1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
#!/bin/sh
################
##
## test python scripts
##
# echo 'get_genome_seq.py'
# /usr/share/fasta3/scripts/get_genome_seq.py chr1:109687874-109687909
echo 'get_protein.py'
/usr/share/fasta3/scripts/get_protein.py 'sp|P09488|GSTM1_HUMAN'
/usr/share/fasta3/scripts/get_protein.py 'P09488'
/usr/share/fasta3/scripts/get_protein.py 'NP_000552'
echo 'get_refseq.py'
/usr/share/fasta3/scripts/get_refseq.py NP_000552
/usr/share/fasta3/scripts/get_refseq.py NP_0000552
echo 'get_uniprot.py'
/usr/share/fasta3/scripts/get_uniprot.py P09488
/usr/share/fasta3/scripts/get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
echo '################################################################'
echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
# (a) produce an appropriate alignment file
fasta36 -q -m 8CBL -V \!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label \!/usr/share/fasta3/scripts/get_protein.py+P30711 \!/usr/share/fasta3/scripts/get_protein.py+P20135 > hum_chk_map_test.m8CBL
# (b) expand chromosome locations on subject and query exons to both genomes
/usr/share/fasta3/scripts/map_exon_coords.py hum_chk_map_test.m8CBL
echo 'rename_exons.py -- look for exon_X in output'
/usr/share/fasta3/scripts/rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
# echo '################################################################'
# echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
# # (a) from FASTA -m8CBl -- no raw score
# echo '.fa_tab no raw score'
# /usr/share/fasta3/scripts/annot_blast_btop4.py --no_raw_score --have_qslen --query /usr/share/doc/fasta3/examples/seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
#
# ## .bl_tab uses --ann_script because of multiple HSPs
# echo '.bl_tab yes raw score'
# /usr/share/fasta3/scripts/annot_blast_btop4.py --raw_score --have_qslen --query /usr/share/doc/fasta3/examples/seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
#
|
