/usr/share/EMBOSS/test/seqformats.dat is in emboss-test 6.6.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 | # Tests for sequence formats
# Input data is from the BioPython project Tests directory
#
# Initial version BioPython 1.52 December 2009
#
# run qatest.pl with -testfile=(this file) and with
# setenv EMBOSS_OUTDIRECTORY to specify location of results
#################
# Ace 3 files
#################
ID ace1
AP seqret
CL Ace/consed_sample.ace -sf acedb -out test.out -osf acedb
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID ace2
AP seqret
CL Ace/contig1.ace -sf acedb -out test.out -osf acedb
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID ace3
AP seqret
CL Ace/seq.cap.ace -sf acedb -out test.out -osf acedb
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
######################################################
# Fasta 3 files + 1 alignment + fasta markx10 outputs
######################################################
ID fasta1
AP seqret
CL -auto ../Fasta/f001 -sf ncbi -out test.out -osf ncbi
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta1f
AP seqret
CL -auto ../Fasta/f001 -sf fasta -out test.out -osf fasta
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta2
AP seqret
CL -auto ../Fasta/f002 -sf ncbi -out test.out -osf ncbi
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta2f
AP seqret
CL -auto ../Fasta/f002 -sf fasta -out test.out -osf fasta
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta3
AP seqret
CL -auto ../Fasta/f003 -sf ncbi -out test.out -osf ncbi
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta3f
AP seqret
CL -auto ../Fasta/f003 -sf fasta -out test.out -osf fasta
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta4
AP seqret
CL -auto ../Fasta/fa01 -sf ncbi -out test.out -osf ncbi
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
ID fasta4f
AP seqret
CL -auto ../Fasta/fa01 -sf fasta -out test.out -osf fasta
FI stderr
FC = 0
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI test.out
FC = 0
//
##########################
# SwissProt 16 files
##########################
##########################
# EMBL 6 files
##########################
#########################################
# GenBank 16 gb, 2 faa 1 ffn 1 fna 1 seq
#########################################
# UniGene 3 data
# Stockholm 2 sth
# PDB 1 pdb
# Nucleic 7 files
# Amino 4 pro
# Clustalw 6 aln
# NBRF 5 pir
# Nexus 2 nex
# Phylip 7 phy 1 tree
# Saf 1 saf
# GFF 4 fna 1 gbk
# IntelliGenetics 3 txt
# Entrez 41 xml
# Emboss 11 output files
# Quality 57 fastq 1 qual 1 fasta
# CodonUsage 1 txt (fasta format)
# BioSQL 2 sql
# Blast 76 bt* (no bt008 ... README says 'too big') 8 xml
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