Mercurial > repos > idot > fastx_toolkit2
comparison seqid_uncollapser.xml @ 0:78a7d28f2a15 draft
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| author | idot |
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| date | Wed, 10 Jul 2013 06:13:48 -0400 |
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| -1:000000000000 | 0:78a7d28f2a15 |
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| 1 <tool id="cshl_seqid_uncollapser" name="Uncollapse rows"> | |
| 2 <description>containing collapsed sequence IDs</description> | |
| 3 <command> | |
| 4 cat '$input' | | |
| 5 fastx_uncollapser -c $idcol -v -o '$output' | |
| 6 </command> | |
| 7 <inputs> | |
| 8 <param format="tabular,pslx" name="input" type="data" label="Library to uncollapse" /> | |
| 9 <param name="idcol" label="Column with collased sequence-identifier" type="data_column" data_ref="input" accept_default="false" > | |
| 10 <help>This column contains the sequence id from a collapsed FASTA file in the form of "(seq number)-(read count)" (e.g. 15-4). Use 10 if you're analyzing BLAT output</help> | |
| 11 </param> | |
| 12 </inputs> | |
| 13 <tests> | |
| 14 <test> | |
| 15 <param name="input" value="fastx_seqid_uncollapse1.psl" /> | |
| 16 <param name="idcol" value="10" /> | |
| 17 <param name="output" file="fastx_seqid_uncollapse1.out" /> | |
| 18 </test> | |
| 19 </tests> | |
| 20 | |
| 21 <outputs> | |
| 22 <data format="input" name="output" metadata_source="input" | |
| 23 /> | |
| 24 </outputs> | |
| 25 <help> | |
| 26 | |
| 27 **What it does** | |
| 28 | |
| 29 This tool reads a row (in a table) containing a collapsed sequence ID, and duplicates the . | |
| 30 | |
| 31 .. class:: warningmark | |
| 32 | |
| 33 You must specify the column containing the collapsed sequence ID (e.g. 15-4). | |
| 34 | |
| 35 -------- | |
| 36 | |
| 37 **Example Input File** | |
| 38 | |
| 39 The following input file contains two collapsed sequence identifiers at column 10: *84-2* and *87-5* | |
| 40 | |
| 41 (meaning the first has multiplicity-count of 2 and the second has multiplicity count of 5):: | |
| 42 | |
| 43 | |
| 44 23 0 0 0 0 0 0 0 + 84-2 ... | |
| 45 22 0 0 0 0 0 0 0 + 87-5 ... | |
| 46 | |
| 47 | |
| 48 **Output Example** | |
| 49 | |
| 50 After **uncollapsing** (on column 10), the line of the first sequence-identifier is repeated *twice*, and the line of the second sequence-identifier is repeated *five* times:: | |
| 51 | |
| 52 23 0 0 0 0 0 0 0 + 84-2 ... | |
| 53 23 0 0 0 0 0 0 0 + 84-2 ... | |
| 54 22 0 0 0 0 0 0 0 + 87-5 ... | |
| 55 22 0 0 0 0 0 0 0 + 87-5 ... | |
| 56 22 0 0 0 0 0 0 0 + 87-5 ... | |
| 57 22 0 0 0 0 0 0 0 + 87-5 ... | |
| 58 22 0 0 0 0 0 0 0 + 87-5 ... | |
| 59 | |
| 60 | |
| 61 Uncollapsing a text file allows analsys of collapsed FASTA files to be used with any tool which doesn't 'understand' collapsed multiplicity counts. | |
| 62 | |
| 63 .. class:: infomark | |
| 64 | |
| 65 See the *Collapse* tool in the *FASTA Manipulation* category for more details about collapsing FASTA files. | |
| 66 | |
| 67 ----- | |
| 68 | |
| 69 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 70 | |
| 71 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 72 | |
| 73 </help> | |
| 74 </tool> | |
| 75 <!-- FASTX-Uncollapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |