Mercurial > repos > iuc > find_nested_alt_orfs

annotate test-data/all_fasta.loc @ 0:14f4c7a8a962 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
author iuc
date Mon, 11 Apr 2022 20:37:19 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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diff changeset
2 #under the "genome" directory (a directory that contains a directory
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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diff changeset
3 #for each build). The script extract_fasta.py will generate the file
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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5 #TAB characters):
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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6 #
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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8 #
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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9 #So, all_fasta.loc could look something like this:
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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10 #
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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14 #
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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17 #such as with hg19 above.
14f4c7a8a962 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
iuc
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18 #