some problems

BioInformaticsStronghold/Completing_a_Tree.py

@@ -0,0 +1,35 @@
+f = open("rosalind_tree.txt", "r")
+
+n = 0
+components = []
+
+first = True
+
+for x in f:
+    if first:
+        n = int(x)
+        first = False
+        for n in range(1, n + 1):
+            adjnode = set()
+            adjnode.add(n)
+            components.append(adjnode)
+    else:
+        nodes = [int(s) for s in x.rstrip().split(' ')]
+        last = 0
+        for i, com in enumerate(components):
+            if nodes[0] in com:
+                last = i
+                for n in nodes:
+                    com.add(n)
+
+        for n in nodes:
+            for i, com in enumerate(components):
+                if n in com and i != last:
+                    union = set.union(components[last], com)
+                    components[last] = union
+                    if i < last:
+                        last -= 1
+                    components.remove(com)
+
+#print(components)
+print(len(components) - 1)

BioInformaticsStronghold/Finding_a_Spliced_Motif.py

@@ -0,0 +1,20 @@
+from Bio import SeqIO
+
+seqs = []
+
+for seq_record in SeqIO.parse("rosalind_sseq.txt", "fasta"):
+    seqs.append(str(seq_record.seq))
+
+result = ""
+
+s = 0
+for t in seqs[1]:
+    while s < len(seqs[0]):
+        if seqs[0][s] == t:
+            result = result + str(s + 1) if len(result) == 0 else result + ' ' + str(s + 1)
+            s += 1
+            break
+        else:
+            s += 1
+
+print(result)

BioInformaticsStronghold/Transitions_and_Transversions.py

@@ -0,0 +1,42 @@
+from Bio import SeqIO
+
+seqs = []
+
+for seq_record in SeqIO.parse("rosalind_tran.txt", "fasta"):
+    seqs.append(str(seq_record.seq))
+
+transitions = {
+    'A': 'G',
+    'G': 'A',
+    'C': 'T',
+    'T': 'C'
+}
+
+transversion_one = {
+    'A': 'C',
+    'C': 'A',
+    'G': 'C',
+    'T': 'A',
+}
+
+transversion_two = {
+    'C': 'G',
+    'A': 'T',
+    'G': 'T',
+    'T': 'G'
+}
+i = 0
+
+transition_num = 0
+transversion_num = 0
+
+while i < len(seqs[0]):
+    p1 = seqs[0][i]
+    p2 = seqs[1][i]
+    if transitions[p1] == p2:
+        transition_num += 1
+    if transversion_one[p1] == p2 or transversion_two[p1] == p2:
+        transversion_num += 1
+    i += 1
+
+print(transition_num/transversion_num)

BioInformaticsStronghold/example.txt

@@ -1,2 +1,7 @@
->Rosalind_23
-AGCUAGUCAU
+10
+1 2
+2 8
+4 10
+5 9
+6 10
+7 9

BioInformaticsStronghold/rosalind_sseq.txt

@@ -0,0 +1,18 @@
+>Rosalind_9978
+GTTTCCAACGAGCTTGTCCCCTTGAACAGAGCGCGATTATGACCCCAATAATTGCTGGTC
+TTTAATATCCGAGAGTACTGCCCAACCAATCGTACTAGAAACTCGACATCCGATTAGCTA
+CATCGCCCATTCTTCGACAGCTGTGAGAGACGATAGTTAAACTATTAAGTTAGATGCACA
+CTACTAATCAAAAACCCCGACCGCCCAGACATTAAGGCATGGCCATGGGCTGTCTTTTGG
+GGAGAGGAAATACGGTGGTGGTAAACATTTTAGGACCAAGAGCACTGTCCCCGTGGGCAC
+ATATAATTGCGCCCCTTTCTACCTAATTCAGTGCTTAGTCTAACGTTTTCATACTGAACG
+CCTGACGAACTAAATCGATCGTATCCCGTAACGCATCAAGTGATCTAGTACGACCCCTGC
+TTTTTAATCCACCGTCTCCTCAGCGTGGCGATGATCATTCGTAAAGAGTCTCTACGCAAG
+GACCCCCAACAACGGCGTTATTACCACCAGCTGGACTTAGAACACAGGACCTGATACAGC
+GGCTCGAGTTTGTACTTCGCGCGATGCAATGCAAAAATAGGTCCAACCTACTGAACGTTC
+TGTGTAGCTTTGTTTGTGTGCCAACATATTCCACGATCCGACCTGCACAACTCCTACACG
+ATTCCAACATAGAACCTAATACAAGGCTGCATTTAAGCAGCTACGAATGAAACCAATAAT
+TTGATCCCGGATCACTGAATTTTGTTACACCACGCGCACCTGAATAGGTTCCGGGCATAT
+CTCGTAAGGTGGAGGTGGAGTCTCTATTCTTGTGCGAACGAAGTCTTTACCATAGGGAGC
+CTAAACTTATTCATTAG
+>Rosalind_6460
+GTCGCATGAACGCGTACACATGTCCACGATCGCTAT

BioInformaticsStronghold/rosalind_tran.txt

@@ -0,0 +1,34 @@
+>Rosalind_5795
+GCCTGAGGTGATCAGAGAGTCCAGTGTAATAGACAGAAGGTATGACTCAAATCTGACCCT
+AATTGTAGATGTCAAAGAGGGTCACGGCTAACAGATATGGTCTACTTATTTCCTTGAACT
+TGACTGCACCCGTTCAGCGAGAAACTATGACGCATACGACCCCGGCCCGCTTTTCAATCG
+GCTACGCCACTGAAAATCCACGCTGGTTCGCATGGCGCGACCTCGTGCCAGCCGTTCGGG
+GTGGTATGCGCTCAGACCCATAGGAGAACCCTTATTGACAACTGACGGGGATTAAATTTC
+GCCTTCTGAGATCGGGTCAAACTGCAAACGCAACGCGAAGATTGAAAGCAGCTCGTTCAT
+ACTCTCTCAGACAGGATAGGTGCCGGCCAATACTTTGCAGGTAACCGGAACAGGTTTGTC
+ACCGTTTGTTAGTCTTGCGATGCGAACCGAGCGAACGCTCAGTCGACCAGTTCCATACCC
+AAGCGATCTATCCGATAACGCATTGTTATACGCTATAGCTGACTAAACAGTCACGATCTC
+ACCGCTATTAAAGTAGGGCAAGGCCAGTGCACGCGCACAATTTGGTAGACAAGGGGTGCT
+TGACAGGCGATATGCCAGTGCATCGGATAAGGCTGCCGATACTCCCTCGAACGCCGGAAG
+CTTGTGGGTGGACTAAGAGCCTCTTCTGCCAATTTCTGCAATGAATTAGCGCTGGTGACC
+CCACTGCTTTATTTAAAACACAATTGGCGGCAAAGGATTTTATGATATTCGGTCGTTCTA
+GCATTTATACTGCGTTGGCTGTTTAAGATCTCGGGAGAGGGTACCGGTTGAGAGATTAAC
+GTTGGGGCCACTCTCTGTATTAACGATCGATTAGGCTTATTCTCCCACACAAATCGCCCG
+TCTACGGGTCCCATGATAGTGGTGAATC
+>Rosalind_9371
+GCCTGAGGTGATCACAAAGTTCAGAAAGATGGTCAGGGGGTATGGCTTAAACATGACCCC
+AATTGTTGCCGGTAAGGCGGATGACGGCAAACGGGTATTACCTACTCATGTCCTTGGACC
+TTACCACGCCCGTCCAGCGAGGAACTGTGACGTGCGCAATTATAGCCCGGTCTACACCCG
+AATATGAAACTAGAAATCCACGATGGCCCGCATGGTGCTATCCCATGCCAGCAGTCCAGG
+GCCGAGTGCATTTAAGCCCTTAGGATGATCCTCATTGGTAAACGTCGAGAACTGAATTTC
+GCCTTATAAGATCGGGTCGGACTGTAAATGCATCGCGAAGATTGAAAGCGGTTTGCCTAT
+GCATCCTCAGATGGTATAGGGGCGCGCCAATACTCTGCAGATTAACGGAGCGGGTTTGTC
+ACCGTCCATCGATCTCGCCGTGCGGACTGAACAAACGCCAAGTGGACCAGCCTCACAACC
+ACACGTGCCATGCGACGATGCGCAGTGGAACGGTGTAATAAGCTAAGCAGTCAGGATCCT
+ACCGATATCAGAGTGGATTAAGGCCACGGTACGCGCACGATTTTGTTGGCACAGGGCGTT
+TGGCAGATGGTTATTCAGTAGGCCAGGTAAGGTTGCCGACGTTCCTTCAAGCGTCGGAAA
+CACGTGGGTGTGCTGAGAGTCTCATCTGTCATTTTTTGCAATAAAGCGGTACGAGTGATC
+CCACCGCTCCATTTGAAGCTTAATCCAGGGCAACGGATCTCTTGATATTCGGTCTACCTG
+ACATTCATGCTGTATTGGCTGTTTAGGTAACCGCAAGGACGCATTAGTTGAGTGGCTAAG
+ATTGCAGCCAGCCTCCGTATTAACGATCGTTTCGGCCTGTCCTTCCACTCACATCGCACG
+TGTACGGGTTCCATGACAAGGGTAATTT