add new sample data

README.md

@@ -12,24 +12,23 @@ Probeit is a software to generate probes which are for pathogen detection and ge
 # 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
+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 
+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
 # 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
+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
+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 
+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
+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
 ```
 
 

azure-pipelines.yml

@@ -32,24 +32,24 @@ jobs:
             cd ..
             
             echo [process] run probeit posnegset
-            python probeit.py posnegset -p sample/positive.fasta -n sample/negative.fasta -o posnegset1
+            python probeit.py posnegset -p sample/positive.fa -n sample/negative.fa -o posnegset1
             echo [process] run probeit snp
-            python probeit.py snp -r sample/ref.fasta -a sample/ref.gff -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 snp1
-            python probeit.py snp -r sample/ref.fasta -a sample/ref.gff -s sample/str.fasta  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C,nt:A21716G" -o snp3
+            python probeit.py snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa  -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 snp1
+            python probeit.py snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C,nt:A21716G" -o snp3
             
             echo [process] compare outputs
             echo posnegset 1
-            diff posnegset1/sorted1.fa sample/posnegset1.fasta -s
+            diff posnegset1/sorted1.fa sample/posnegset1.fa -s
             echo posnegset 2
-            diff posnegset1/sorted2.fa sample/posnegset2.fasta -s
+            diff posnegset1/sorted2.fa sample/posnegset2.fa -s
             echo snp aa 1
-            diff snp1/sorted1.fa sample/snp_aa1.fasta -s
+            diff snp1/sorted1.fa sample/snp_aa1.fa -s
             echo snp aa 2
-            diff snp1/sorted2.fa sample/snp_aa2.fasta -s
+            diff snp1/sorted2.fa sample/snp_aa2.fa -s
             echo snp nt 1
-            diff snp3/sorted1.fa sample/snp_nt1.fasta -s
+            diff snp3/sorted1.fa sample/snp_nt1.fa -s
             echo snp nt 2
-            diff snp3/sorted2.fa sample/snp_nt2.fasta -s
+            diff snp3/sorted2.fa sample/snp_nt2.fa -s
             exit 0
 - job: macOS
   timeoutInMinutes: 120
@@ -80,24 +80,24 @@ jobs:
             cd ..
 
             echo [process] run probeit posnegset
-            python probeit.py posnegset -p sample/positive.fasta -n sample/negative.fasta -o posnegset2
+            python probeit.py posnegset -p sample/positive.fa -n sample/negative.fa -o posnegset2
             echo [process] run probeit snp
-            python probeit.py snp -r sample/ref.fasta -a sample/ref.gff -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 snp2
-            python probeit.py snp -r sample/ref.fasta -a sample/ref.gff -s sample/str.fasta  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C,nt:A21716G" -o snp4
+            python probeit.py snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa  -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 snp2
+            python probeit.py snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa  -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C,nt:A21716G" -o snp4
 
             echo [process] compare outputs
             echo posneget 1
-            diff posnegset2/sorted1.fa sample/posnegset1.fasta -s
+            diff posnegset2/sorted1.fa sample/posnegset1.fa -s
             echo posnegset 2
-            diff posnegset2/sorted2.fa sample/posnegset2.fasta -s
+            diff posnegset2/sorted2.fa sample/posnegset2.fa -s
             echo snp aa 1
-            diff snp2/sorted1.fa sample/snp_aa1.fasta -s
+            diff snp2/sorted1.fa sample/snp_aa1.fa -s
             echo snp aa 2
-            diff snp2/sorted2.fa sample/snp_aa2.fasta -s
+            diff snp2/sorted2.fa sample/snp_aa2.fa -s
             echo snp nt 1
-            diff snp4/sorted1.fa sample/snp_nt1.fasta -s
+            diff snp4/sorted1.fa sample/snp_nt1.fa -s
             echo snp nt 2
-            diff snp4/sorted2.fa sample/snp_nt2.fasta -s
+            diff snp4/sorted2.fa sample/snp_nt2.fa -s
             exit 0
 
 

sample/posnegset1.fa

@@ -0,0 +1,2 @@
+>p1_0	HM440559.1:10601:10641;HM440560.1:10597:10637;HM440563.1:10600:10640;NC_003687.1:10602:10642
+TGAGACCAAAAGGCCTCCTGGAAGGCTCACCAGGAGTTAG

sample/posnegset2.fa

@@ -0,0 +1,2 @@
+>p2_0	p1_0
+AACTCGGGAGGAGGGGGGAA

sample/snp_aa1.fasta → sample/snp_aa1.fa

@@ -1,72 +1,72 @@
 >A21716G=S:Q52R;10
+ATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATGT
 >A21716G=S:Q52R;11
+CATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATG
 >A21716G=S:Q52R;19
+CAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCTT
 >A21716G=S:Q52R;20
+TCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCT
 >A21716G=S:Q52R;21
+CTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTC
 >A21716G=S:Q52R;22
+CCTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTT
 >C26304T=E:L21F;10
+CTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACAC
 >C26304T=E:L21F;11
+ACTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACA
 >C26304T=E:L21F;19
+AATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTGC
 >C26304T=E:L21F;20
+TAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTG
 >C26304T=E:L21F;21
+TTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTT
 >C26304T=E:L21F;22
+GTTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCT
 >G23011A=S:E484K;10
+AATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAAT
 >G23011A=S:E484K;11
+TAATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAA
 >G23011A=S:E484K;19
+ACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTTC
 >G23011A=S:E484K;20
+CACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTT
 >G23011A=S:E484K;21
+GCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTT
 >G23011A=S:E484K;22
+AGCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACT
 >G23592C=S:Q677H;10
+TCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGTA
 >G23592C=S:Q677H;11
+ATCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGT
 >G23592C=S:Q677H;19
+CGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGCA
 >G23592C=S:Q677H;20
+GCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGC
 >G23592C=S:Q677H;21
+TGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGG
 >G23592C=S:Q677H;22
+ATGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGG
 >T24223C=S:F888L;10
+GGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCAT
 >T24223C=S:F888L;11
+TGGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCA
 >T24223C=S:F888L;19
+ATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTAC
 >T24223C=S:F888L;20
+AATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTA
 >T24223C=S:F888L;21
+CAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATT
 >T24223C=S:F888L;22
+ACAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCAT
 >T26766C=M:I82T;10
+GAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGTG
 >T26766C=M:I82T;11
+GGAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGT
 >T26766C=M:I82T;19
+TCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTAGG
 >T26766C=M:I82T;20
->T26766C=M:I82T;21
->T26766C=M:I82T;22
-AATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTGC
-AATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTA
-AATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAAT
-ACAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCAT
-ACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTTC
-ACTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACA
-AGCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACT
 ATCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTAG
-ATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTAC
-ATCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGT
-ATGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGG
-ATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATGT
-CAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATT
-CACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTT
-CAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCTT
-CATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATG
-CCTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTT
-CGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGCA
-CTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTC
-CTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACAC
-GAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGTG
+>T26766C=M:I82T;21
 GATCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTA
-GCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTT
-GCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGC
-GGAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGT
+>T26766C=M:I82T;22
 GGATCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGT
-GGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCAT
-GTTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCT
-TAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTG
-TAATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAA
-TCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTAGG
-TCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGTA
-TCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCT
-TGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGG
-TGGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCA
-TTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTT

sample/snp_aa2.fa

@@ -0,0 +1,12 @@
+>A21716G=S:Q52R
+CGAAGACCCAGTCCCTACTT
+>C26304T=E:L21F
+TTATGATGAACCGACGACGA
+>G23011A=S:E484K
+AACTGGAAAGATTGCTGATT
+>G23592C=S:Q677H
+CTATTGCCATACCCACAAAT
+>T24223C=S:F888L
+CCACAGCAAGTGCACTTGGA
+>T26766C=M:I82T
+TCCTTCGTGGACATCTTCGT

sample/snp_nt1.fasta → sample/snp_nt1.fa

@@ -1,84 +1,72 @@
 >A21716G;10
->A21716G;10
->A21716G;11
+ATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATGT
 >A21716G;11
+CATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATG
 >A21716G;19
->A21716G;19
->A21716G;20
+CAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCTT
 >A21716G;20
+TCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCT
 >A21716G;21
->A21716G;21
->A21716G;22
+CTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTC
 >A21716G;22
+CCTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTT
 >C26304T;10
+CTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACAC
 >C26304T;11
+ACTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACA
 >C26304T;19
+AATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTGC
 >C26304T;20
+TAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTG
 >C26304T;21
+TTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTT
 >C26304T;22
+GTTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCT
 >G23011A;10
+AATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAAT
 >G23011A;11
+TAATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAA
 >G23011A;19
+ACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTTC
 >G23011A;20
+CACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTT
 >G23011A;21
+GCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTT
 >G23011A;22
+AGCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACT
 >G23592C;10
+TCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGTA
 >G23592C;11
+ATCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGT
 >G23592C;19
+CGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGCA
 >G23592C;20
+GCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGC
 >G23592C;21
+TGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGG
 >G23592C;22
+ATGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGG
 >T24223C;10
+GGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCAT
 >T24223C;11
+TGGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCA
 >T24223C;19
+ATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTAC
 >T24223C;20
+AATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTA
 >T24223C;21
+CAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATT
 >T24223C;22
+ACAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCAT
 >T26766C;10
+GAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGTG
 >T26766C;11
+GGAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGT
 >T26766C;19
+TCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTAGG
 >T26766C;20
->T26766C;21
->T26766C;22
-AATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTGC
-AATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTA
-AATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAAT
-ACAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCAT
-ACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTTC
-ACTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACA
-AGCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACT
 ATCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTAG
-ATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATTAC
-ATCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGT
-ATGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGG
-ATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATGT
-ATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATGT
-CAATCACTTCTGGTTGGACCCTTGGTGCAGGTGCTGCATT
-CACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTTT
-CAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCTT
-CAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCTT
-CATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATG
-CATTCAACTCGGGACTTGTTCTTACCTTTCTTTTCCAATG
-CCTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTT
-CCTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTT
-CGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGCA
-CTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTC
-CTCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTC
-CTTCTTTTTTTTGCTTTCGTGGTATTCTTGCTAGTTACAC
-GAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGTG
+>T26766C;21
 GATCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTA
-GCACACCTTGTAATGGTGTTAAAGGTTTTAATTGTTACTT
-GCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGGC
-GGAATTGCTACCGCAATGGCTTGTCTTGTAGGCTTGATGT
+>T26766C;22
 GGATCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGT
-GGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCAT
-GTTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCT
-TAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTTG
-TAATGGTGTTAAAGGTTTTAATTGTTACTTTCCTTTACAA
-TCACCGGTGGAATTGCTACCGCAATGGCTTGTCTTGTAGG
-TCAGACTCACACTAATTCTCCTCGGCGGGCACGTAGTGTA
-TCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCT
-TCAGTTTTACATTCAACTCGGGACTTGTTCTTACCTTTCT
-TGCGCTAGTTATCAGACTCACACTAATTCTCCTCGGCGGG
-TGGTTGGACCCTTGGTGCAGGTGCTGCATTACAAATACCA
-TTAATAGCGTACTTCTTTTTTTTGCTTTCGTGGTATTCTT

sample/snp_nt2.fa

@@ -0,0 +1,12 @@
+>A21716G
+TCGAAGACCCAGTCCCTACT
+>C26304T
+TTATGATGAACCGACGACGA
+>G23011A
+AACTGGAAAGATTGCTGATT
+>G23592C
+CTATTGCCATACCCACAAAT
+>T24223C
+TTCCACAGCAAGTGCACTTG
+>T26766C
+ATCCTTCGTGGACATCTTCG