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annotate all_fasta.loc.sample @ 2:dc4c9490fac8 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
author eric-rasche
date Wed, 01 Mar 2017 22:49:11 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
5 #TAB characters):
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
6 #
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
8 #
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
10 #
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
14 #
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
17 #such as with hg19 above.
dc4c9490fac8 planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff changeset
18 #