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RNA diff and patching tool

Java 97.96% CSS 2.04%

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luke-rnawalker's Issues

Delete in patching error

The code is taking into consideration previous deletes , inserts which it should not.
The patch sequence describes operations as if the previous inserts, deletes and updates weren't present. for ex seq: ACUGA with update script <delete,1> <delete,2> would
result in AGA but if we take into account previous ops => ACUGA after executing <delete,1> would be => AUGA and after <delete,2> => AUA which is wrong.

an easy solution would be based on the observation that the patching script is in increasing order so operations on a character that comes earlier in the sequence are listed before ops. on characters that come later in the sequence.

use a global index i which is set to 0 in the beginning and that gets incremented with inserts and decremented with deletes. And for every update,delete and insert we do the operation at the (source index + i) ( I think )

These input files result in the errors described below:

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: begin 6, end 5, length 5
	at java.base/java.lang.String.checkBoundsBeginEnd(String.java:3734)
	at java.base/java.lang.String.substring(String.java:1903)
	at java.base/java.lang.String.substring(String.java:1876)
	at patching.main(patching.java:80)

Process finished with exit code 1

Source Sequence

<?xml version= "1.0"?>
<RNADataBank>
    <RNA>
        <accession>AB000263</accession>
        <description>Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.</description>
        <length>207</length>
        <sequence>
            ACGCCGUUU
        </sequence>
    </RNA>
    <DNA></DNA>
</RNADataBank>

Destination Sequence

<?xml version= "1.0"?>
<RNADataBank>
    <RNA>
        <accession>AB000263</accession>
        <description>Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.</description>
        <length>207</length>
        <sequence>
            AUUU
        </sequence>
    </RNA>
    <DNA></DNA>
</RNADataBank>

Sequence difference script

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE Diff SYSTEM "DiffScriptDefinition.dtd">
<Diff>
    <meta>
        <SourceString>c68e2e283162b8b8379a77740aaa8e20</SourceString>
        <DestinationString>882711e4374e36ab999a950ac5dae669</DestinationString>
    </meta>
    <EditScript>
        <Delete>
            <index>1</index>
        </Delete>
        <Delete>
            <index>2</index>
        </Delete>
        <Delete>
            <index>3</index>
        </Delete>
        <Delete>
            <index>4</index>
        </Delete>
        <Delete>
            <index>5</index>
        </Delete>
    </EditScript>
</Diff>

patching problem

patching produces wrong sequence

expected sequence : GAGUGGGUGGUGGUGGU
produced sequence : GUGGUGGUGGUGGGUGA

Source seq:

<?xml version= "1.0"?>
<RNADataBank>
    <RNA>
        <accession>AB000263</accession>
        <description>Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.</description>
        <length>207</length>
        <sequence>
            A
        </sequence>
    </RNA>
    <DNA></DNA>
</RNADataBank>

Destination seq:

<?xml version= "1.0"?>
<RNADataBank>
    <RNA>
        <accession>AB000263</accession>
        <description>Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.</description>
        <length>207</length>
        <sequence>
            GAGUGGGUGGUGGUGGU
        </sequence>
    </RNA>
    <DNA></DNA>
</RNADataBank>

diff script:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Diff>
    <meta>
        <SourceString>7fc56270e7a70fa81a5935b72eacbe29</SourceString>
        <DestinationString>4cdcd78f0cde50ac95bdf0a4c2b3aea7</DestinationString>
    </meta>
    <EditScript>
        <Insert>
            <getIndex>0</getIndex>
            <dropIndex>0</dropIndex>
        </Insert>
        <Insert>
            <getIndex>2</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>3</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>4</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>5</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>6</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>7</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>8</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>9</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>10</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>11</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>12</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>13</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>14</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>15</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
        <Insert>
            <getIndex>16</getIndex>
            <dropIndex>1</dropIndex>
        </Insert>
    </EditScript>
</Diff>

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