Commit 38260da9 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.0.1+dfsg

parent 7c68ec94

README.md

+1 −1
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# SeqSero 1.0

# SeqSero

Salmonella serotyping from genome sequencing data

SeqSero.py

+5 −2
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@@ -11,7 +11,8 @@ def main(): 
  parser = argparse.ArgumentParser(usage='SeqSero.py -m <data_type> -i <input_data> [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com')

  parser.add_argument("-m", choices=['1','2','3', '4'],help="<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly)")

  parser.add_argument("-i", nargs="+", help="<string>: path/to/input_data")

  parser.add_argument("-b",choices=['sam','mem'],default="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam") 

  parser.add_argument("-b",choices=['sam','mem','nanopore'],default="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam")

  parser.add_argument("-d",help="<string>: output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number")

  args=parser.parse_args()

  dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))

  if len(sys.argv)==1:
@@ -19,6 +20,8 @@ def main(): 
  else:

    request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())

    request_id += str(random.randint(1, 10000000))

    make_dir=args.d

    if make_dir is None:

      make_dir="SeqSero_result_"+request_id

    os.system("mkdir "+make_dir)

    os.system("cp -rf "+dirpath+"/database "+make_dir)

database/FliC_Family_k,z_special_genes.fasta

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@@ -46,7 +46,5 @@ GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGG 
GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTGGCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCTGATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGAACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAGCTGCTTTGACTGCTGGTGGTGTCGATGCTGCTGATGTAGCTACG

>fliC_z41_Salmonella.enterica_Ottawa_AY353510

GATAGCAAAGCTGTTACTGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGGATCAGTGCAGGTAATCCTGCTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACGAAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTACTCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGATTGCTGGAGATATTGATACTGCTGATGCAGATGCTGCTGAAATG

>fliC_z44_Salmonella.enterica_Bulovka_AY353512_k,z

CAAGCTACAGTTGAAAACAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCCTCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGGCTGACTCAGGTAAAAATGGTTTCCTTAAAGTTGATGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAAATACTGTAGCAGCAAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCAAGTTCGGCTGTACAAGATCAGTTAACAGCTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAA

>fliC_z69_Salmonella.enterica_Pietersburg_AY353520

GATAGTAAAGCTGTAACAGTAGCTGCTGATTTAGATATTACCGCTCTTAATACCGATGCAGCTCTTAAAGCAGGAACGGGAGCTACAACAGGTACTCCATCAATAAAAGATGACAAAGTTTATTATGATAGTGCCAGCAAAAACTACTACGTTGAAGTTACCGGATTAACCGCCCCTGATGATGCTAAGAATGGCTTCTATAAAGTAAATGTTGCTGATGACGGTACAGTATCCATGGCCGCTAATACAGCTATAGAGGCGGGTAAACCAGCCGGTGCAGTAGAAGTAACAAAAACTCAAGAAGAAAAAAACCCATTACCATTATCAGCAGATCTCAAAACTTCTCTTAAATCTGGCGAGATTACAGATCCAGACATT

database/FliC_Family_l,v_special_genes.fasta

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@@ -6,8 +6,6 @@ AATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGG 
AGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG

>fliC_l,z13_Salmonella.enterica_Kenya_AY353449

AGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTCATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACTACG

>fliC_l,v,z13_Salmonella.enterica_Kimberley_AY353448

AATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG

>fliC_l,w_Salmonella.enterica_Glidji_AY353447

AATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG

>fliC_l,z28_Salmonella.enterica_Javiana_AY353455

database/FljB_1_2_7_whole.fasta

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>fljB_1,5_Salmonella.enterica_IIIb.61:k:1,5_AY353278

ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAACAACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGACTGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTGTATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA

>fljB_1,5_Muenster_DTU-unknown_another_1,5

ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAACCACGAAAACTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATCAAAGCGGCCATAGGTGGTACGACTGGTACGCCTGCTGTAACGGGCGGTACAGTTAAATTTGACGCAGATAATAATAAGTATTTTGTTTCTATTGGTGGCTATACTGGTGCTGATGCATCCAAAAATGGCGATTATGAAGTTAACGTTGCTGCTGACGGTAAAGTTACACTTGCTACAGGTGCAACTAAAACCACAATACCGGCAGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAACAGTTGTTTCAGCAGATGCGAAAAATGCCTTAATCGCTGGCGGCGTGGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCGCTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA

>fljB_1,7_Salmonella.enterica_Bredeney_AY353296

ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCCTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAACAACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGCTGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTGTTTCCGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA

>fljB_1,2_Salmonella.enterica_Typhimurium_AY353264