1# Tests for sequence formats 2# Input data is from the BioPython project Tests directory 3# 4# Initial version BioPython 1.52 December 2009 5# 6# run qatest.pl with -testfile=(this file) and with 7# setenv EMBOSS_OUTDIRECTORY to specify location of results 8 9################# 10# Ace 3 files 11################# 12 13ID ace1 14AP seqret 15CL Ace/consed_sample.ace -sf acedb -out test.out -osf acedb 16FI stderr 17FC = 2 18FP 0 /Warning: / 19FP 0 /Error: / 20FP 0 /Died: / 21FI test.out 22FC = 0 23// 24 25 26ID ace2 27AP seqret 28CL Ace/contig1.ace -sf acedb -out test.out -osf acedb 29FI stderr 30FC = 2 31FP 0 /Warning: / 32FP 0 /Error: / 33FP 0 /Died: / 34FI test.out 35FC = 0 36// 37 38 39ID ace3 40AP seqret 41CL Ace/seq.cap.ace -sf acedb -out test.out -osf acedb 42FI stderr 43FC = 2 44FP 0 /Warning: / 45FP 0 /Error: / 46FP 0 /Died: / 47FI test.out 48FC = 0 49// 50 51###################################################### 52# Fasta 3 files + 1 alignment + fasta markx10 outputs 53###################################################### 54 55ID fasta1 56AP seqret 57CL -auto ../Fasta/f001 -sf ncbi -out test.out -osf ncbi 58FI stderr 59FC = 0 60FP 0 /Warning: / 61FP 0 /Error: / 62FP 0 /Died: / 63FI test.out 64FC = 0 65// 66 67 68 69ID fasta1f 70AP seqret 71CL -auto ../Fasta/f001 -sf fasta -out test.out -osf fasta 72FI stderr 73FC = 0 74FP 0 /Warning: / 75FP 0 /Error: / 76FP 0 /Died: / 77FI test.out 78FC = 0 79// 80 81 82 83ID fasta2 84AP seqret 85CL -auto ../Fasta/f002 -sf ncbi -out test.out -osf ncbi 86FI stderr 87FC = 0 88FP 0 /Warning: / 89FP 0 /Error: / 90FP 0 /Died: / 91FI test.out 92FC = 0 93// 94 95 96 97ID fasta2f 98AP seqret 99CL -auto ../Fasta/f002 -sf fasta -out test.out -osf fasta 100FI stderr 101FC = 0 102FP 0 /Warning: / 103FP 0 /Error: / 104FP 0 /Died: / 105FI test.out 106FC = 0 107// 108 109 110ID fasta3 111AP seqret 112CL -auto ../Fasta/f003 -sf ncbi -out test.out -osf ncbi 113FI stderr 114FC = 0 115FP 0 /Warning: / 116FP 0 /Error: / 117FP 0 /Died: / 118FI test.out 119FC = 0 120// 121 122 123 124ID fasta3f 125AP seqret 126CL -auto ../Fasta/f003 -sf fasta -out test.out -osf fasta 127FI stderr 128FC = 0 129FP 0 /Warning: / 130FP 0 /Error: / 131FP 0 /Died: / 132FI test.out 133FC = 0 134// 135 136 137 138ID fasta4 139AP seqret 140CL -auto ../Fasta/fa01 -sf ncbi -out test.out -osf ncbi 141FI stderr 142FC = 0 143FP 0 /Warning: / 144FP 0 /Error: / 145FP 0 /Died: / 146FI test.out 147FC = 0 148// 149 150 151 152ID fasta4f 153AP seqret 154CL -auto ../Fasta/fa01 -sf fasta -out test.out -osf fasta 155FI stderr 156FC = 0 157FP 0 /Warning: / 158FP 0 /Error: / 159FP 0 /Died: / 160FI test.out 161FC = 0 162// 163 164########################## 165# SwissProt 16 files 166########################## 167 168########################## 169# EMBL 6 files 170########################## 171 172######################################### 173# GenBank 16 gb, 2 faa 1 ffn 1 fna 1 seq 174######################################### 175 176# UniGene 3 data 177 178# Stockholm 2 sth 179 180# PDB 1 pdb 181 182# Nucleic 7 files 183 184# Amino 4 pro 185 186# Clustalw 6 aln 187 188# NBRF 5 pir 189 190# Nexus 2 nex 191 192# Phylip 7 phy 1 tree 193 194# Saf 1 saf 195 196# GFF 4 fna 1 gbk 197 198# IntelliGenetics 3 txt 199 200# Entrez 41 xml 201 202# Emboss 11 output files 203 204# Quality 57 fastq 1 qual 1 fasta 205 206 207# CodonUsage 1 txt (fasta format) 208 209# BioSQL 2 sql 210 211# Blast 76 bt* (no bt008 ... README says 'too big') 8 xml 212