Week2

students/Abusagit/rosalind/10 Base Quality Distribution.py

@@ -0,0 +1,28 @@
+def get_incorrect_phred(file):
+    with open(rf"D:\Downloads\{file}.txt") as f_read, open(rf"filtered{file}.fastaq", 'w') as f_write:
+        cut_off = int(f_read.readline())
+        lines = iter(f_read.readlines())
+        while lines:
+            try:
+                print(next(lines), end='', file=f_write)  # print seq name
+                sequence = next(lines).strip()
+                delimiter = next(lines)  # '+'
+                quality = next(lines).strip()
+
+                i = 0
+                j = len(sequence) - 1
+                while all((i < len(sequence), j >= 0, i < j,
+                           ord(quality[i]) - 33 < cut_off or ord(quality[j]) - 33 < cut_off)):
+                    i += (ord(quality[i]) - 33) < cut_off
+                    j -= (ord(quality[j]) - 33) < cut_off
+                print(i, j)
+                print(sequence[i:j + 1], file=f_write)
+                print(delimiter, file=f_write, end='')
+                print(quality[i:j + 1], file=f_write)
+            except StopIteration:
+                break
+    print("DONE")
+
+
+if __name__ == '__main__':
+    get_incorrect_phred(input())

students/Abusagit/rosalind/4 MEME.py

@@ -0,0 +1,20 @@
+import os
+from subprocess import call
+
+data = input("data: ")
+width = input("width: ")
+output = input("otput: ")
+CMD = f"meme {data} -text -nostatus -protein -minw {width} > {output}"
+
+if __name__ == '__main__':
+    c = call(CMD, shell=True)
+
+    with open(output) as outfile:
+        for line in outfile:
+            if 'regular expression' in line:
+                separator = outfile.readline()
+                regex = outfile.readline().rstrip()
+                break
+
+    os.remove('outfile')
+    print(regex)

students/Abusagit/rosalind/7 Read Quality Distribution.py

@@ -0,0 +1,18 @@
+import sys
+from functools import reduce
+
+
+def get_incorrect_phred(file):
+    with open(rf"D:\Downloads\{file}.txt") as f_read:
+        threshold = int(f_read.readline())
+
+        a = f_read.readlines()
+        qualities = [None for _ in range(len(a) // 4)]
+        for i in range(3, len(a), 4):
+            qualities[i // 4] = sum(ord(char) - 33 for char in a[i].strip()) // len(a[i].strip())
+
+        return reduce(lambda x, y: x + (y < threshold), qualities, 0)
+
+
+if __name__ == '__main__':
+    print(get_incorrect_phred(input()))

students/Abusagit/rosalind/8 Read Filtration by Quality.py

@@ -0,0 +1,19 @@
+from functools import reduce
+
+
+def get_incorrect_phred(file):
+    with open(rf"D:\Downloads\{file}.txt") as f_read:
+        threshold, percentage = map(int, f_read.readline().split())
+
+        a = f_read.readlines()
+        filtered = 0
+
+        for i in range(3, len(a), 4):
+            qualities = [ord(char) - 33 for char in a[i].strip()]
+            filt = reduce(lambda x, y: x + (y >= threshold), qualities, 0) / len(qualities) * 100
+            filtered += filt >= percentage
+
+    return filtered
+
+if __name__ == '__main__':
+    print(get_incorrect_phred(input()))

students/Abusagit/rosalind/9 Base Filtration by Quality.py

@@ -0,0 +1,17 @@
+def get_incorrect_phred(file):
+    with open(rf"D:\Downloads\{file}.txt") as f_read:
+        threshold = int(f_read.readline())
+
+        a = f_read.readlines()
+
+        below = 0
+        for i in range(len(a[1].strip())):
+            qualities = sum(ord(a[j][i]) - 33 for j in range(3, len(a), 4)) / (len(a) // 4)
+
+            below += qualities < threshold
+
+    return below
+
+
+if __name__ == '__main__':
+    print(get_incorrect_phred(input()))

students/Abusagit/rosalind/filteredrosalind_bfil.fastaq

@@ -0,0 +1,12 @@
+@Rosalind_0049
+GCAGAGACCAGTAGATGTGTTTGCGGACGGTCGGGCTCCATGTGACAC
++
+FD@@;C<AI?4BA:=>C<G=:AE=><A??>764A8B797@A:58:527
+@Rosalind_0049
+ATGGGGGGGGGAGACAAAATACGGCTAAGGCAGGGGTCCT
++
+<<65:793967<4:92568-34:.>1;2752)24')*15;
+@Rosalind_0049
+ACCCCATACGGCGAGCGTCAGCATCTGATATCCTCTTTCAATCCTAGCT
++
+B:EI>JDB5=>DA?E6B@@CA?C;=;@@C:6D:3=@49;@87;::;;?8

students/Abusagit/rosalind/test.txt

@@ -0,0 +1,15 @@
+>Rosalind_7142
+PFTADSMDTSNMAQCRVEDLWWCWIPVHKNPHSFLKTWSPAAGHRGWQFDHNFFVYMMGQ
+FYMTKYNHGYAPARRKRFMCQTFFILTFMHFCFRRAHSMVEWCPLTTVSQFDCTPCAIFE
+WGFMMEFPCFRKQMHHQSYPPQNGLMNFNMTISWYQMKRQHICHMWAEVGILPVPMPFNM
+SYQIWEKGMSMGCENNQKDNEVMIMCWTSDIKKDGPEIWWMYNLPHYLTATRIGLRLALY
+>Rosalind_4494
+VPHRVNREGFPVLDNTFHEQEHWWKEMHVYLDALCHCPEYLDGEKVYFNLYKQQISCERY
+PIDHPSQEIGFGGKQHFTRTEFHTFKADWTWFWCEPTMQAQEIKIFDEQGTSKLRYWADF
+QRMCEVPSGGCVGFEDSQYYENQWQREEYQCGRIKSFNKQYEHDLWWCWIPVHKKPHSFL
+KTWSPAAGHRGWQFDHNFFSTKCSCIMSNCCQPPQQCGQYLTSVCWCCPEYEYVTKREEM
+>Rosalind_3636
+ETCYVSQLAYCRGPLLMNDGGYGPLLMNDGGYTISWYQAEEAFPLRWIFMMFWIDGHSCF
+NKESPMLVTQHALRGNFWDMDTCFMPNTLNQLPVRIVEFAKELIKKEFCMNWICAPDPMA
+GNSQFIHCKNCFHNCFRQVGMDLWWCWIPVHKNPHSFLKTWSPAAGHRGWQFDHNFFQMM
+GHQDWGTQTFSCMHWVGWMGWVDCNYDARAHPEFYTIREYADITWYSDTSSNFRGRIGQN