Mercurial > repos > cpt > cpt_gff_extract_seq

annotate all_fasta.loc.sample @ 10:3d9f283ff09d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e14699677f337fd1324aa6898c1388796c5446c1-dirty
author cpt
date Fri, 01 Dec 2023 05:01:01 +0000
parents ab40380424c9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
5 #TAB characters):
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
6 #
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
8 #
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
10 #
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
14 #
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
17 #such as with hg19 above.
ab40380424c9 planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
cpt
parents:
diff changeset
18 #