# 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