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
|
/*****************************************************************************
*
* seqget.c
* entrez version
*
* "Fasta style" SeqIds include a string indicating the class of SeqId,
* vertical bar, then fields from the SeqId separated by vertical bar
* If an (OPTIONAL) field is missing, the vertical bar must still be
* there.
*
* local = lcl|integer or string
* gibbsq = bbs|integer
* gibbmt = bbm|integer
* giim = gim|integer
* genbank = gb|accession|locus
* embl = emb|accession|locus
* pir = pir|accession|name
* swissprot = sp|accession|name
* patent = pat|country|patent number (string)|seq number (integer)
* other = oth|accession|name|release
* general = gnl|database(string)|id (string or number)
* gi = gi|integer
* ddbj = dbj|accession|locus
* prf = prf|accession|name
* pdb = pdb|entry name (string)|chain id (char)
*
*****************************************************************************/
#include <accentr.h>
#include <sequtil.h>
#include <tofasta.h>
#include <asn2ff.h>
#define NUMARGS 5
Args myargs[NUMARGS] = {
{"Filename for output ","stdout", NULL,NULL,FALSE,'o',ARG_FILE_OUT, 0.0,0,NULL},
{"Output type: 1=text asn.1 2=binary asn.1 3=genbank 4=genpept 5=fasta",
"1", "1", "5", FALSE, 't', ARG_INT, 0.0, 0, NULL } ,
{"GI id for single Bioseq to dump" ,"0","1","99999999",TRUE,'g',ARG_INT,0.0,0,NULL},
{"Maximum complexity of SeqEntry: 0=as stored, 1=Bioseq, 2=Seq-set, 3=nuc-prot set " ,"0","0","3",TRUE,'c',ARG_INT,0.0,0,NULL},
{"Fasta style SeqId ENCLOSED IN QUOTES:\nlcl|int or str bbs|int bbm|int gb|acc|loc\nemb|acc|loc pir|acc|name sp|acc|name\npat|country|patent|seq gi|int\ndbj|acc|loc prf|acc|name pdb|entry|chain ",
NULL,NULL,NULL,TRUE,'s',ARG_STRING,0.0,0,NULL}};
Int2 Main(void)
{
Int2 retcode, /* Default is nuc-prot */
outtype;
SeqIdPtr sip=NULL; /* Same as a ValNodePtr, generic data ptr implemented */
/* as a choice and a union. */
Int4 gi;
SeqEntryPtr sep;
AsnIoPtr asnout=NULL;
FILE * fp=NULL;
Boolean is_network;
Char tbuf[40];
CharPtr outmode;
/*
** Get program arguments
*/
if ( !GetArgs("SeqGet 1.0", NUMARGS, myargs) ) return 1;
/*
** Set parameters from the command line
*/
outtype = (Int2)myargs[1].intvalue;
gi = myargs[2].intvalue;
retcode = (Int2)myargs[3].intvalue;
if (myargs[4].strvalue != NULL)
{
if (gi)
{
ErrPostEx(SEV_FATAL, 1,0, "Use only one of -g or -s");
return 1;
}
sip = SeqIdParse((CharPtr)(myargs[4].strvalue));
if (sip == NULL)
{
ErrPostEx(SEV_FATAL, 1,0, "Can't parse [%s]",
(CharPtr)(myargs[4].strvalue));
return 1;
}
}
else if (! gi)
{
ErrPostEx(SEV_FATAL, 1,0, "Must supply one of -g or -s");
return 1;
}
/*
** Initialize, open and otherwise prepare for CD-ROM or Network access.
*/
if ( !EntrezInit("SeqGet", FALSE, &is_network) ) {
ErrPostEx(SEV_FATAL, 1,0, "Can't initialize Entrez");
return 1;
}
if (sip != NULL)
{
gi = EntrezFindSeqId(sip);
if (! gi)
{
EntrezFini();
SeqIdPrint(sip, tbuf, PRINTID_FASTA_SHORT);
ErrPostEx(SEV_FATAL, 1,0, "Couldn't find SeqId [%s]", tbuf);
return 1;
}
SeqIdFree(sip);
}
sep = EntrezSeqEntryGet(gi, retcode);
EntrezFini();
if (sep == NULL)
{
ErrPostEx(SEV_FATAL, 1,0,"Could not retrieve entry for GI %ld", (long)gi);
return 1;
}
outmode = "w";
switch (outtype)
{
case 2:
outmode = "wb";
case 1:
asnout = AsnIoOpen((CharPtr)myargs[0].strvalue, outmode);
if (asnout == NULL)
{
ErrPostEx(SEV_FATAL, 1,0, "Could not open [%s] for asn output",
myargs[0].strvalue);
return 1;
}
break;
case 3:
case 4:
case 5:
fp = FileOpen((CharPtr)myargs[0].strvalue, outmode);
if (fp == NULL)
{
ErrPostEx(SEV_FATAL, 1,0, "Could not open [%s] for asn output",
myargs[0].strvalue);
return 1;
}
break;
}
switch (outtype)
{
case 1:
case 2:
SeqEntryAsnWrite(sep, asnout, NULL);
break;
case 3:
SeqEntryToFlat(sep, fp, GENBANK_FMT, RELEASE_MODE);
break;
case 4:
SeqEntryToFlat(sep, fp, GENPEPT_FMT, RELEASE_MODE);
break;
case 5:
SeqEntryToFasta(sep, fp, TRUE); /* nuc acids */
SeqEntryToFasta(sep, fp, FALSE); /* proteins */
break;
}
AsnIoClose(asnout);
FileClose(fp);
SeqEntryFree(sep);
return 0;
}
|
