGCCTCATATAAGATCTTCAAAATGGAAAAA
+GGGAAAGTAGTTAAATCAGTCGAATTGAATGCCCCTAATTATCACTATGAGGAGTGCTCCTGTTATCCTGATGCTGGCGA
+AATCACATGTGTGTGCAGGGATAATTGGCATGGCTCAAATCGGCCATGGGTATCTTTCAATCAAAATTTGGAGTATCAAA
+TAGGATATATATGCAGTGGAGTTTTCGGAGACAATCCACGCCCCAATGATGGAACAGGCAGTTGTGGTCCGGTGTCCCCT
+AACGGGGCATATGGAGTAAAAGGGTTTTCATTTAAATACGGCAATGGTGTTTGGATCGGGAGAACCAAAAGCACTAATTC
+CAGGAGCGGCTTTGAAATGATTTGGGATCCAAATGGGTGGACTGGAACGGACAGTAGCTTCTCGGTGAAACAAGATATCG
+TAGCAATAACTGATTGGTCAGGATATAGCGGGAGTTTTGTCCAGCATCCAGAACTGACAGGATTAGATTGCATAAGACCT
+TGTTTCTGGGTTGAGCTAATCAGAGGGCGGCCCAAAGAGAGCACAATTTGGACTAGTGGGAGCAGCATATCTTTTTGTGG
+TGTAAATAGTGACACTGTGGGTTGGTCTTGGCCAGACGATGCCGAGTTGCCATTCACCATTGACAAGTAGTTTGTTCAAA
+AAACTCCTTGTTTCTACT
+>NC_007363.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) segment 7, complete sequence
+AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTCCCGTCAGGCC
+CCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTCTTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAATGG
+CTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCG
+AGGACTGCAGCGTAGACGCTTTGTCCAGAATGCCTTAAATGGAAATGGAGATCCAAACAATATGGATAGGGCAGTTAAGC
+TATACAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCC
+AGTTGTATGGGTCTCATATACAACAGGATGGGAACGGTGACCACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGA
+GCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACTACCACCAACCCACTAATCAGGCATGAGAACAGAA
+TGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCTGGATCGAGTGAGCAGGCAGCGGAAGCCATGGAGGTT
+GCTAGTCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAGCTCCAGTGCCGGTCTGAAAGATAA
+TCTTCTTGAAAATTTGCAGGCCTACCAAAAACGAATGGGAGTGCAAATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCC
+GCAAGTATCATTGGGATACTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAA
+ATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAGCAGAGTG
+CTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT
+>NC_007364.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) segment 8, complete sequence
+GTGACAAAGACATAATGGATTCCAACACGATAACCTCGTTTCAGGTAGATTGTTATCTATGGCACATAAGAAAGCTACTC
+AGTATGAGAGACATGTGTGATGCCCCCTTTGATGACAGGCTCCGAAGAGACCAAAAGGCATTAAAGGGAAGAGGCAGCAC
+ACTTGGACTCGATTTAAGAGTGGCTACAATGGAGGGGAAAAAGATCGTTGAGGACATCCTGAAGAGTGAGACAAATGAAA
+ACCTCAAAATAGCCATTGCTTCCAGTCCTGCTCCTCGGTATATCACCGATATGAGCATAGAGGAGATGAGCCGAGAATGG
+TACATGCTGATGCCTAGGCAGAAAATAACTGGAGGCCTTATGGTGAAAATGGACCAAGCCATAATGGATAAAAGAATTAT
+CCTTAAAGCAAATTTCTCAGTTCTATTTGATCAACTAGAGACATTAGTCTCTCTGAGGGCATTCACAGAAAGTGGTGCTA
+TTGTGGCTGAAATATTTCCCATTCCCTCCGTACCAGGACATTTTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATC
+GGTGGACTTGAATGGAATGATAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAATCCATGATGAGAA
+TGGGGGACCTTCACTCCCTCCAAAACAGAAACGCTACATGGCGAAACGAGTTGAGTCAGAAGTTTGAAGAGATCAGATGG
+CTCATTGCTGAATGTAGAAATATACTGACAAAGACTGAAAATAGCTTTGAACAGATAACATTTTTGCAAGCATTGCAACT
+CTTACTTGAAGTTGAGAGTGAGATAAGGACCTTCTCTTTTCAGCTTATTTAATACTAAAAAACAC

data/test.fna

+>lcl|NC_007357.1_cds_YP_308664.1_1 [gene=PB2] [locus_tag=FLUAVH5N1_s1gp1] [db_xref=GeneID:3654615] [protein=polymerase] [protein_id=YP_308664.1] [location=28..2307] [gbkey=CDS]
+ATGGAAAGAATAAAAGAACTAAGAGATCTAATGTCGCAGTCCCGCACTCGCGAGATACTAACAAAAACCACTGTGGATCA
+TATGGCCATAATCAAGAAATACACATCAGGAAGACAAGAGAAGAACCCTGCTCTCAGAATGAAATGGATGATGGCAATGA
+AATATCCAATCACAGCAGACAAGAGAATAATGGAGATGATTCCTGAAAGGAATGAGCAAGGACAAACGCTTTGGAGCAAG

kmc.md

+Résultats kmc avec k-mer de 27:
+Stage 1: 100%
+Stage 2: 100%
+1st stage: 12.2781s
+2nd stage: 24.6005s
+Total    : 36.8785s
+Tmp size : 1809MB
+
+Stats:
+   No. of k-mers below min. threshold :    243017427
+   No. of k-mers above max. threshold :            0
+   No. of unique k-mers               :    315431169
+   No. of unique counted k-mers       :     72413742
+   Total no. of k-mers                :   1644690745
+   Total no. of reads                 :     28282964
+   Total no. of super-k-mers          :    186607305

main.py

+import gzip
+import re
+from IOalignment import IOAlignment
+from Bio import SeqIO
+from Bio.Seq import Seq
+import parasail
+
+label = "NC_007357.1 Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) polymerase (PB2) gene, complete cds"
+# seqs = ParseFasta("data/grippe.fasta")
+# seq = seqs[label]
+# print([i for i in range(len(seq))])
+# for record in SeqIO.parse("example.fasta", "fasta"):
+#    print(record.id)
+
+# for line in file.readlines():
+#     print(line)
+
+# Lectures des reads :
+reads = {}
+with gzip.open('SRR10971381_1.fastq.gz', 'rt') as fastq:
+    counter = 0
+    for i, record in enumerate(SeqIO.parse(fastq, 'fastq'), start=1):
+        reads[i] = (str(record.seq))
+        counter+=1
+        if counter >= 1000:
+            break
+
+# Lectures de Grippe A :
+genes_grippe = IOAlignment('data/covid.fna')
+genes_grippe = genes_grippe.ParseFasta() # ID long => garder l'entier en entier ?
+
+#label = 'lcl|NC_007357.1_cds_YP_308664.1_1 [gene=PB2] [locus_tag=FLUAVH5N1_s1gp1] [db_xref=GeneID:3654615] [protein=polymerase] [protein_id=YP_308664.1] [location=28..2307] [gbkey=CDS]'
+#genome_grippe = genomes_grippe[label]
+
+#genome="BGAABCGHJ"
+
+
+
+
+# découpe le genome en n kmers de taille k
+def split_kmers(genome, k):
+    i = 0
+    res = []
+
+    # chaque k lettres, découper un nouveau mot et le placer dans la liste des kmers
+    for i in range(0, len(genome), k):
+        res.append(genome[i:i+k])
+
+    # si le kmer de fin est trop petit le retirer
+    if len(res[len(res)-1]) < k:
+        res.pop()
+
+    return res
+
+# crée la table des indices des suffixes triés
+def create_suffix_table(genome):
+    # génère indices de 0 à la taille du génome
+    indices = [i for i in range(len(genome))]
+    return sorted(indices, key=get_suffix)
+
+# obtenir le suffixe à la position i
+def get_suffix(i):
+    return gene_grippe[i:]
+
+def search_suffix(genome, suffix_table, kmer, i1, i2):
+    # kmer non trouvé
+    if i2 - i1 < 1:
+        return -1
+
+    m = (i1 + i2) // 2
+
+    # si le kmer est trouvé au début du suffixe, renvoyer la position
+    if genome[suffix_table[m]:].startswith(kmer):
+        return suffix_table[m]
+    # si le kmer est plus grand que le suffixe du milieu, parcourir la droite du tableau des suffixes
+    if kmer > genome[suffix_table[m]:]:
+        return search_suffix(genome, suffix_table, kmer, m+1, i2)
+    # s'il est plus petit, parcourir la gauche
+    else:
+        return search_suffix(genome, suffix_table, kmer, i1, m)
+
+#print(split_kmers(reads[1], 10))
+for read in reads.values():
+    kmers = split_kmers(read, 11)
+
+    for gene_grippe in genes_grippe.values():   
+        suffix_table = create_suffix_table(gene_grippe)
+
+        for kmer in kmers:
+            pos = search_suffix(gene_grippe, suffix_table, kmer, 0, len(suffix_table))
+
+            if pos != -1:
+                start = pos - len(read)
+                end = pos + len(read)
+
+                # aligner le genome sur le read (les gaps du genome ne sont pas pénalisés)
+                # print(str(max(start,0)) + " " + str(min(end, len(gene_grippe)-1)))
+                # print(str(start) + " " + str(end))
+                al = parasail.sg_dx_scan_sat(read, gene_grippe[max(start,0):min(end, len(gene_grippe)-1)], 16, 4, parasail.dnafull)
+                print(al.score / len(read))
+                al=parasail.sg_dx_trace_scan_sat(gene_grippe[start:end], read, 5, 1, parasail.dnafull)
+                traceback=al.get_traceback()
+                print(traceback.ref)
+                print("--------------------------")
+                print(traceback.query)
+
+
+
+#al=parasail.sg_dx_trace_scan_sat("TGTTGCATCTTCAGCTAGTCTGGAGCAA", genome[m]", 5,1,parasail.dnafull)
+#traceback=al.get_traceback()
+#print(traceback.ref+""+traceback.query)
\ No newline at end of file

notes.py

+# Comparer reads (humains mais pas uniquement) avec génome (virus)
+# Output final = séparer les reads issus et non issus du génome
+
+# Table des suffixes => génome du virus => série de positions => pas stocker listes des suffixes
+# Fragmenté read en k-mer => chercher si k-mer dans génome virus
+# seed -> extend 
+
+# Lecture avec Biopython 
+#Alignement avec Parasail
+
+from IOalignment import IOAlignment
+import gzip
+from Bio import SeqIO
+from Bio.Seq import Seq
+import parasail
+
+sequence_dict = {}
+
+# Lectures des reads :
+# with gzip.open('SRR10971381_1.fastq.gz', 'rt') as fastq:
+#     for i, record in enumerate(SeqIO.parse(fastq, 'fastq'), start=1):
+#         sequence_dict[i] = (str(record.seq))
+#         print(sequence_dict)
+
+# Lectures de Grippe A :
+# seq = IOAlignment('Grippe_A.fna')
+# seq = seq.ParseFasta() # ID long => garder l'entier en entier ?
+# print('séq = ', seq)
+
+print('----------------')
+# [ i for i in range(len(genome))]
+        
+# from multiprocessing.pool import ThreadPool
+# from time import sleep
+# from random import random
+
+# array=[("AACG",1),("AGGA",2),("TGCA",3),("GGAA",4),("ATTT",5),("CCAC",6),("GCAC",7),("TAGG",8)]
+
+# def process(data1,data2):
+#     print(data1,data2)
+#     sleep(1)
+
+# pool = ThreadPool(processes=2)
+# for data in array:
+#     pool.apply_async(process,data)
+# pool.close()
+# pool.join()
+
+#  This function performs a semi-global alignment. The "dx" in the function name stands for "do not penalize gaps at the beginning of the query sequence and at the end of the 
+# database sequence" 1. The "sat" part indicates that the function attempts to allocate profiles for both 8-bit and 16-bit solutions, choosing the appropriate one based on the size of the data 1.
+# 5 et 1 gap opening/extension
+# parasail.dnafull, specifies the substitution matrix to use for scoring the alignment. parasail.dnafull is a predefined substitution matrix for DNA sequences that includes all possible nucleotide substitutions
+al = parasail.sg_dx_scan_sat("TGTTGCATCTTCAGCTAGTCTGGAGCAA", "GGACAGGGCTTTGAGTGGATGTGATGGATCATCACCTACACTGGGAACCCAACGTATACC", 5, 1, parasail.dnafull)
+print(al.score)
+
+al=parasail.sg_dx_trace_scan_sat("TGTTGCATCTTCAGCTAGTCTGGAGCAA", "GGACAGGGCTTTGAGTGGATGTGATGGATCATCACCTACACTGGGAACCCAACGTATACC", 5,1,parasail.dnafull)
+traceback=al.get_traceback()
+print(traceback.ref+"||||||||"+traceback.query)
+
+import tqdm
+import time
+import tqdm
+j=0
+for i in tqdm.tqdm(range(int(10e8))):
+    j=j+i
+
+progress=tqdm(total=100)
+for i in range(100):
+    time.sleep(.1) #Justepourralentirleprogrammepourvoirl"effetdetqdm
+    progress.update(1)
+progress.close()
+
+def compare_my_tuples(tuple):
+    return tuple[1]
+
+l=[(2.5,"A"),(4.1,"D"),(1.1,"C"),(3.7,"F"),(2.8,"B")]
+sorted(l,key=compare_my_tuples)
+

test.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'parasail'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mparasail\u001b[39;00m\n\u001b[1;32m      3\u001b[0m al \u001b[38;5;241m=\u001b[39m parasail\u001b[38;5;241m.\u001b[39msg_dx_scan_sat(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTGTTGCATCTTCAGCTAGTCTGGAGCAA\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGGACAGGGCTTTGAGTGGATGTGATGGATCATCACCTACACTGGGAACCCAACGTATACC\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;241m5\u001b[39m, \u001b[38;5;241m1\u001b[39m, parasail\u001b[38;5;241m.\u001b[39mdnafull)\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28mprint\u001b[39m(al\u001b[38;5;241m.\u001b[39mscore)\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'parasail'"
+     ]
+    }
+   ],
+   "source": [
+    "import parasail\n",
+    "\n",
+    "al = parasail.sg_dx_scan_sat(\"TGTTGCATCTTCAGCTAGTCTGGAGCAA\", \"GGACAGGGCTTTGAGTGGATGTGATGGATCATCACCTACACTGGGAACCCAACGTATACC\", 5, 1, parasail.dnafull)\n",
+    "print(al.score)\n",
+    "\n",
+    "al=parasail.sg_dx_trace_scan_sat(\"TGTTGCATCTTCAGCTAGTCTGGAGCAA\", \"GGACAGGGCTTTGAGTGGATGTGATGGATCATCACCTACACTGGGAACCCAACGTATACC\", 5,1,parasail.dnafull)\n",
+    "traceback=al.get_traceback()\n",
+    "print(traceback.ref+\"\"+traceback.query)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'C'"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "genome_grippe[172]"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}