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test_runs.txt
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This file contains sample commands with their associated output.
All of these runs were done using Python 2.7 on Windows 8.1.
Test Run 1: Showing help message
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
-h
usage: Mutation_Detector.py [-h] [-o OUTFILE]
[-d | -r | -p | -a | -c {DNA,mRNA,protein,all}]
infile1 infile1 infile1 infile2 infile2 infile2
Mutation Detector v2.0.0
A utility for finding mutations between FASTA sequences.
positional arguments:
infile1 Takes three strings indicating 1) coding, template, or
mRNA, 2) 3' or 5', and 3) filename.
infile2 Takes three strings indicating 1) coding, template, or
mRNA, 2) 3' or 5', and 3) filename.
optional arguments:
-h, --help show this help message and exit
-o OUTFILE, --outfile OUTFILE
Filename for the output file
-d, --DNA Compare as 5' coding DNA.
-r, --mRNA Compare as mRNA.
-p, --protein Compare as proteins (default).
-a, --all Compare as DNA, mRNA, and protein.
-c {DNA,mRNA,protein,all}, --compare-as {DNA,mRNA,protein,all}
Compare as DNA, mRNA, protein, or all.
Test Run 2: Running against two custom FASTA sequences
==============================================================================
Contents of my_fastaA.fasta:
>my_fastaA
ATGGGGAGGCGGTGGTGA
Contents of my_fastaB.fasta:
>my_fastaB
ATGGGGAGGCGGTCGTGA
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/mine/my_fastaA.fasta coding 5 test/mine/my_fastaB.fasta
W5S
1 mutation found.
Test Run 3: Same as Test Run 2, but comparing all sequence types
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/mine/my_fastaA.fasta coding 5 test/mine/my_fastaB.fasta --all
DNA sequence mutations:
G14C
1 mutation found.
mRNA sequence mutations:
G14C
1 mutation found.
Amino acid sequence mutations:
W5S
1 mutation found.
Test Run 4: Same as Test Run 2, but comparing only mRNA mutations and using a
text file as output.
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/mine/my_fastaA.fasta coding 5 test/mine/my_fastaB.fasta -r -o resu
lts.txt
Contents of results.txt:
G14C
1 mutation found.
Test Run 5: Comparing a template strand with a coding strand
==============================================================================
Contents of my_fastaA_template.fasta:
>my_fastaA_template
TACCCCTCCGCCACCACT
Contents of my_fastaB.fasta:
>my_fastaB
ATGGGGAGGCGGTCGTGA
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
template 5 test/mine/my_fastaA_template.fasta coding 5 test/mine/my_fastaB.fasta
--all
DNA sequence mutations:
G14C
1 mutation found.
mRNA sequence mutations:
G14C
1 mutation found.
Amino acid sequence mutations:
W5S
1 mutation found.
Test Run 6: Comparing mutantA sequence with humanCFTRcodingsequence
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 3 test/humanCFTRcodingsequence.fasta coding 3 test/mutantA.fasta -a
DNA sequence mutations:
G19T
1 mutation found.
mRNA sequence mutations:
G19U
1 mutation found.
Amino acid sequence mutations:
E7_
1 mutation found.
Test Run 7: Comparing mutantB sequence with humanCFTRcodingsequence
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 3 test/humanCFTRcodingsequence.fasta coding 3 test/mutantB.fasta --compar
e-as all
DNA sequence mutations:
C36T
1 mutation found.
mRNA sequence mutations:
C36U
1 mutation found.
Amino acid sequence mutations:
No mismatches found - strings are identical
Test Run 8: Comparing Human_CFTR_coding_sequence with Mary Allele A
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/Human_CFTR_coding_sequence.fasta coding 5 test/Mary_CFTR_coding_se
quence_allele_A.fasta -a
DNA sequence mutations:
G360A
1 mutation found.
mRNA sequence mutations:
G360A
1 mutation found.
Amino acid sequence mutations:
No mismatches found - strings are identical
Test Run 9: Comparing Human_CFTR_coding_sequence with Mary Allele A1
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/Human_CFTR_coding_sequence.fasta coding 5 test/Mary_CFTR_coding_se
quence_allele_A_1.fasta -a
DNA sequence mutations:
G360A
1 mutation found.
mRNA sequence mutations:
G360A
1 mutation found.
Amino acid sequence mutations:
No mismatches found - strings are identical
Test Run 10: Comparing Human_CFTR_coding_sequence with Mary Allele B
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/Human_CFTR_coding_sequence.fasta coding 5 test/Mary_CFTR_coding_se
quence_allele_B.fasta -a
DNA sequence mutations:
G1652A
1 mutation found.
mRNA sequence mutations:
G1652A
1 mutation found.
Amino acid sequence mutations:
G551D
1 mutation found.
Test Run 11: Comparing Human_CFTR_coding_sequence with Tom Allele A
==============================================================================
C:\Users\chorton\Documents\GitHub\Mutation-Detector>python Mutation_Detector.py
coding 5 test/Human_CFTR_coding_sequence.fasta coding 5 test/Tom_CFTR_coding_seq
uence_allele_A.fasta -a --outfile Tom_A.txt
Contents of Tom_A.txt:
DNA sequence mutations:
Sequences are not the same length; they differ by 3 characters.
C1521T
T1522G
T1523G
G1526T
G1528T
T1529C
T1530C
C1532A
C1533T
T1534G
T1539A
G1540T
A1542T
T1543A
A1544G
T1545A
A1546T
G1547A
A1548C
T1549A
A1550G
C1551A
A1554C
A1555G
G1556T
G1558A
T1562A
C1563A
A1564G
A1565C
G1567T
C1568G
A1569C
T1570C
G1571A
C1572A
A1574T
C1576G
T1577A
A1581G
G1584C
G1585A
A1586T
A1588T
T1589C
T1591A
C1592A
C1593G
A1594T
A1595T
G1596T
T1597G
T1598C
T1599A
C1601A
A1602G
G1603A
G1605A
A1606G
A1608C
G1609A
C1611T
A1613T
T1614A
A1615G
A1617T
G1618C
C1621G
T1622G
T1623A
G1625A
A1628G
A1629T
T1632A
G1633A
G1634T
A1635C
T1637C
C1638A
A1639C
C1640T
A1641G
C1642A
T1643G
G1644T
A1645G
T1647A
A1650T
G1651C
G1652A
T1653A
A1655G
C1657G
G1658C
G1660A
C1661G
G1664T
A1665T
A1666T
T1667C
C1670T
T1671A
T1672G
T1673C
G1675A
C1676G
A1678G
G1679C
C1682T
G1684T
T1685A
A1686C
T1687A
C1689A
A1690G
A1692T
A1694C
C1697A
G1699T
A1700T
T1701G
T1703A
G1704T
A1706T
T1707A
T1711G
T1712A
A1713C
G1714T
A1715C
C1716T
T1717C
C1720T
C1721T
T1723G
T1724G
T1725A
G1726T
G1727A
A1728C
T1729C
A1730T
C1731A
C1732G
T1733A
A1734T
A1736T
G1738T
T1740A
T1741A
T1742C
A1744G
C1745A
G1747A
A1750G
G1753A
A1754T
A1756T
A1758T
T1759G
T1760A
T1761A
G1762A
A1763G
A1764C
A1765T
C1767T
T1768G
G1769T
T1770C
G1771T
T1772G
C1773T
T1774A
G1775A
T1776A
A1777C
A1778T
A1779G
C1780A
A1783G
T1784C
G1785T
G1786A
C1787A
T1788C
C1791A
A1793C
A1794T
C1796G
T1797G
G1799T
G1800T
A1801T
T1803G
T1804G
G1806C
G1807A
T1808C
C1809T
A1810T
T1813A
C1814A
T1815A
A1817T
A1818G
A1819G
T1820A
G1821A
G1822C
A1824T
C1825T
A1826T
T1827A
T1828A
T1829A
A1830G
G1833A
A1834G
A1835C
A1836T
C1838A
T1839C
G1840A
C1842A
A1844T
A1846T
T1849A
A1851T
A1852T
T1854G
T1855C
T1856A
G1857T
C1858G
T1860A
A1862G
A1863T
G1864A
T1866C
A1870T
G1871A
C1872T
A1874T
T1877A
T1879G
A1880G
T1881G
G1882A
G1883C
G1884A
A1885T
C1886T
A1887T
T1889C
T1890A
T1891G
C1892A
G1894C
A1895T
A1896C
T1898A
C1899A
C1900A
A1902T
A1903C
A1904T
T1905A
T1907A
A1908G
A1910C
G1911A
C1912G
C1913A
A1914C
G1915T
A1916T
C1917T
T1918A
T1919G
T1920C
A1921T
G1922C
C1923A
T1924A
C1925A
A1927C
A1928T
A1929C
C1930A
C1932G
A1933G
T1934G
G1935A
G1936T
A1938T
T1939G
G1940A
G1942T
A1943C
C1946T
T1947C
T1948G
T1949A
G1951C
C1953A
C1954T
A1955T
A1956T
T1957A
T1958G
A1960G
G1961C
T1962A
C1964A
G1966A
A1967G
G1973A
A1974T
A1975T
A1976C
T1977A
T1978A
C1979T
A1980C
A1981C
C1983A
C1984A
T1985C
A1986T
A1987G
C1988A
T1989G
G1990A
A1991C
G1992C
A1993T
C1994T
C1995A
T1996C
T1997A
A1998C
A2000G
C2001T
C2002T
G2003T
T2004C
T2006C
C2007A
C2009T
T2011G
T2012A
A2015G
G2018A
A2019T
A2021C
G2023C
C2026G
C2027T
T2028C
G2029T
T2030C
C2033G
C2034G
T2035A
G2036C
G2037A
A2038G
C2039A
G2041A
A2042C
C2045A
A2050C
C2053T
A2054C
A2055T
C2057T
T2059A
T2060A
T2061A
A2062C
A2064G
C2065A
A2066C
G2067T
A2068G
C2069G
T2070A
G2072A
A2073G
G2074T
A2075T
G2076T
T2077G
T2078G
T2079G
G2081A
G2082A
G2083A
A2087G
A2088G
G2090A
G2094T
A2095T
A2096C
T2098A
C2099T
A2101C
T2103C
C2104A
T2105A
C2106T
A2107C
A2108C
T2109A
C2110A
C2111T
A2112C
T2114A
A2116T
A2117C
C2118T
T2119A
C2120T
T2121A
A2122C
T2123G
C2125A
G2126A
A2128T
A2129T
A2130T
T2132C
T2133C
T2134A
C2135T
C2136T
A2137G
T2139G
G2140C
T2141A
G2142A
C2143A
A2145G
A2147C
G2148T
A2149C
T2151C
C2152T
C2153T
C2154A
T2155C
T2156A
C2158A
A2159T
A2160G
T2162A
G2163T
A2164G
A2165G
T2166C
G2167A
G2168T
A2170G
T2171A
C2172A
A2175G
G2178T
G2179T
A2180C
T2182G
C2183A
T2187G
G2188C
A2189C
G2190T
C2191T
C2192T
T2193A
T2194G
T2195A
A2196G
G2197A
A2198G
G2199A
A2202G
A2203C
G2204T
C2206T
T2207C
G2208C
C2210T
C2211A
T2212G
G2215C
T2216C
C2218G
C2219A
A2220T
G2221T
A2222C
T2224G
C2225A
T2226G
G2227C
C2230G
A2231G
G2232A
G2234A
A2235G
A2237C
G2239A
C2240T
G2241A
A2242C
A2244G
T2246C
G2247T
C2249G
T2250C
C2251A
G2252T
T2255G
A2257G
G2258T
C2259G
G2260A
G2262C
T2264G
G2267C
C2268T
A2269G
C2270G
T2271C
G2272C
G2273C
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